REVIEW OF COLIPHAGES AS POSSIBLE
INDICATORS OF FECAL CONTAMINATION
FOR AMBIENT WATER QUALITY
820-R-15-098
EPA Office of Water
Office of Science and Technology
Health and Ecological Criteria Division
April 17, 2015
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NOTICES
This document has been drafted and approved for publication by the Health and Ecological
Criteria Division, Office of Science and Technology, United States (U.S.) Environmental
Protection Agency (EPA), and is approved for publication. Mention of trade names or
commercial products does not constitute endorsement or recommendation for use.
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ACKNOWLEDGMENTS
The development of this criteria document was made possible through an effort led by Sharon
Nappier, EPA Project Manager, EPA, Office of Science and Technology, Office of Water. EPA
acknowledges the valuable contributions of EPA Internal Technical Reviewers who reviewed
this document: Jamie Strong and Elizabeth Doyle.
The project described here was managed by the Office of Science and Technology, Office of
Water, EPA under EPA Contract EP-C-11-005 to ICF International. EPA also wishes to thank
Audrey Ichida, Kirsten Jaglo, Jeffrey Seller, Arun Varghese, Alexandria Boehm, Kara Nelson,
Margaret Nell or, and Kaedra Jones for their contributions and invaluable support.
The primary contact regarding questions or comments to this document is:
Sharon Nappier
U.S. EPA Headquarters
Office of Science and Technology, Office of Water
1200 Pennsylvania Ave., NW
Washington, DC 20460
Mail Code 4304T
Phone: (202) 566-0740
Email: nappier.sharon@epa.gov
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EXTERNAL PEER REVIEW WORKGROUP
The External Peer Review was managed by the Office of Science and Technology, Office of
Water, EPA under EPA Contract No. EP-C-13-010 to Versar, Inc. The following professionals
were part of the External Peer Review Workgroup that provided excellent technical and
scientific review on the Draft regarding the content and technical approach in response to EPA
Charge to the Peer Reviewers:
Valerie J. Harwood
University of South Florida
Tampa, Florida 33620
Sunny Jiang
University of California, Irvine
Irvine, California 92697
Mark D. Sobsey
University of North Carolina, Chapel Hill
Chapel Hill, NC 27599
EPA reviewed and incorporated their comments, where appropriate, to develop this literature
review.
Potential areas for conflict of interest were investigated with the Peer Reviewers, including a
review of their current affiliations. No conflicts of interest were identified.
in
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TABLE OF CONTENTS
Notices i
Acknowledgments ii
External Peer Review Workgroup iii
Table of Contents iv
Tables vi
Figures vii
1. Introduction 1
1.1. Context and Purpose 1
1.2. Background 1
1.3. General Attributes of an Ideal Indicator of Enteric Viral Degradation 3
2. Bacteriophage Characteristics 5
2.1. Origin and Replication 5
2.2. Morphology 7
2.2.1 Morphological Properties Affecting Persistence 9
2.3. Detection Methods 10
2.3.1 Culture-Based Methods 10
2.3.2 Rapid Methods 12
3. Epidemiological Relationships 16
3.1 Von Schirnding et al. (1992) 17
3.2 Lee etal. (1997) 18
3.3 Medema et al. (1995) and Van Asperen et al. (1998) 19
3.4Wiedenmannetal. (2006) 20
3.5Colfordetal. (2005, 2007) 21
3.6 Wade etal. (2010) 22
3.7Abdelzaheretal. (2011) 23
3.8 Griffith et al. (personal communication, 2015) 24
3.9 General Conclusions from Epidemiological Studies 24
4. Occurrence in the Environment 27
4.1. Associations between Coliphages and Viruses 27
4.1.1 Coliphage- Virus Associations in Freshwater 31
4.1.2 Coliphage-Virus Associations in Saline or Brackish Water 31
5. Environmental Factors and Fate 37
5.1. Temperature 37
5.2. Sunlight 39
iv
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5.3. Salinity 44
5.4. Predation and Enzymatic Degradation 47
5.5. Organic and Inorganic Matter 49
5.6. Environmental Factors Impacts Summary 51
6. Wastewater Treatment 56
6.1. Primary Treatment 60
6.2. Secondary Treatment 61
6.3. Wastewater Treatment Ponds 63
6.4. Tertiary Treatment and Advanced Treatment 63
6.5. Disinfection 66
6.5.1 Free Chlorine 66
6.5.2 Combined Chlorine 68
6.5.3 Ozone 71
6.5.4 UVC 72
6.5.SUVA and UVB 75
7. Conclusions 78
8. References 81
APPENDIX A: Literature Search Strategy and Summary of Literature Search Results 110
APPENDIX B: Coliphage and NoV Densities during Wastewater Treatment 114
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Tables
Table 1. Morphology of a subsection of bacteriophages 8
Table 2. Morphology of human enteric viruses that may be transmitted in aquatic
environments 9
TableS. Advantages and disadvantages of methods to detect coliphages 14
Table 4. Summary of epidemiological studies 26
Table 5. Number of cases and outcome of the logistical regression analysis of the
association between coliphages and pathogens in water 28
Table 6. Logistic regression of the association between indicators and different pathogens
in water 29
Table 7. Comparison of common methods for the detection of pathogenic human enteric
viruses from environmental sources 30
Table 8. Summary table of coliphages - virus correlations in ambient water 33
Table 9. Comparison of mean exponential decay rates of coliphages, fecal indicators and
human viruses in different media at different temperatures 40
Table 10. Mean exponential decay rates of coliphages and fecal indicators in fresh river
water contaminated with raw sewage or effluent under different light conditions 42
Table 11. Comparison of mean exponential decay rates of coliphages and human viruses
under different light conditions 43
Table 12. Comparison of mean exponential decay rates of coliphages and MNV at
different concentrations of salt and at different temperatures 47
Table 13. Summary of environmental factors influencing viral inactivation in aquatic
environments 52
Table 14. Logioremovals of enteric viruses and indicator organisms 60
Table 15. Virus densities in secondary treated wastewater samples from five Australian
WWTPs 62
Table 16. Average (and percent positive) microorganism effluent densities in a WWTP
with free chlorine treatment of nitrified and filtered secondary wastewater 67
Table 17. Logic reduction of FIB, enteric virus, and F-specific coliphages in sewage
matrix due to chlorine (adapted from Tree etal., 2003) 69
Table 18. Logic reduction of bacteriophages and enteroviruses in spiked secondary
effluent after chlorination with 20 mg/L of chlorine.* 70
Table 19. Inactivation of FIB and F-specific RNA coliphage in ozone disinfected water.* 72
Table 20. Average (and percent positive) microorganism densities in a WWTP with UV
treatment of filtered secondary effluent (n=5) 73
Table 21. UVC inactivation of F-specific RNA coliphage MS2 74
Table 22. Logic reduction in coliphages and enteric viruses in secondary effluent after
lagooning in sunlight or UVC treatment 76
Table 23. Attributes of fecal contamination indicators 80
Table A. Coliphage andNoV densities during wastewater treatment 114
VI
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Figures
Figure 1. Comparison of coliphage and enteric viruses in raw sewage and secondary
effluent 59
vn
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Acronyms and Abbreviations
AOP advanced oxidation processes
AOR adjusted odds ratio
BOD biochemical oxygen demand
C Celsius
CDOM colored dissolved organic matter
CPU colony forming unit
CI confidence interval
CLAT culture latex agglutination and typing
CT disinfectant concentration multiplied by contact time
cm centimeter
DNA deoxyribonucleic acid
ds double-stranded
EPA Environmental Protection Agency
E. coli Escherichia coli
Famp E. coli resistant to streptomycin and ampicillin (host)
FCV feline calicivirus
FIB fecal indicator bacteria
F-specific male-specific or F+ coliphage ("F" refers to the genetic fertility factor that is
required for bacteria to produce a sex pilus necessary for conjugation)
GE gastroenteritis
GI genogroup I
Gil genogroup II
GUI genogroup III
GIV genogroup IV
HCGI highly credible gastrointestinal illness
ICC integrated cell culture
ISO International Standards Organization
kDa kilodalton
L liter
mg milligram
MJ megajoule
ml millijoule
mL milliliter
mm millimeter
mM millimolar
MNV murine norovirus
MPN most probable number
MST microbial source tracking
um micrometer
NEEAR National Epidemiological and Environmental Assessment of Recreational Water
nm nanometer
NOAEL no observed adverse effect level
NoV norovirus
NTU nephelometric turbidity unit
Vlll
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OR odds ratio
PCR polymerase chain reaction
PFU plaque forming units
QA/QC quality assurance/quality control
QMRA quantitative microbial risk assessments
qPCR quantitative polymerase chain reaction
RNA ribonucleic acid
RR relative risk
RT-PCR reverse transcriptase polymerase chain reaction
RT-qPCR reverse transcriptase quantitative polymerase chain reaction
SAL single agar layer
SD standard deviation
ss single-stranded
U.S. United States
UV ultraviolet
W Watt
WERF Water Environment Research Foundation
WRF Water Research Foundation
WWTP wastewater treatment plant
IX
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1. Introduction
1.1. Context and Purpose
The United States (U.S.) Environmental Protection Agency (EPA) recommended the use of the
fecal indicator bacteria (FIB) Escherichia coli (E. coif) and enterococci to determine the level of
fecal contamination present in environmental waters and to establish the 2012 Recreational
Water Quality Criteria (RWQC), which protect the designated use of primary contact recreation
(U.S. EPA, 2012). The purpose of this review is to summarize the scientific literature on
coliphage properties to assess their suitability as indicators of fecal contamination in ambient
water. This review covers background information on coliphage characteristics and enumeration
methods (Section 2); their relationship with human health risks in epidemiological studies
(Section 3); their occurrence and associations with pathogens in the environment (Section 4); and
the fate and transport of coliphages in the environment (Section 5) and during wastewater
treatment (Section 6). Appendix A describes the literature search strategy and summarizes the
results of literature search.
At this time, EPA is considering the use of F-specific and somatic coliphages, as possible viral
indicators of fecal contamination in ambient water. Coliphages are a subset of bacteriophages
that infect E. coli. Other types of bacteriophages [i.e., those that infect Enterococcus and various
Bacteroides species (spp.)] have also been evaluated for their use as indicators of fecal
contamination. While some information on other types of bacteriophages is presented, this
review primarily focuses on coliphages because there is more literature available on their
occurrence, fate, and epidemiological relationships. Additionally, two standardized enumeration
methods published by EPA are available for both coliphages.
1.2. Background
For over a century, FIB (i.e., total coliforms, fecal coliforms, E. coli, fecal streptococci, and
enterococci) have been used to detect sewage contamination in water in order to protect the
public from waterborne pathogens associated with fecal material (e.g., bacteria, protozoa, and
viruses) (Kehr et al., 1941; NRC, 2004). The use of FIB as indicators of sewage contamination
facilitated tremendous gains in public health protection, particularly by indicating the likely
presence of bacterial pathogens such as Vibrio cholerae (which causes cholera) and Salmonella
typhi (which causes typhoid fever). Although advances in wastewater treatment over the last half
century have facilitated gains in public health, it has been suggested that viral pathogens are the
leading causative agents of recreational waterborne illnesses (Jiang et al., 2007; Sinclair et al.,
2009). Unfortunately, because bacteria respond to water treatment processes and environmental
degradation processes differently than viruses, traditional FIB may not be the best indicators of
viral pathogens associated with fecal contamination. This review considers coliphages as
possible indicators of fecal contamination in ambient water. Because FIB have long been used
for managing water quality, much of this review compares coliphages to other commonly used
FIB, such asE1. coli and enterococci.
EPA conducted a series of prospective cohort epidemiological studies at multiple locations from
1972 to 1979 to better understand the relationship between FIB and swimming-associated
illnesses (Cabelli et al., 1982; Dufour, 1984). Symptoms of the swimming-associated illnesses
1
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included acute, self-limiting gastroenteritis (GE) with a short incubation period and duration.
From their studies, Cabelli et al. (1982) concluded that human noroviruses (NoV) or rotaviruses
were the most likely cause of the symptoms.1 Seller et al. (2010) reached similar conclusions
regarding the causative agent of the illnesses observed in the EPA National Epidemiological and
Environmental Assessment of Recreational Water (NEEAR) study. Additionally, numerous
studies have identified the presence of viruses in wastewater treatment effluent, often when
traditional FIB are non-detectable (Kageyama et al., 2003; da Silva et al., 2007; Haramoto et al.,
2007; Kitajima et al., 2009; Kuo et al., 2010; Simmons et al., 2011).
The human viruses most frequently associated with recreational waterborne illnesses are NoV,
adenoviruses, human enteroviruses, rotaviruses, astroviruses, and hepatitis E, with NoV
responsible for the large majority of viral-based gastrointestinal illnesses (U.S. EPA, 2009a). For
example, Sinclair et al. (2009) found that 18 of the 27 (67%) reported viral outbreaks in ambient
recreational water (does not include pools) from 1951 to 2006 were due to NoV, and 2 (7%)
were due to adenovirus. As viruses are an important cause of recreational waterborne illness, it
has been suggested they may also be appropriate indicators of fecal contamination in water.
Currently, there are limitations associated with using individual pathogenic viruses as indicators.
For one, the measurement of densities of individual pathogenic viruses in water is expensive and
time consuming, as culture-based techniques to propagate them can take over a week. Secondly,
human NoV has only recently been cultured and methods for culture-based quantification of
environmental water samples have not been developed yet (Papafragkou et al., 2013; Jones et al.,
2014; Thorne and Goodfellow, 2014). NoV viral ribonucleic acid (RNA) can be detected and
amplified through reverse transcriptase polymerase chain reaction (RT-PCR) (a semi-
quantitative method) and RT-quantitative PCR (RT-qPCR, a quantitative method) (Kageyama et
al., 2003; Trujillo et al., 2006; Atmar et al., 2008; Tajiri-Utagawa et al., 2009; Cashdollar et al.,
2013). However, polymerase chain reaction (PCR) methods do not differentiate between
infective and non-infective viruses. Human enteric adenoviruses are also difficult and slow to
culture, and therefore are frequently detected using integrated cell culture (ICC) RT-PCR assays,
which are semi-quantitative. Methods for these assays are improving, but they are still
technically difficult and relatively slow to produce results (i.e., days) (Rodriguez et al., 2013;
Polston et al., 2014). Therefore, numerous authors have proposed using bacteriophages (viruses
that infect bacteria) as an indicator of human enteric viruses in water impacted by fecal
contamination (Hilton and Stotzky, 1973; Gerba, 1987; Havelaar, 1987; Sobsey et al., 1995;
Chung et al., 1998; Contreras-Coll et al., 2002; Hot et al., 2003; Skraber et al., 2004a, b; Moce-
Llivina et al., 2005). In particular, coliphages, or viruses that infect E. coli, have been the most
thoroughly investigated for this purpose.
Coliphages, particularly F-specific (also known as "male-specific" or "F+ phage") and somatic
coliphages, have been proposed as more reliable indicators of human viral pathogens associated
with fecal contamination than FIB (Gerba, 1987; Palmateer et al., 1991; Havelaar et al., 1993;
1 Cabelli et al. (1982) suggested that "human rotavirus and/or the parvo-like viruses" were the etiological agents. In
the 1970s the virus now called NoV was described morphologically as "picorna or parvovirus-like" (Kapikian et al.,
1972).
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Duran et al., 2002; Rose et al., 2004; Skraber et al., 2004a, b).2 This is based on their greater
similarity to human enteric viruses in their physical structure, composition, and morphology,
survivability in the environment, and persistence in treatment processes compared to FIB
(Funderburg and Sorber, 1985; Havelaar et al., 1993; Gantzer et al., 1998; Grabow, 2001;
Nappier et al., 2006). For example, F-specific RNA coliphages are morphologically similar to
enteroviruses, caliciviruses, astroviruses, and hepatitis A and E viruses, and some somatic
coliphages are similar to adenovirus (King et al., 2011). Coliphages can also be detected and
quantified by simple, inexpensive, rapid, and reliable methods (Gerba, 1987; Havelaar, 1987).
Although they are abundant in domestic wastewater, raw sewage sludge, and polluted waters
(Havelaar et al., 1990; Debartolomeis and Cabelli, 1991; Leclerc et al., 2000; Mandilara et al.,
2006), coliphages are present at lower densities in fresh feces than in wastewater (Dhillon et al.,
1976; Osawa et al., 1981; Calci et al., 1998; Gantzer et al., 2002; Long et al., 2005). They
originate almost exclusively from the feces of humans and other warm-blooded animals and can
undergo limited multiplication in sewage under some conditions (i.e., high densities of
coliphages and susceptible host E. coli at permissive temperatures) (Sobsey et al., 1995; Grabow,
2001). Coliphages (detected by EPA Method 1601, 1602, or approved equivalent methods) are
one of the fecal indicator organisms that can be selected for microbial monitoring of groundwater
systems (U.S. EPA, 2006).
1.3. General Attributes of an Ideal Indicator of Enteric Viral Degradation
Methodological constraints limit reliable enumeration of individual pathogens in water (see
Section 2). Because pathogen enumeration methods are not advanced enough at this time for use
in routine water quality monitoring, FIB have been used to detect the presence of fecal
contamination. Important attributes of an ideal indicator for fecal contamination include the
following (NRC, 2004; Bitton, 2005):
• the indicator should be a member of the intestinal microflora of warm-blooded animals
(see Section 2);
• the indicator should be present when pathogens are present and absent in uncontaminated
samples (see Section 4);
• the indicator should be present in greater numbers than the pathogen (see Sections 4
and 6);
• the indicator should be at least as resistant as the pathogen to environmental factors (see
Section 5) and to disinfection in water and wastewater treatment plants (WWTPs) (see
Section 6);
• the indicator should not multiply in the environment (see Section 2);
• the indicator should be detectable by easy, rapid, and inexpensive methods (see
Section 2);
• the indicator should be nonpathogenic (see Section 2);
• the indicator should be correlated to health risk (see Section 3); and
• the indicator should be specific to a fecal source or identifiable as to source of origin
(microbial source tracking [MST] is not included in this review).
2 Coliphages are broken into two groups, F-specific (also referred to as male-specific or F+) RNA or DNA
coliphages and somatic coliphages. Both infect E. coli; somatic coliphages infect E. coli cells through their outer
membrane and F-specific coliphages infect E. coli via the pilus appendage, found on the surface of some types of
bacteria for conjugative or motile functions.
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While there is no true "ideal" indicator that fits all of the criteria above, coliphages exhibit most
of these attributes, including the following:
• they are part of the intestinal microflora of warm-blooded animals (Sobsey et al., 1995;
Grabow, 2001);
• they are present in greater numbers than pathogens (Havelaar et al., 1990; Debartolomeis
and Cabelli, 1991; Leclerc et al., 2000);
• they are detectable by easy and rapid (1 day or less) methods (Wentsel et al., 1982;
Gerba, 1987; Havelaar, 1987); and
• they are nonpathogenic (Grabow, 2001; Pillai, 2006; Johczyk et al., 2011).
Coliphages partially meet some of the other criteria, including the following:
• they co-occur with pathogens in water in some studies (for example, Havelaar et al.,
1993; Jiang et al., 2001; Ballester et al., 2005; Pillai, 2006; Wu et al., 2011);
• they are at least equally resistant as some viral pathogens to environmental factors and to
disinfection in water and WWTPs (Havelaar, 1987, 1990; Yahya and Yanko, 1992;
Nasser et al., 1993; Gantzer et al., 1998; Sinton et al., 2002; Hot et al., 2003; Bitton,
2005; Lodder and de Roda Husman, 2005; Pillai et al., 2006; Charles et al., 2009;
Bertrand et al., 2012; Seo et al., 2012; Silverman et al., 2013);
• they undergo very limited to no multiplication in the environment (Grabow et al., 1980;
Grabow, 2001; Luther and Fujioka, 2004; Muniesa and Jofre, 2004; Jofire, 2009; Johczyk
etal., 2011); and
• they have been shown to correlate with health risk in some studies (Lee et al., 1997;
Colford et al., 2005, 2007; Wiedenmann et al., 2006; Abdelzaher et al., 2011).
Additionally, while not the focus of this review, assays for bacteriophages have been developed
to identify some sources of origin (Pina et al., 1998; Brion et al., 2002; Schaper et al., 2002a;
Cole et al., 2003; Noble et al., 2003; Payan et al., 2005; Savichtcheva and Okabe, 2006; Stewart-
Pullaro et al., 2006; Ebdon et al., 2007, 2012; Lee et al., 2009; Wolf et al., 2010; Gomez-Donate
et al., 2011; Jofre et al., 2011; Lee et al., 2011; Nnane et al., 2011; Boehm et al., 2013).
This review evaluates the potential for coliphages to be useful as viral indicators of fecal
contamination. The above attributes are considered in more detail throughout the review.
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2. Bacteriophage Characteristics
Bacteriophages (commonly referred to as phages) are viruses that infect bacteria. Phages were
first described as a component of the human microbiome in the early 1900s and are
nonpathogenic. They exist for all known bacterial species, and a wide variety have been isolated.
Based on their size and morphology, bacteriophages are classified into 13 different phylogenetic
families (Pillai, 2006). Genetically, the bacteriophage virion (entire virus particle) consists of
either double-stranded (ds) or single-stranded (ss) RNA or deoxyribonucleic acid (DNA), a
protein capsid, and in some cases, a lipid membrane envelope (Pillai, 2006). Bacteriophages
under evaluation as indicators of fecal contamination are nonenveloped, like many viral
pathogens of interest. See Tables 1 and 2 below for more details.
In recent years, bacteriophages that infect E. coli, Enterococcus, and various Bacteroides spp.
have been considered as possible indicators of fecal contamination (Chung and Sobsey, 1993;
Grabow et al., 1995; Jofre et al., 1995; Bradley et al., 1998; Gantzer et al., 1998; ISO, 1999;
Duran et al., 2002; Lucena et al., 2003; Mandilara et al., 2006; Bonilla et al., 2010; Santiago-
Rodriguez et al., 2010; Vijayavel et al., 2010; Purnell et al., 2011). The majority of research on
using bacteriophages as fecal indicators has been conducted on coliphages, which are
bacteriophages that infect E. coli (U.S. EPA, 2001a). Coliphages, specifically F-specific and
somatic coliphages, are the primary focus of this document and are described in detail below.
2.1. Origin and Replication
Bacteriophages are considered the most abundant form of "life" on earth and can be found in all
environments where bacteria grow, including in soil, water, and inside other larger organisms
(e.g., humans) harboring host bacteria (e.g., E. coli) (Clokie et al., 2011; Dutilh et al., 2014;
Diaz-Mufioz and Koskella, 2014). However, these viruses only reproduce inside metabolizing
bacterial hosts and are thus considered obligate intracellular parasites that cannot multiply
independently in any environment outside of the host bacterial cell (Grabow, 2001; Briissow et
al., 2004; Johczyk et al., 2011). For replication to occur in a given environment, such as in
recreational waters, their host must be both viable in that environment (Grabow, 2001; Bitton,
2005; Jofre, 2009) and susceptible to bacteriophage infection (Wiggins and Alexander, 1985;
Woody and Cliver, 1995, 1997). Bacteriophages use the host cell's ribosomes, protein-
synthesizing machinery, amino acids, and energy generating systems to replicate. Some
bacteriophage species possess fewer than 10 genes and use essentially all of the host's cellular
functions to replicate. In contrast, other bacteriophages have 30 to 100 genes and are less
dependent on the host. For example, larger bacteriophage may not require host genes for DNA
replication because their own genomes contain the necessary genes (Grabow, 2001).
Bacteriophage replication includes the following steps:
1) adsorption: the virion attaches itself to a host cell;
2) penetration: the genome enters the host cell;
3) viral synthesis: the host cell manufactures viral components;
4) maturation: the components are assembled into intact new virions; and
5) release: virus particles leave the infected cell (Goldman and Green, 2009).
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The host-specificity of bacteriophages is determined by protein molecules that serve as receptor
sites on the surface of potential host bacteria. Only specific bacteriophages will recognize and
attach to these specific bacterial receptor sites. Attachment leads to infection of the bacterium
host as described above (Grabow, 2001).
Coliphages are generally found in the gut and are excreted in the feces of humans and other
warm-blooded animals. Coliphages are present in large numbers in sewage (approximately 107
plaque forming units [PFU] per milliliter [mL]) (Ewert and Paynter, 1980; Lucena et al., 2004;
Lodder and de Roda Husman, 2005). They have been investigated for years as possible viral
indicators of fecal contamination (Simkova and Cervenka, 1981; Gerba, 1987; Havelaar et al.,
1993; Sobsey et al., 1995; Chung et al., 1998; Contreras-Coll et al., 2002; Cole et al., 2003; Hot
et al., 2003; Lucena et al., 2003; Moce-Llivina et al., 2005; Brezina and Baldini, 2008; Wu et al.,
2011). Coliphages can be divided into seven major morphological groups, or families; four of
which contain somatic coliphages and three of which contain F-specific coliphages (Cole et al.,
2003; Mesquita et al., 2010). Somatic coliphages infect E. coli cells through their outer
membrane; F-specific coliphages infect E. coli via the pilus appendage, found on the surface of
many types of bacteria. Studies indicate that somatic coliphages are excreted at higher levels
than F-specific RNA coliphages and that somatic coliphages are likely to be more persistent in
water than F-specific RNA coliphages (Grabow, 2001; Schaper et al., 2002a; Lee and Sobsey,
2011). Both F-specific and somatic coliphages, including their taxonomy, are described below.
Somatic coliphages are an abundant group of bacteriophages in feces and encompass DNA
bacteriophages that infect coliform bacteria, including E. coli, via the outer membrane. The
bacteriophage families Myoviridae, Siphoviridae, Podoviridae, and Microviridae have somatic
coliphage representatives (Hayes, 1968; Grabow, 2001). E. coli strains that are used for
propagating somatic coliphages include E. coli CN13 andE. coli WG5 (Muniesa et al., 2003).
Coliphage strain OX174 from the Microviridae family is a model somatic coliphage that is
widely used in laboratory settings. Coliphages in the Microviridae family have circular ds DNA.
Coliphages in the Myoviridae, Siphoviridae, and Podoviridae families have linear ds DNA. For
more information on coliphage families, see Section 2.2 (Table 1) below.
Male-specific, or F-specific, coliphages are another broad group of coliphages that infect Gram-
negative bacteria, including E. coli, which possess a plasmid coding for an F, or sex, pilus (Vinje
et al., 2004). F-specific coliphages are in the bacteriophage families Inoviridae, Leviviridae, and
Tectiviridae (Cole et al., 2003; Lute et al., 2004; Ogorzaly et al., 2009; Mesquita et al., 2010). F-
specific coliphages in the Inoviridae family are filamentous, ssDNA phages, whereas F-specific
coliphages in the Leviviridae family are small, icosahedral, ssRNA phages and F-specific
coliphages in the Tectiviridae family are cubic capsid (icosahedral) with linear dsDNA and no
tail (Cole et al., 2003; Mesquita et al., 2010). Based on serological cross-reactivity, replicase
template activity, and phylogenetic analysis, the F-specific RNA coliphages in the Leviviridae
family have been further broken down into genogroups GI, Gil, GUI, and GIV (Vinje et al.,
2004). In general, Gil and GUI F-specific RNA coliphages are mainly found in environments
associated with human waste, and GI and GIV F-specific RNA coliphages are mostly associated
with animal waste, although these associations are not absolute (Schaper et al., 2002a; Cole et
al., 2003; Vinje et al., 2004). Several host strains of bacteria are used to enumerate F-specific
coliphages in water samples, including E. coli resistant to streptomycin and ampicillin (Famp) and
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Salmonella enterica serovar Typhimurium WG49 (Stm WG49).3 Common laboratory strains of
F-specific coliphages include MS2 (GI), GA (Gil), QP (GUI), and SP (GIV) (Vinje et al., 2004).
Despite being frequently detected in the environment, data indicate that somatic and F-specific
coliphages rarely, if ever, replicate inE1. coli under environmental conditions (Contreras-Coll et
al., 2002; Jofre, 2009). Lack of replication in the environment is partially because coliphages do
not replicate below a bacterial host density of 104 colony-forming units per mL (Wiggins and
Alexander, 1985; Woody and Cliver, 1997). Additionally, Woody and Cliver (1997)
demonstrated that the F-specific RNA coliphage QP cannot replicate in E. coli in nutrient-poor
environments, and Cornax et al. (1991) asserted that the low survivability of the E. coli bacterial
host in marine environments does not support the replication of coliphages.
F-specific coliphages have not been observed to multiply in E. coli suspended in water (Grabow,
2001). As described above, F-specific coliphages require the presence of F-pili on the host
bacteria for infection to occur. In addition to requiring high densities of bacterial hosts for
replication, the F-pili production requires optimum temperatures between 30 and 37°Celsius (°C)
with F-pili production decreasing rapidly below temperatures of 25°C (Franke et al., 2009).
Additionally, most environmental isolates of E. coli have not been observed to produce pili even
at elevated temperatures and are generally considered unsuitable hosts for F-specific RNA
coliphages (Luther and Fujioka, 2004). F-specific coliphages can replicate in E. coli in certain
water environments if fertility fimbriae are present and when the temperature is at least 30°C.
However, replication under these conditions is unlikely as environmental conditions are not
likely to support fertility fimbriae production (Grabow et al., 1980). However, some argue that F-
specific RNA coliphages may reproduce under environmental conditions according to the "mud
puddle hypothesis." This hypothesis argues that the presence of animal waste lagoons and
stagnant small puddles in a watershed may provide an environment for the generation of
coliform bacteria and F-specific and somatic coliphages (Jiang et al., 2007; Reyes and Jiang,
2010). However, additional research to test whether the coliphages detected on environmental E.
coli strains can also infect the E. coli strains used in laboratory assays is needed.
2.2. Morphology
Bacteriophages are incredibly diverse in size, morphology, surface properties, and composition.
Table 1 briefly describes the structure and morphology of the seven bacteriophage families that
include coliphages.
1 Stm WG49 contains an E. coli plasmid that codes for sex pili.
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Table 1. Morphology of a subsection of bacteriophages.
Type
Somatic coliphages
Somatic coliphages and
Bacteroides
bacteriophages
Somatic coliphages
Somatic coliphages
F-specific DNA
coliphages
Family (Examples)
Myoviridae (T2, T4)
Siphoviridae (k, Tl, T5)
Podoviridae (T3, T7, P22)
Microviridae (
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Table 2. Morphology of human enteric viruses that may be transmitted in aquatic
environments.
Genus &
Common name(s)
Astrovirus
Astrovirus
Calicivirus
Norovirus
Coronavirus
Coronavirus
Enterovirus
Poliovirus,
Coxsackieviras A & B,
Echoviras
Enterovirus
Hepatitis A
Hepevirus
Hepatitis E
Mastadenovirus
Adenovirus
Parvovirus
Parvoviras
Reovirus
Reovirus
Rotavirus
Rotaviras
Torovirus
Toroviras
Nucleic acid
Spherical ssRNA
Spherical ssRNA
Linear ssRNA
Linear ssRNA
Spherical ssRNA
Spherical ssRNA
Linear dsDNA
Linear ssDNA
Linear dsRNA (segmented)
Spherical dsRNA (segmented)
Linear ssRNA
Structure
Nonenveloped
Nonenveloped
Enveloped
Nonenveloped
Nonenveloped
Nonenveloped
Nonenveloped
Nonenveloped
Nonenveloped
Nonenveloped
Enveloped
Source: Bosch, 1998; King et al, 2011
2.2.1 Morphological Properties Affecting Persistence
Coliphages can be inactivated, or made noninfective by various environmental factors, including
temperature (Feng et al., 2003), pH (Feng et al., 2003), salinity (Sinton et al., 2002), sunlight
(Sinton et al., 1999), and ultraviolet (UV) light (Sang et al., 2007). Viral inactivation occurs
when viral components (nucleic acids, proteins, lipids) are destroyed. Therefore, characteristics
that influence survival include coliphage morphology, including size and surface properties
(Johczyk et al., 2011).
Of greatest importance, surface conformations, such as whether the virus is enveloped or
nonenveloped, affects virus inactivation. Due to their nonenveloped nature, NoV, poliovirus,
coxsackievirus, and echovirus are presumed to be highly resistant to environmental degradation
and chemical inactivation (Bae and Schwab, 2008). The lipid content of a viral envelop renders
the virus more sensitive to environmental stress including desiccation and heat, and are generally
believed to be less resistant to inactivation than non-enveloped viruses (Rosenthal, 2009).
Coliphages are nonenveloped and are resistant to environmental degradation and chemical
inactivation similar to other enteric nonenveloped viruses (Havelaar, 1987; Havelaar et al., 1990;
Yahya and Yanko, 1992; Nasser et al., 1993; Gantzer et al., 1998; Sinton et al., 2002; Hot et al.,
2003; Ackermann et al., 2004; Bitton, 2005; Lodder and de Roda Husman, 2005; Pillai et al.,
2006; Johczyk et al., 2011; Bertrand et al., 2012; Seo et al., 2012; Silverman et al., 2013).
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Of additional consideration, differences in tail structure as well as capsid size and structure affect
bacteriophage survival. For example, Ackermann et al. (2004) found that tailed bacteriophages
were the most stable in adverse conditions, but found no difference in stability among
bacteriophages with contractile, noncontractile, or short tails. Bacteriophages with a large capsid
(100 nanometers [nm] in diameter) were found to have better preservation rates than
bacteriophages with a smaller capsid (60 nm in diameter) (Ackermann et al., 2004). Lee and
Sobsey (2011) found small diameter Microviridae to be among the most persistent of several
tested somatic coliphages in water. Romero et al. (2011) attributed differences in solar
inactivation rates between MS2 and rotavirus to their differing protein capsid structure and
genomes, which the authors conclude may be responsible for observed differences in reactivity
with individual reactive oxygen species. Overall, it is difficult to make generalizations given the
complexity of interactions between physical characteristics and factors that affect bacteriophage
survival.
While there are differences in survival among viruses of different families, there are also
differences in survival among viruses within the same family (Sobsey and Meschke, 2003;
Nappier et al., 2006). A study that estimated the survival of several virus families and genera,
including adenovirus, poliovirus, and coxsackievirus, found that survival varied by virus type
(Mahl and Sadler, 1975). Siphoviridae with flexible tails are the most persistent in freshwater
environments under adverse conditions (Muniesa et al., 1999). Additionally, coliphages within
the same family and with similar structural similarities do not necessarily share the same survival
characteristics (Johczyk et al., 2011). For example, results from laboratory studies showed that
different F-specific RNA coliphages differ in their survival in water (Brion et al., 2002; Schaper
et al., 2002b; Long and Sobsey, 2004; Nappier et al., 2006). There is also demonstrated
variability within taxonomic types (Brion et al., 2002).
2.3. Detection Methods
Currently a variety of methods are available to detect bacteriophages. These include culture-
based methods and "rapid" methods (defined as one day or less) which include immunology- and
molecular-based methods. Each type of method has advantages and disadvantages (see Table 3).
Plaque assays are a typical culture-based technique used for enumerating infectious virus
particles (ISO, 1995, 2000, 2001; Grabow, 2001; U.S. EPA, 2001a, b; Eaton et al., 2005;
Rodriguez et al., 2012a). Additionally, there are three bacteriophage methods published by the
International Organization for Standardization (ISO) for F-specific RNA bacteriophages, somatic
coliphages, and bacteriophages infecting Bacteroides fragilis (B.fragilis) (ISO, 1995, 2000,
2001). Rapid methods include immunology based methods (i.e., culture latex agglutination and
typing [CLAT]), molecular methods (multiple types of PCR), and Fast Phage (a modified rapid
version of EPA Method 1601) (Brussaard, 2004, 2009; Fong and Lipp, 2005; Kirs and Smith,
2007; Love and Sobsey, 2007; Gentilomi et al., 2008; Salter et al., 2010; Rodriguez et al.,
2012b).
2.3.1 Culture-Based Methods
Standardized culture-based methods are available in both the United States and the European
Union for the detection of coliphages in water (ISO, 1995, 2000, 2001; U.S. EPA, 2001a, b;
10
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Eaton et al., 2005). The ISO methods have been optimized and tested through interlaboratory
comparison (Mooijman et al., 2001, 2002, 2005; Muniesa and Jofre, 2007). The ISO Standard
Method 9224A-F provides protocols for detecting or enumerating coliphages (Eaton et al.,
2005). Two methods for coliphage monitoring in groundwater were approved by EPA in 2001
(U.S. EPA 2001a, b). These methods include EPA Method 1601 (two-step enrichment process)
and EPA Method 1602 (single agar layer [SAL] method). EPA Methods 1601 and 1602 have
undergone multi-laboratory validation (U.S. EPA 2003a, b). The results of these inter-laboratory
comparisons support the use of these methods in the determination and enumeration of F-specific
and somatic coliphages in groundwater (U.S. EPA, 2003a, b). These methods are approved in 40
Code of Federal Regulations Part 136 and can be used for detection of coliphages in wastewater.4
These culture-based methods have been applied to rivers, estuaries, drinking water, surface
water, storm water, and wastewater (Havelaar, 1987; Davies et al., 2003; Borchardt et al., 2004;
Lucena et al., 2004; Sobsey et al., 2004; Ballester et al., 2005; Lodder and de Roda Husman,
2005; Nappier et al., 2006; Stewart-Pullaro et al., 2006; Bonilla et al., 2007; Locas et al., 2007,
2008; Gomila et al., 2008; Love et al., 2010; Francy et al., 2011; Rodriguez et al., 2012a).
EPA Method 1601 describes a qualitative two-step enrichment procedure for coliphages and was
developed to help determine if groundwater is affected by fecal contamination (U.S. EPA,
2001a). However, this validated4 procedure determines the presence or absence of F-specific and
somatic coliphages in groundwater, surface water, and other waters (U.S. EPA, 2003a). Method
1601 may be used as a quantitative assay of coliphage densities in a most probable number
(MPN) format (spot-plating). The Method 1601 protocol directs that a 100 mL or 1 liter (L)
groundwater sample be enriched with a log-phase host bacteria (E. coli Famp for F-specific
coliphages and E. coli CN-13 for somatic coliphages) for coliphages. After an overnight
incubation, samples are put on to a lawn of host bacteria specific for each type of coliphage,
incubated, and examined for circular lysis zones, which indicate the presence of coliphages. For
quality control purposes, both a coliphage positive reagent (enumerated sewage filtrate or pure
cultures of F-specific RNA coliphage MS2 or somatic coliphage OX174) water sample and a
negative reagent water sample (method blank) are analyzed for each type of coliphage with each
sample batch. This method is considered more sensitive than EPA Method 1602, a SAL
procedure discussed below (U.S. EPA, 2001a), due to the larger sample volumes used in 1601
(100 mL to 1 L) compared to Method 1602 (100 mL). In total, EPA Method 1601 requires 28 to
40 hours for a final result, depending on incubation times (Salter et al., 2010).
The EPA Method 1602 SAL procedure can be used to quantify coliphages in a sample. The
Method 1602 protocol directs that a 100 mL water sample may be assayed by adding the log-
phase host bacteria (E. coli Famp for F-specific coliphage and E. coli CN-13 for somatic
coliphage) and 100 mL of double-strength molten tryptic soy agar to the sample. The sample is
then thoroughly mixed and the total volume is poured into multiple plates. After an incubation of
16 to 24 hours, circular lysis zones (plaques) are counted and summed for all plates from a single
sample. The quantity of coliphages in a sample is expressed as PFU per 100 mL. For quality
control purposes, both a coliphage-positive reagent (enumerated sewage filtrate or pure cultures
of F-specific RNA coliphage MS2 or somatic coliphage OX174) water sample and a negative
4http://water.epa.gov/scitech/methods/cwa/methods_index.cfm
Method validation is defined as a process that demonstrates the suitability of an analytic method for its intended purpose (U.S.
EPA, 2009b).
11
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reagent water sample (method blank) are analyzed for each type of coliphage with each sample
batch. In total, EPA Method 1602 typically requires an overnight incubation (18 to 24 hours) up
to 3 days, but results can be obtained in as few as 8 to 10 hours (Salter et al., 2010).
There are also methods for coliphage detection that use membrane filters to concentrate
coliphages from a water sample (Sobsey et al., 1990; Sobsey et al., 2004; Eaton et al., 2005).
Volumes of water of 100 mL and greater can be concentrated on a membrane filter after addition
of salts and or pH adjustments. Coliphages can then be eluted off the filter and used in one of the
standard assays above, or they can be enumerated directly on the membrane filter (Eaton et al.,
2005). For direct filter assays, a single assay dish is utilized for each coliphage-adsorbed filter.
This significantly reduces the time and materials required. However, extraneous material on the
filter can interfere with the plaque assay. Both 47-millimeter (mm) membrane and 90-mm
membrane filters have been used and the membrane filtration method can be used to detect both
F-specific and somatic coliphages.
One study evaluated the use of a single E. coli host (Escherichia coll host strain CBS90) for the
simultaneous detection of both somatic and F-specific coliphages (Guzman et al., 2008). This
host could be useful for detecting total coliphages. However, more independent and multi-
laboratory validation of this method is needed. Rose et al. (2004) usedE1. coli C-3000 (ATCC
#15597), which they report can host both somatic and F-specific coliphages.
EPA is currently evaluating a membrane filtration culture method and may also evaluate an
ultrafiltration culture method for use in coliphage enumeration. The intralaboratory (single
laboratory) method validation study is underway.
2.3.2 Rapid Methods
Recently, multiple methods have been published that are faster than EPA Methods 1601 and
1602. Each method has advantages and disadvantages in terms of speed, accuracy, form of
results (i.e., quantitative, qualitative, infectivity of virus), and level of training and equipment
required. The rapid methods are outlined below in more detail.
Polymerase Chain Reaction Methods
The most common type of molecular method used to detect coliphages is PCR. PCR is a method
of amplifying nucleic acids and involves cycling the reaction mixture through temperatures that
allow for denaturing, annealing, and extension of new DNA fragments or amplicons. With each
cycle, specific DNA fragments targeted by primers are doubled. This exponential amplification
of DNA fragments allows samples with very small numbers of target sequences to be amplified
into an amount of DNA that can be visualized on an agarose gel (Innis et al., 1990). Depending
on the type of information needed (quantitative, qualitative), different types of PCR are used and
are described in more detail below. Currently, there are no universal primers for the detection of
coliphages, but primers are available for individual coliphage strains.
RT-PCR: RT-PCR is used to determine the presence of RNA or RNA viruses, such as F-specific
RNA coliphages. The viral RNA is first reverse transcribed into complementary DNA, which is
used as a template for the PCR reaction (Fong and Lipp, 2005; Kirs and Smith, 2007).
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Quantitative (q) PCR and RT-qPCR: Both qPCR and RT-qPCR assays, which detect and
quantify the amount of nucleic acid present, have been developed for the quantification of
coliphages (Smith, 2006). These assays can determine the amount of a given coliphage present in
a given sample (Yong et al., 2006; Kirs and Smith, 2007; U.S. EPA, 2007, 2010; Gentilomi et
al., 2008). These PCR assays often detect only a subgroup of the total coliphages that would be
quantified by plaque assays. Most recently, PCR has been performed on digital microfluidic
platforms (Hua et al., 2010; Jebrail and Wheeler, 2010; Mark et al., 2010) and has been used to
detect bacteriophages (Tadmor et al., 2011) and coliphages (Reitinger et al., 2012). Digital PCR
on microfluidic chips promises to be a fast and accurate high-throughput technique to determine
phage genome quantification.
Multiplex PCR: Multiplex PCR (also including multiplex qPCR, RT-PCR, and RT-qPCR) was
developed to detect multiple target sequences in the same reaction tube. Thus, multiplex PCR
can detect more than one type of phage in one sample (U.S. EPA, 2007, 2010). For example, RT-
qPCR only quantitatively detects one type of coliphage per tube (i.e., Gil F-specific RNA
coliphage) while multiplex RT-qPCR quantitatively detects multiple phage targets per tube (i.e.,
GI, Gil, and GUI F-specific RNA coliphages) (Kirs and Smith, 2007).
Culture Latex Agglutination and Typing
The CLAT method has been validated for the detection of coliphages from fecal contamination
in beach waters (Griffith et al., 2009; Wade et al. 2010) and combines a two-step enrichment
process and latex agglutination serotyping to monitor for the presence of coliphages (Love and
Sobsey, 2007; Rodriguez et al., 2012a). This rapid antibody-based method detects F-specific
coliphages in water samples in 5 to 24 hours. Samples are generally scored as positive based on
formation of clumps visible on the agglutination card after 60 seconds. Absence of such clumps
signifies negative samples (Love and Sobsey, 2007). The assay is relatively inexpensive as
reagents can be stored at ambient temperatures for months, unlike the reagents used for PCR-
based assays (Love and Sobsey, 2007).
Fast Phage Modified Method 1601
A modification to EPA Method 1601 called Fast Phage has been described by Salter et al.
(2010). This modification incorporates the use of shelf-stable, ready-to-use reagents in a
simplified format. Within the Fast Phage method, isopropyl-p-D-1-thiogalactopyranoside is used
as an enrichment medium to induce transcription of the host E. coli lac operon. Lysis of E. coli
by coliphages is coupled with lac operon expression. Therefore, a large amplification and a rapid
extracellular beta-galactosidase enzyme release during coliphage-induced lysis of the infected
host are reported in comparison to the growing, uninfected host (Salter et al., 2010). Fast Phage
is approved under EPA's Alternative Test Procedure program for detection of coliphages in
groundwater (Salter and Durbin, 2012).
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Table 3. Advantages and disadvantages of methods to detect coliphages.
Method
Advantages
Disadvantages
Culture EPA Method
1601
Qualitative (presence/absence);
Differentiates between F-specific and somatic
coliphages;
Infectivity is determined;
More sensitive than Method 1602 (depending
on sample volume: Method 1601 with >100
mL is more sensitive than Method 1602 and
Method 1601 with <100 mL is less sensitive
than Method 1602); and
Inexpensive.
• Not validated as a quantitative assay;
and
• Requires 24 hours-3 days for results.
Culture EPA Method
1602
Both qualitative and quantitative (PFU);
Differentiates between F-specific and somatic
coliphages;
Infectivity is determined; and
Inexpensive.
Requires 16-24 hours for results; and
May be less sensitive than Method
1601 (depending on sample volume:
Method 1601 with >100 mL is more
sensitive than Method 1602 and
Method 1601 with <100 mL is less
sensitive than Method 1602).
SM9224F Membrane
Filtration
Both qualitative and quantitative (PFU);
Differentiates between F-specific and somatic
coliphages;
Infectivity is determined;
Similar material requirements to EPA Methods
1601 and 1602; and
Greater than 100 mL volume samples can be
evaluated, which increases sensitivity in
ambient waters.
• Requires 16-24 hours for results; and
• May have recovery loss due to
filtration and elution steps; and
• Turbidity in the sample may interfere
with plaque identification.
PCR/(reverse-
transcriptase) RT-PCR
Rapid (-2-10 hours);
Increased sensitivity compared to culture
methods; and
Can test for specific types of DNA (PCR) or
RNA (RT-PCR) phages.
Qualitative only;
Infectivity (live vs. dead) not
determined;
Inhibitors may be present in the
environmental matrix; and
Expensive (PCR equipment) and
quality assurance/quality control
(QA/QC) expertise required.
qPCR/RT-qPCR
(quantitative)
• Rapid (-2-10 hours);
• Quantitative;
• Increased sensitivity compared to culture
methods; and
• Can test for specific types of DNA (qPCR) or
RNA (RT-qPCR) phages.
Infectivity not determined;
Inhibitors may be present in the
environmental matrix; and
Expensive (qPCR equipment) and
QA/QC expertise required.
Multiplex qPCR/RT-
qPCR
Rapid (-2-10 hours).
Increased sensitivity compared to culture
methods; and
Can quantitatively distinguish between F-
specific DNA (qPCR) and RNA (RT-qPCR)
subgroups in one reaction tube.
Infectivity not determined;
Inhibitors may be present in the
environmental matrix;
Expensive (qPCR equipment) and
QA/QC expertise required; and
Multiple sets of primers and probes in
the multiplex qPCR reactions may
cross-react, creating issues in method
specificity (Batra et al., 2013).
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Method
Advantages
Disadvantages
CLAT
Same day results (2-24 hours);
Detects F-specific coliphages and has been
applied to some somatic coliphage groups
(Lee, 2009);
Can differentiate among F-specific
genogroups;
Detects infectious coliphages;
Inexpensive;
Field portable; and
When used in an enrichment-CLAT format it
is as sensitive as EPA Methods 1601 and 1602
(Love, 2007).
Not quantitative unless implemented
in an MPN format (Love and Sobsey,
2007).
Culture Fast Phage
Results within 16-24 hours;
Differentiates between F-specific and somatic
coliphages;
Infectivity is determined; and
Considered "equivalent" to EPA Method 1601
for groundwater monitoring by EPA's
Alternate Test Procedures program.
Qualitative only; and
Requires laboratory equipment,
reagents (Fast Phage kit), and
training.
Note: CLAT and PCR can be field portable, but all the quantitative methods require laboratory facilities.
Sources: ISO, 1995, 2000, 2001; Grabow, 2001; U.S. EPA, 2001a, b, 2007, 2010; Brussaard, 2004; Fong and Lipp,
2005; Kirs and Smith, 2007; Love and Sobsey, 2007; Gentilomi et al., 2008; Brussaard, 2009; Salter et al., 2010;
Rodriguez, et al., 2012a, b; Salter and Durbin, 2012.
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3. Epidemiological Relationships
Since the 1950s, epidemiological studies have been performed to evaluate relationships between
fecal indicators and recreational swimming-associated illnesses in surface waters. The incidence
of symptoms associated with gastrointestinal, eye, ear, and respiratory illnesses has been found
to be higher in swimmers than in nonswimmers in ambient waters (Priiss, 1998; Wade et al.,
2003; Zmirou et al., 2003).
Over the past several decades, EPA has conducted numerous epidemiological studies in both
marine and freshwaters to evaluate the relationship of water quality indicators and human health
risks. The results of an epidemiological study conducted by Cabelli et al. (1982) found that
densities of enterococci in marine and freshwaters correlated with incidences of swimming-
associated gastrointestinal illness, whereas densities of E. coli were correlated with swimming-
associated gastrointestinal illness only in freshwaters. EPA's NEEAR study found that the
occurrence of gastrointestinal illness in swimmers was positively associated with exposure to
levels of enterococci enumerated by EPA's Enterococcus qPCR Method 1611 in marine and
freshwater (Wade et al., 2008, 2010; U.S. EPA, 2012). The correlation between gastrointestinal
illness and culturable enterococci in the NEEAR studies was positive, but not as strong as the
relationship between illness and enterococci enumerated by qPCR. The odds of gastrointestinal
illness was higher among swimmers compared to non-swimmers on days were coliphages were
detected, but the associations did not achieve statistical significance (Wade et al., 2010). The
statistical power was limited due to the relatively few positive results. In addition, only data on
coliphage presence or absence in 100 mL volume samples were used for the analysis even
though quantitative data may be available. Thus, further analyses of these data may be needed to
fully understand the results of the study.
In 1982, Cabelli et al. suggested that viruses were a primary cause of gastrointestinal illness, in
agreement with quantitative microbial risk assessment (QMRA) modeling that used data from
the NEEAR freshwater study (Seller et al., 2015). QMRA modeling demonstrated that the
illnesses reported during the NEEAR study were consistent with a virus that had an incubation
period similar to NoV (Seller et al., 2015). However, NoV has not been confirmed as the cause
of illness in these primary contact recreators. Interestingly, adenovirus (detected by qPCR) has
been positively associated with gastrointestinal illness at a freshwater beach in Ohio (Lee, 2011).
A consistent association between FIB (E. coli and enterococci) and illness has not been reported
at all beaches where epidemiological studies have been conducted (Colford et al., 2007). This
may be due partially to the fact that FIB in surface waters can come from sources other than
wastewater, such as rainfall, plants, runoff, animals, and human shedding. In some subtropical
and temperate climates, bacteria, such as E. coli and enterococci, can multiply in the
environment, giving a false impression of an increase in fecal pollution (Solo-Gabriele et al.,
2000; Yamahara et al., 2009). Additionally, compared to non-spore-forming FIB, human enteric
viruses have been found to be more persistent in water environments and more resistant to
physical antagonism, such as heat (55°C) (Lee and Sobsey, 2011). There are clear advantages to
having alternative indicators (e.g., other than E. coli or enterococci) that have the following
attributes compared to E. coli and enterococci: The alternative indicators are more closely
associated with viral gastrointestinal illnesses (e.g., that are present in intestinal microflora of
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humans); they do not come from other, non-fecal related sources; they offer improved detection
methods; they do not multiply in the aquatic environment; and they are more closely linked to
the pathogens of concern (i.e., often present when viruses are present and absent in
uncontaminated samples and as resistant to environmental factors as some viral pathogens).
Numerous studies have been conducted to determine whether both somatic and F-specific
coliphages are associated with fecal contamination (Chung and Sobsey, 1993; Moce-Llivina et
al., 2005; Love and Sobsey, 2007). However, only a limited number of epidemiological studies
have evaluated the use of coliphages as an indicator of human fecal contamination in recreational
water. These results are summarized below in chronological order. When available, data on E.
coli and enterococci are also presented for comparative purposes.
3.1 Von Schirnding et al. (1992)
Von Schirnding et al. (1992) conducted a prospective cohort study at two marine beaches in
South Africa with 733 participants (including adults and children). Beach 1 was described as
moderately impacted by human sources of fecal contamination, including septic tank overflows,
feces-contaminated river water, and stormwater runoff. Beach 2 was considered to be less
impacted by known sources of fecal contamination. Participants were recruited at the two
beaches. Those who entered the water above their waist were considered "swimmers" and those
who entered the water up to their waist or who did not enter the water were designated as
"nonswimmers." A telephone follow-up call 3 to 4 days later recorded symptoms that developed
after the beach visit. The symptoms were grouped as gastrointestinal (i.e., diarrhea, vomiting,
stomachache, and nausea), respiratory (i.e., sore throat, cough, cold, runny/stuffy nose), and skin
symptoms.
Water samples were collected on study days at three locations at each beach, both before and
during maximum swimming activity. The following indicators were evaluated using culture-
based methods: fecal coliforms, enterococci, staphylococci, somatic coliphages, and F-specific
coliphages. The density of fecal coliforms and enterococci was statistically significantly higher
at Beach 1 than at Beach 2 (median levels of fecal coliforms: 76.5 colony forming units (CPU)
per 100 mL at Beach 1 and 8.0 CPU per 100 mL at Beach 2; median levels of enterococci: 51.5
CPU per 100 mL at Beach 1 and 2.0 CPU per 100 mL at Beach 2). Insignificant densities of
staphylococci and coliphages were detected at both beaches.
The rates for gastrointestinal, respiratory, and skin symptoms (but not other symptoms including
wheezing, earache, rashes, allergy, headache, backache) were higher for swimmers than
nonswimmers at Beach 1, but the differences were not statistically significant. The relative risks
(RR) of symptoms when comparing swimmers and nonswimmers were 2.45 (95% confidence
interval [CI]: 0.55-10.9) for gastrointestinal symptoms, 3.28 (95% CI: 0.76-15.26) for
respiratory symptoms, and 4.06 (95% CI: 0.52-31.72) for skin symptoms. The differences were
not statistically significant for children younger than 10 years of age or for adults.
The authors suggested that a possible explanation for the higher rates of symptoms among
swimmers than nonswimmers at Beach 1 was that the main sources of contamination were likely
the bathers themselves or the sanitary facilities at the informal settlements close to the study
beaches. This conclusion is supported by the known sources of contamination at Beach 1 and the
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fact that insignificant densities of F-specific coliphages were detected at Beach 1 (because
coliphages are more closely associated with sewage and septage than direct human fecal inputs).
At Beach 2, higher rates of respiratory symptoms were observed among nonswimmers than
swimmers (but the differences were not statistically significant). The authors suggested that this
apparent anomaly may reflect the presence of a respiratory outbreak in the community (and thus
children perceived as sick were restricted from swimming by the parents), but because the
numbers were low and not statistically significant, these findings should not be over-interpreted.
Overall, the authors felt that the study findings suggested a relationship between swimming-
associated illness and water quality, but that larger study sizes (4,000 subjects) would be needed
to detect statistically significant differences.
3.2 Lee et al. (1997)
Lee et al. (1997) studied the risk of gastrointestinal illness associated with white-water canoeing
and rafting in a cohort study of 473 canoeists and rafters using an artificial white-water course
fed by the River Trent in England. The River Trent is a lowland river that receives considerable
volumes of treated sewage and, during heavy rainfall, untreated sewage from storm overflows.
The study was conducted on 11 nonconsecutive days between March and December 1995.
Participants were recruited on the day of the study and given a questionnaire about their
activities on the course, previous use of the course, medical history, and food eaten in the
previous week. A second questionnaire (to be returned by prepaid postage 1 to 2 weeks after the
study) included questions on the range of symptoms (respiratory tract, gastrointestinal, ear and
eye, and general symptoms), date of onset and duration, additional water sports conducted
(including at same course), and food eaten in the week after visiting the course. Gastrointestinal
illness was defined as either vomiting or diarrhea (four or more loose stools in 24 hours), or fever
combined with nausea, stomach pain, or loose bowels.
On each study day, water was tested hourly for levels of E. coli, enterococci (fecal streptococci),
sulfite-reducing clostridia, F-specific RNA coliphages (using ISO method 10705-1), and
culturable enteroviruses.
The study found a statistically significant association between risk of gastrointestinal illness and
density of F-specific RNA coliphages. When comparing the exposure ranges of 26 to 32 PFU per
10 mL and 69 to 308 PFU per 10 mL to the reference levels of 1 to 3 PFU per 10 mL, the RR of
gastrointestinal illnesses was 2.6 (95% CI: 1.3-5.2) and 2.8 (95% CI: 1.3-6.0), respectively.
Other variables significantly associated with increased risk of gastrointestinal illness were
ingestion of water (RR = 1.9, 95% CI: 1.0-3.6 for swallowing two or more times compared to
none), accidentally swimming in slalom course (RR = 2.3, 95% CI: 1.2-4.3), and eating and
drinking before changing clothes (RR = 2.1, 95% CI: 1.1-4.0). Being a regular user of the course
was associated with a reduced risk of gastrointestinal illness (RR = 1.6, 95% CI: 0.8-3.3) for one
to six times per year compared to none; and RR = 0.3 (95% CI: 0.1-0.7) for seven or more uses
compared to none).
18
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The authors stated the observed association between fecal streptococci and E. coli levels and
gastrointestinal illness risk was not seen after controlling for the stronger association seen with
F-specific coliphages. The authors concluded that this study demonstrates the value of F-specific
RNA coliphages as indicators of human fecal contamination associated with risk of
gastrointestinal illness in recreational water.
3.3 Medema et al. (1995) and Van Asperen et al. (1998)
Medema et al. (1995) conducted a pilot study to determine the relationship between
microbiological freshwater quality parameters and the occurrence of health complaints among
triathletes (n = 314) using run-bike-runners as controls (n = 81). Information on the occurrence
of health complaints during the competition and in the week thereafter was collected through a
written questionnaire. The authors did not link reported illnesses to water quality, other than to
report the water quality during the time of the triathlon. The geometric means of FIB were 170 E.
coli CFU 100 per mL and 13 fecal streptococci CFU per 100 mL. F-specific RNA coliphages
geometric mean was 5.6 PFU per 100 mL. Enteroviruses were present at densities of 0.1 PFU per
L. Triathletes reported higher rates of symptoms than run-bike-runners: gastrointestinal (7.7
versus 2.5%), respiratory (5.5 versus 3.7%), skin/mucosal (2.6 versus 1.2%), general (3.5 versus
1.2%), and total symptoms (14.8 versus 7.4%) in the week after the event. Approximately 75%
of triathletes reported ingesting water during the swim event.
Van Asperen et al. (1998) extended the Medema et al. (1995) study over two summers. In a
prospective cohort design, they followed 827 triathletes and 773 run-bike-run controls. A mailed
detailed questionnaire collected data about age, sex, general health, medical, and race history,
exposure to surface freshwaters in the week before and after the race, and occurrence of
gastrointestinal complaints 2 days before, during, and 6 days after the race. Triathletes were also
asked about goggle and wetsuit use during the race and if they ingested water during the
swimming portion of the race. Four different GE endpoints were defined as follows:
• GE_UK: (diarrhea AND three or more bowel movements per day) OR vomiting OR
(nausea AND fever);
• GE_US: vomiting OR (diarrhea AND fever) OR (nausea AND fever) OR (stomach pains
AND fever);
• GE_NL-1: (diarrhea AND three or more loose stools movements per day) AND (at least
two of fever OR nausea OR vomiting OR stomach pains); and
• GE_NL-2: diarrhea OR nausea OR vomiting OR stomach pains.
On each exposure day, water samples were collected along the swimming course. Samples were
analyzed for densities of E. coli, thermotolerant coliforms, fecal streptococci, enteroviruses, and
reoviruses, F-specific RNA coliphages, Salmonella, Campylobacter, Aeromonas, Plesiomonas
shigelloides, Pseudomonas aeruginosa, and Staphylococcus aureus. The geometric mean
(ranges) of the microorganisms during triathlons were: thermotolerant coliforms 78 CFU per 100
mL (0.6 to 650 CFU per 100 mL), E. coli 204 CFU per 100 mL (11 to 2,600 CFU per 100 mL),
fecal streptococci 16 CFU per 100 mL (0.2 to 1,800 CFU per 100 mL), enteroviruses 0.04 PFU
per L (0.007 to 7 PFU per L), and F-specific RNA coliphages 0.7 PFU per L (0.01 to 13.6 PFU
per L).
19
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Depending on the case definition, the attack rates of GE in the week after the event were
observed to be higher among triathletes than among run-bike-runners, with odds ratios (ORs)
ranging from 1.6 to 2.3. The adjusted risk of GE ranged from 2.9 to 4.7, depending on the case
definition. All ORs were statistically significant.
The study showed that both E. coli and thermotolerant coliforms were associated with risk of
gastrointestinal illness after bathing in freshwaters. The authors noted that levels of E. coli were
higher than the levels of thermotolerant coliforms, and that the densities of E. coli were much
more closely correlated with illness rates than the densities of thermotolerant coliforms. A
relationship between health and fecal streptococci, enteroviruses, and F-specific RNA coliphages
was not observed (Van Asperen et al., 1998).
3.4 Wiedenmann et al. (2006)
Wiedenmann et al. (2006) conducted a randomized control epidemiological study at five
freshwater bathing beaches in Germany. The probable or possible sources of fecal contamination
at these sites varied, but included raw and treated municipal effluent, agricultural runoff, and
contamination from water fowl. Only one of the five lakes had a known point-source of
contamination. A cohort of 2,196 participants (including adults, children, and teenagers) was
recruited from the local population and randomized into bathers and nonbathers. Two to three
days prior to exposure, participants were interviewed and underwent a brief medical
examination. Bathers were exposed to water for 10 minutes and were asked to immerse their
heads at least three times. Nonbathers made no contact with the water. One week after exposure,
all participants were interviewed and underwent medical inspection of the throat, eyes, and ears.
Three different GE endpoints were defined as follows:
• GE_UK: (diarrhea AND three or more bowel movements per day) OR vomiting OR
(nausea AND fever) OR (indigestion AND fever);
• GE_UK-wf (GE_UK without consideration of stool frequency: diarrhea OR vomiting
OR (nausea AND fever) OR (indigestion AND fever); and
• GE_NL-2: diarrhea OR nausea OR vomiting OR stomach pains.
Water samples were collected at 20-minute intervals from swimming and nonswimming zones
during the study period. The following microbiological parameters were evaluated: E. coli,
enterococci, Clostridiumperfringens, aeromonads, pyocyanine-positive Pseudomonas
aeruginosa, and somatic coliphages. The median densities (ranges) of the microorganisms were:
20 somatic coliphages PFU per 100 mL (10 to 3,780 PFU per 100 mL; method ISO 10705-2);
136 E. coli CPU per 100 mL (4.7 to 5,344 CPU per 100 mL), 37 intestinal enterococci CPU per
100 mL (3.0 to 1,504 CPU per 100 mL), 15 Clostridiumperfringem CPU per 100 mL (9 to 260
CPU per 100 mL), 8,200 aeromonads CPU per 100 mL (600 to 31,400 CPU per 100 mL), and 10
Pseudomonas aeruginosa CPU per 100 mL (10 to 100 CPU per 100 mL).
For somatic coliphages, the no observed adverse effect level (NOAEL) was 10 PFU per 100 mL
for the two less stringent (broader) illness definitions (GE_UK-wf and GE_NL-2) and 150 PFU
per 100 mL for the most stringent (most narrowly defined) illness definition (GE_UK). The RRs
of GE_NL-2, GE_UK-wf, and GE_UK when comparing bathing in waters with somatic
coliphage levels above the NOAEL, with nonbathing were statistically significant and ranged
from 1.8 (95% CI: 1.2-2.6), 2.5 (95% CI: 1.5-4.0), and 4.6 (95% CI: 2.1-10.1), respectively. For
20
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all three illness definitions, swallowing water with somatic coliphage levels above the NOAEL
resulted in a significantly higher attributable risk of illness than not swallowing water.
The authors concluded that reasonable estimates for NOAELs at an average bathing intensity site
are 100 E. coli CPU per 100 mL, 25 enterococci CPU per 100 mL, and 10 somatic coliphages
PFU per 100 mL. Wiedenmann et al. (2006) concluded that a NOAEL approach would be
practical for setting recreational water standards. The authors suggested that somatic coliphages
would be appropriate alternative fecal indicators that could be used to set standards for
freshwater just as well as E. coli and enterococci, especially in tropical climates, where E. coli
and enterococci may be less reliable as indicator organisms.
3.5 Colford et al. (2005, 2007)
Colford et al. (2005, 2007) conducted a prospective cohort epidemiological study at six beaches
near Mission Bay, California in 2003. The study cohort consisted of nearly 8,000 participants.
The authors reported that MST evaluation at Mission Bay suggested that only a minor portion of
fecal input was from human point sources during the study period.
Water quality was monitored using traditional FIB enumeration methods (culturable enterococci,
fecal coliforms, and total coliforms) and a subset of samples was also evaluated using: (1) new
methods for measuring traditional FIB (chromogenic substrate or qPCR), (2) Bacteroides, (3)
coliphages (somatic and F-specific coliphages), and (4) human enteric viruses (adenovirus and
NoV). F-specific and somatic coliphages were detected and quantified in 1 L volumes of water
by a modification of EPA Method 1601 for enrichment and spot plating that provides a MPN
estimate of coliphage density. Roughly 68% of the samples had detectable levels of somatic
coliphages and maximum densities were observed near 36 MPN per 100 mL. F-specific
coliphages were detected in 11% of the samples and maximum densities reached only one MPN
per 100 mL. No NoV was found and adenovirus was found only in one sample. The observed
geometric means for enterococci (measured by qPCR) and fecal coliforms were 65 estimated
number per 100 mL and 25 MPN per 100 mL, respectively.
Interviewers recorded which water sampling site was closest to the location of the individual or
family on the beach. Participants were asked to complete a questionnaire prior to their departure
from the beach. The questionnaire assessed possible exposures at the beach, and exposures or
illnesses experienced during the previous two to three days. A follow-up telephone interview was
conducted 10 to 14 days after the study to gain information on health outcomes. Health outcomes
measured in the investigation included gastrointestinal illness, respiratory symptoms, and skin
ailments. Two definitions of highly credible gastrointestinal illness (HCGI) were measured. One
(HCGI-1) was defined as (1) vomiting; (2) diarrhea and fever; or (3) cramps and fever. The
second (HCGI-2) was defined as vomiting plus fever. Multivariate analysis was conducted to
assess relationships between health outcomes and degree of water contact or levels of water
quality indicators. These analyses were adjusted for confounding covariates such as age, gender,
and ethnicity.
Of the measured health outcomes, only skin rash and diarrhea were consistently significantly
elevated in swimmers compared to nonswimmers. For diarrhea, this risk was strongest among
children 5 to 12 years old. No correlation was found between increased risk of illness and levels
21
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of Bacteroides or Enterococcus, as detected using rapid methods (qPCR) or for somatic
coliphages. A significant association was observed between the levels of F-specific coliphages
and HCGI-1, HCGI-2, nausea, cough, and fever. The adjusted odds ratio (AOR) was 1.26 (95%
CI: 1.06-1.48) for HCGI-1; 1.43 (95% CI: 1.13-1.82) for HCGI-2; 1.34 (95% CI: 1.16-1.55) for
nausea; 1.22 (95% CI: 1.02-1.48) for cough; and 1.25 (95% CI: 1.09-1.44) for fever. Colford et
al. (2005, 2007) suggested that these associations be interpreted cautiously because only a small
number of participants were exposed to the water at times when F-specific coliphages were
detected.
3.6 Wade et al. (2010)
Wade et al. (2010) enrolled 6,350 participants in prospective cohort epidemiological studies
conducted at three marine beaches. These beaches were located in Mississippi (Edgewater
Beach), Rhode Island (Goddard Beach), and Alabama (Fairhope Beach), and were known to be
impacted by discharge from nearby WWTPs. The study in Mississippi was conducted in 2005
and studies in Rhode Island and Alabama were conducted in 2007. Upon study enrollment,
participants were interviewed to gather information on exposure and health status and completed
a questionnaire prior to exiting the beach for the day. Based on their activities for the day,
participants were divided into cohorts that included swimmers and nonswimmers. Swimming
was defined as body immersion (i.e., immersion to the waist or higher). Nonswimmers were
considered unexposed to recreational water. Health endpoints evaluated during the study
included upper respiratory illness (defined as any two of the following: sore throat, runny nose,
cough, cold, or fever), earache, eye irritation, rash, and gastrointestinal illness (defined as any of
the following: (1) diarrhea (three or more loose stools in a 24-hour period); (2) vomiting; (3)
nausea and stomachache; or (4) nausea or stomachache, and interference with regular activities
(missed regular activities as a result of the illness).
Water samples were collected in duplicate at three different time points along three transects
perpendicular to the shoreline on each study day. A total of 1,242 water samples were collected.
Water samples were tested for a variety of indicators, including a faster test for F-specific
coliphages based on a CLAT assay, which also distinguishes F-specific RNA coliphages and
F-specific DNA coliphages. F-specific coliphages were also evaluated using a modified version
of EPA Method 1601, called the 24-hour SPOT assay. Samples were tested for Enterococcus
spp. using EPA Method 1600 (a culture-based method) and Enterococcus and Bacteroidales by
qPCR.
Wade et al. (2010) reported that 56% (100 of 222) of samples at Fairhope Beach and 65% (203
of 425) of samples at Goddard Beach were positive for F-specific coliphages by the modified
EPA Method 1601.5 Fewer samples were positive for F-specific coliphages by the CLAT assay.
At Fairhope Beach, 4% (8 of 228) and 6% (14 of 224) of samples were positive for F-specific
RNA and F-specific DNA coliphages, respectively. At Goddard Beach, 7% (31 of 425) and 9%
(37 of 423) of samples were positive for F-specific RNA and F-specific DNA coliphages,
respectively. The AOR of gastrointestinal illness was significantly higher among swimmers
compared to nonswimmers on days when F-specific RNA (AOR = 1.80, 95% CI: 1.22-2.66) or
5 Edgewater Beach, data collection was stopped several days early due to the effects of Hurricane Katrina.
Bacteriophage results were not reported for Edgewater Beach.
22
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F-specific DNA coliphages (AOR = 1.69, 95% CI: 1.16-2.47) were detected by the CLAT assay
or F-specific coliphages were detected by a modified 1601 method (AOR = 1.70, 95% CI: 1.12-
2.57). An increased, but not statistically significant risk of gastrointestinal illness among
swimmers was observed for a 1-logio increase in each of the three F-specific coliphages
measured. F-specific coliphages measured by the modified 1601 method were not associated
with gastrointestinal illness among swimmers. Other illnesses (i.e., respiratory illness, earache)
did not show a relationship with the presence of coliphages.
The risks of both gastrointestinal illness and diarrhea were significantly associated with exposure
to Enterococcus and Bacteroidales (enumerated using qPCR). F-specific coliphages, using the
modified 1601 method, had a positive correlation with gastrointestinal illness in marine waters,
but like culturable enterococci, the association was not significant over the full range of water
quality (Wade et al., 2010).
3.7 Abdelzaher et al. (2011)
Abdelzaher et al. (2011) performed a randomized control exposure epidemiological study to
evaluate water quality and daily cumulative health effects for bathers at a nonpoint source
subtropical marine recreational beach in Miami, Florida. Study participants were randomly
assigned to either the 'bather' or the 'nonbather' categories. Those assigned to the bather
category were asked to spend 15 minutes in the water and nonbathers were asked to spend 15
minutes on the beach only. The daily number of bathers varied over the course of the study, with
a total of 652 bathers (daily average = 43, daily range = 29-55). Similarly, for nonbathers, the
total number was 651 (daily average = 43, and daily range = 25-60).
Health effects considered during the study included gastrointestinal illness, skin ailments, and
respiratory illness. Gastrointestinal illness was defined as all cases of vomiting or diarrhea, or all
reported cases of indigestion or nausea accompanied by a fever. 'Diarrhea' was defined as
having three or more runny stools within a 24-hour period.
Water samples were categorized as "daily composite samples," which were combined water
samples collected throughout each sampling day either by bathers or study staff. Bather-collected
samples were analyzed for a variety of indicator organisms, including enterococci (using three
detection methods: membrane filtration, chromogenic substrate, and qPCR), fecal coliform, E.
coli, Clostridium perfringens (all measured by membrane filtration), somatic and F-specific
coliphages (measure by EPA Method 1602), human- and dog-associated MST markers
(Bacteroides thetaiotaomicron, BacHum-UCD, HF8, and DogBac), human polyomavirus, and
the esp gene of Enterococcus faecium. Pathogens evaluated in the study included:
Staphylococcus aureus, Vibrio vulnificus, the protozoa Cryptosporidium spp. and Giardia spp.,
NoV, enterovirus, and hepatitis A virus. Investigator-collected composite samples were used for
pathogen analysis using traditional large-volume concentration methods.
Average daily excess illness percentage rates (calculated by subtracting the daily illness rates for
nonswimmers from that for swimmers) for gastrointestinal, skin, and acute febrile respiratory
illness were 2.0% (standard deviation [SD] = 3.3), 5.6% (SD = 4.7), and 1.2% (SD = 2.9),
respectively. No statistically significant correlations between health outcomes and any of the
indicator organisms, including coliphages, were identified in this investigation.
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Somatic coliphages were detected (range 0.3 to 1.7 PFU per 100 mL) on four of 15 days tested.
On three of five days where the greatest level of excess gastrointestinal illness occurred, somatic
coliphages were detected. Although no statistically significant associations between water
quality and illness were observed, the authors state that this overlap is suggestive of a potential
correspondence between the presence of somatic coliphages and increased risk of gastrointestinal
illness. Given the low number of positive samples and that F-specific coliphages were not
detected in any of the samples, no apparent association between this potential indicator and
health outcomes was observed in this study. The authors suggest that a possible reason F-specific
coliphages were not detected may be due to the small volume of water for each sample (100 mL)
compared to other studies, such as Colford et al. (2005, 2007) who used 1 L samples, thereby
increasing detection limits.
3.8 Griffith et al. (personal communication, 2015)
The Southern California Coastal Water Research Project Authority conducted two prospective
cohort studies at California beaches (Avalon Bay (Avalon), Doheny State Beach (Doheny)) in
2007 and 2008. Both Avalon and Doheny were impacted by faulty sanitary sewer infrastructure,
which allowed microbial contamination to reach the beach via groundwater.
The studies enrolled 8,226 swimmers across the two beaches and each swimmer's water
exposure was recorded. Water samples were collected several times per day at multiple locations
at each beach and analyzed for up to 30 target indicators using more than 50 different
methodologies. Interviewers contacted participants by phone 10 to 14 days later and recorded
symptoms of gastrointestinal illness occurring after their beach visit. Regression models were
used to evaluate the association between water quality indicators and gastrointestinal illness
among swimmers at each beach.
In these two studies, F-specific coliphages measured by EPA Method 1602 had a stronger
association with health outcomes than did culturable enterococci measured by EPA Method 1600
at Doheny and Avalon beaches. When all environmental conditions were considered in aggregate
at Doheny, the OR for F-specific coliphages was 1.9 and statistically greater than 1 (p<0.05),
whereas the OR for enterococci was only 1.2 and not significant (p>0.05). At Avalon, the OR for
F-specific coliphages was 1.9 compared to less than 1.1 for enterococci, though neither was
significantly different than 1.0 (p>0.05). Under highrisk conditions, F-specific coliphages were
significantly associated with gastrointestinal illness (p<0.05) and the estimated OR was more
than double that for culturable enterococci at both Avalon and Doheny. Associations were also
found between F-specific coliphages and adenovirus observed at Doheny Beach (Love et al.
2014). The authors noted that when the contamination source is primarily human fecal material,
indicators like F-specific coliphages are better predictors of the health risk.
3.9 General Conclusions from Epidemiological Studies
Eight epidemiological investigations have evaluated the relationship between swimming-
associated illness and presence of coliphages. Studies specifically evaluating the link between
levels of somatic or F-specific coliphages and incidence of illness resulting from exposure to
fresh and marine waters are summarized in Table 4.
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With the exception of one small study (Von Schirnding et al., 1992), all of the epidemiological
investigations that evaluated coliphages detected somatic or F-specific coliphages. There is
considerable heterogeneity in the results of these studies, even within similar designs. For
example, some studies found a significant association between the levels of F-specific coliphages
and two definitions of gastrointestinal illness, cough, fever, and nausea, but found no association
between increased risk of illness and levels of somatic coliphages, Bacteroides, or Enterococcus
(Colford et al., 2005, 2007). Similarly, when comparing swimmers to nonswimmers on days
when F-specific RNA or DNA coliphages were detected, Wade et al. (2010) found statistically
significant increases in risk of gastrointestinal illness. In these cases, F-specific coliphages were
potentially useful indicators.
On the other hand, at a marine recreational beach in Miami with no known point source of
contamination, Abdelzaher et al. (2011) detected somatic coliphages (range 0.3 to 1.7 PFU per
100 mL) on four of 15 days tested, three of which were on days characterized by the highest
excess gastrointestinal illness. However, F-specific coliphages were not detected in any of the
samples, and no statistically significant correlations between water quality and illness were
found. In this case somatic coliphages may have been useful, but F-specific coliphages were not
useful, due to being below the detection limits of methods.
Overall, the epidemiological evidence is suggestive of a potential relationship between
coliphages and human health. In more than half the studies (Lee et al., 1997; Colford et al., 2005,
2007; Wiedenmann et al., 2006; Abdelzaher et al., 2011, Wade et al., 2010), the presence of
coliphages was associated with swimming-associated gastrointestinal illness. Wade et al. (2010)
found that the AOR of gastrointestinal illness was higher among swimmers compared to
nonswimmers on days when F-specific RNA and DNA coliphages were detected. These studies
suggest that somatic (Wiedenmann et al., 2006) and F-specific coliphages (Lee et al., 1997;
Colford et al., 2005, 2007; Wade et al., 2010; Griffith et al., personal communication, 2015) hold
potential as feasible alternative water quality indicators in marine and freshwaters, with and
without point-source contamination (Lee et al., 1997; Colford et al., 2005, 2007; Wiedenmann et
al., 2006; Wade et al., 2010; Abdelzaher et al., 2011). As mentioned in Section 1.3, a good
indicator should be correlated to health risk. Evaluation of the results of these eight
epidemiological studies suggests that overall the studies support coliphages as potential
indicators of gastrointestinal illness from recreational exposures.
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Table 4. Summary of epidemiological studies.
Von Schirnding et al.
(1992),
n=733,
marine
Lee etal. (1997),
n=473,
fresh
van Asperen (1998),
827 triathletes and
773 run-bike-run
controls,
Fresh
Wiedenmann et al.
(2006),
n=2,196,
fresh
Colford et al. (2005,
2007),
n= 8,000,
marine
Wade etal. (2010),
n= 6,350,
marine
Abdelzaher et al.
(2011),
n=652,
marine
Griffith etal.
(personal
communication,
2015)
Somatic
coliphages and F-
specific coliphages,
fecal coliforms,
enterococci
F-specific RNA
coliphages, E. coli,
enterococci, culturable
enteroviruses
F-specific coliphages,
E. coli, fecal
streptococci,
thermotolerant
coliforms,
enteroviruses
Somatic coliphages, E.
coli, enterococci
F-specific coliphages
(qPCR), somatic
coliphages, culturable
enterococci, fecal
coliforms, total
coliforms, adenovirus,
andNoV
F-specific RNA
coliphages (CLAT), F-
specific DNA
coliphages (CLAT), F-
specific coliphages
(modified EPA
Method 1601),
enterococci
Somatic coliphages,
enterococci, fecal
coliforms, E. coli
F-specific coliphages
(Method 1602);
enterococci, and 30
target indicators with
50 different
methodologies.
Low densities of coliphages were detected at
both beaches. Rates for gastrointestinal,
respiratory, and skin symptoms were higher for
swimmers than nonswimmers at Beach 1, but
the results were not statistically significant.
Statistically significant association between risk
of gastrointestinal illness and density of F-
specific RNA coliphages. The observed
association between fecal streptococci and E.
coli levels and risk of gastrointestinal illness
was not seen after controlling for the stronger
association seen with F-specific coliphages.
Risk of gastrointestinal illness increased
significantly at levels with thermotolerant
coliforms (>220 CPU per 100 mL) or E. coli
(>355 CPU per 100 mL), compared to lower
levels (< 120 CPU per 100 mL tolerant
coliforms or <238 CPU per 100 mL for E. coli).
No exposure-response relationship observed for
F-specific coliphages, fecal streptococci, or
enteroviruses.
Significantly increased RR of gastroenteritis for
bathing in waters with somatic coliphage levels
above the NOAEL (10 PFU per 100 mL) versus
nonbathing.
Significant association between the levels of F-
specific coliphages and HCGI-1, HCGI-2,
nausea, cough, and fever.
Significantly higher risk of gastrointestinal
illness comparing swimmers with nonswimmers
on days when coliphages were present.
No statistically significant correlations between
health outcomes and any indicator organisms,
including somatic coliphages.
F-specific coliphages (measured using EPA
Method 1602) had a stronger association with
health outcomes than EPA Method 1600 at the
two beaches studied.
Coliphage levels
were too low to
evaluate.
Yes; F-specific
coliphages
No
Yes; somatic
coliphages
Yes; F-specific
coliphages
Yes; F-specific
coliphages
Somatic coliphages
detection overlaps
with highest illness
days.
Yes; F-specific
coliphages
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4. Occurrence in the Environment
Coliphages, including F-specific DNA, F-specific RNA coliphages, and somatic coliphages have
been detected and proposed as indicators of fecal contamination in a variety of environments.
Most studies investigating coliphages as fecal indicators focused on environments that may be
contaminated with human or animal fecal matter, such as water entering or exiting sewage
treatment facilities, stormwater, natural lakes, rivers, streams, groundwater, seawater, and beach
sand (Zaiss 1981; Sogaard, 1983; Payment et al., 1988; Araujo et al., 1997; Paul et al., 1997;
Gantzer et al., 1998; Davies et al., 2003; Bonilla et al., 2007; Charles et al., 2009; Haramoto et
al., 2009, 2011; Payment and Locas, 2011; Wu et al., 2011).
Studies investigating the presence of coliphages and viruses in different types of environmental
waters are described below (Section 4.1). A review of the literature shows that generalizations
across studies are difficult because the detection of microorganisms from fecal contamination,
including viruses and coliphages are inconsistent and dependent on a number of important
factors (WHO, 2001). Generally, when any two studies on coliphages and viruses are compared,
there are differences between the type of detection method used - both for the coliphages and the
pathogen. In addition to different detection methods, the differences between studies might
include the following: type of coliphage tested (i.e., somatic, F-specific DNA, F-specific RNA);
specific pathogens tested; number of samples taken; volume of sample taken; level of
contamination; type of environment from which samples were taken; location of the
environment; resistance of the coliphages and pathogens to environmental stressors and growth;
transport characteristics of the coliphages and pathogens; carriage rates and shedding patterns of
the coliphages and pathogens among host populations; presence of host populations; waste
management practices; rainfall; time of year; and statistical analyses used (WHO, 2001; Bonilla
et al., 2007; Wu et al., 2011). Given these differences along with the variable occurrence of
viruses in fecal sources, it is not surprising that the presence of fecal indicators including
coliphages and the presence of enteric viruses varies between studies.
4.1. Associations between Coliphages and Viruses
Some studies have reported an association between the presence of coliphages and human
viruses (Havelaar et al., 1993; Jiang et al., 2001; Ballester et al., 2005), while other studies have
found no association between their presence (Ibarluzea et al., 2007; Jiang et al., 2007; Boehm et
al., 2009; Viau et al., 201 Ib). Meta-analyses of peer-reviewed studies looking at the occurrence
of microbial indicators and pathogens, including coliphages and viruses, can give an overview of
the field.
In one recent study, Wu et al. (2011) analyzed a broad range of 540 indicator-pathogen pairs
from studies conducted between 1970 and 2009 in a variety of water environments including:
rivers, lakes, reservoirs, ponds, estuaries, costal and marine waters, and wastewater (Wu et al.,
2011). Groundwaters, treated drinking waters, and sand/sediments were not included in the
study. The data were analyzed using a logistic regression model adjusted for indicator classes,
pathogen classes, water types, pathogen sources, sample size, the number of samples with
pathogens, the detection method, year of publication, and statistical method. The association is
presented as an OR, where an OR greater than one signifies that the presence of the indicator is
associated with the presence of the pathogen. Not surprisingly, no single indicator was
27
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significantly correlated with all the pathogens evaluated.6 Coliphages (F-specific and somatic
together) and F-specific coliphage densities were more likely to be correlated with pathogens
than the other traditional indicators (E. coli, enterococci, and fecal coliforms) (Wu et al., 2011).
The associations between coliphages and pathogens were not statistically significant (OR = 1.29,
p-va\ue = 0.186 and OR = 1.27, p-va\ue = 0.625, respectively). See Table 5 below for specific
OR and/>-values between different categories of coliphages or indicators and pathogens in water.
Silva et al. (2010) also found that in water samples collected from 16 beaches along the
Portuguese coast there was no relationship between viral detection (hepatitis A and NoV) and the
European regulatory-based bacterial indicators total coliform, fecal coliform, E. coli, and fecal
enterococci.
Table 5. Number of cases and outcome of the logistical regression analysis of the
association between coliphages and pathogens in water.
Fee ;il indicator
Coliphagesb
F-specific
coliphages
F-specific RNA
coliphages
Somatic coliphages
E. coli
Enterococci
Fecal coliforms
Number of cases"
Uncorrelated
45
24
15
20
29
34
78
Correlated
40
16
8
10
11
12
48
OR Value
1.29
1.27
0.75
0.70
0.52
0.47
0.84
/7-Value
0.186
0.625
0.518
0.364
0.070
0.032
0.405
95% Confidence limits
0.82
0.48
0.31
0.32
0.25
0.24
0.56
2.05
3.35
1.80
1.52
1.06
0.94
1.27
Source: Based on Table 2 in Wu et al. (2011).
a An individual case of an indicator-pathogen pair represents a statistical analysis of a published dataset of one
indicator type with one pathogen type where the methods of statistical analysis, correlation coefficients, andp-
values were reported.
b Includes F-specific and somatic coliphages.
OR values above 1 are in bold.
Studies have evaluated the association between pathogens and different subsets of coliphages
(i.e., somatic, F-specific DNA and RNA) and report variable results which are influenced by the
environments in which the studies are conducted (Ballester et al., 2005; Savichtcheva and Okabe,
2006; Payment and Locas, 2011). For example, Wu et al. (2011) report that no indicator-
pathogen pairs were significantly associated, except for F-specific coliphage-adenovirus pairs
(OR = 25.5,/7-value = 0.019) (see Table 6 below). Wu et al. (2011) also found that the
association between indicators and pathogens is significantly stronger in brackish and saline
water than in freshwater. Therefore, the papers in this chapter are separated into those studies
conducted in freshwater and those conducted in saline or brackish water. Because Wu et al.
(2011) conducted a meta-analysis, which is summarized above, that includes most of the studies
comparing coliphages to human viruses, only a few of the illustrative studies that compare
coliphages to human viruses in ambient water are summarized in Sections 4.1.1 and 4.1.2 below.
6 Individual articles evaluated different pathogens. Pathogens (and pathogen genes) paired with indicators included
Giardia, Cryptosporidium, Campylobacter, Helicobacter pylori, Salmonella, shiga toxin genes, Pseudomonas
aeruginosa,Aeromonads, Vibrio, Staphylococcus aureus, hepatitis A virus, adenoviruses, astroviruses, NoVs,
sapoviruses, enteroviruses, human enteric viruses, filamentous fungi, yeasts, and Candida albicans.
28
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Table 6. Logistic regression of the association between indicators and different pathogens
in water.
Indicators
Pathogens
Adenoviruses
Cryptosporidium
spp.
Enteroviruses
Giardia spp.
F-specific coliphages
OR value (/?-value);
[95% Confidence
Limits]
25.5 (p = 0.019);
[1.72, 377.92]
NR
1.2 (p = 0.810);
[0.27, 5.29]
NR
Somatic coliphages
OR value (/?-value);
[95% Confidence
Limits]
1.25 (p = 0.862);
[0.10, 15.50]
0.74 (p = 0.791);
[0.08, 6.97]
NR
1.06 (p = 0.965);
[0.09, 12.42]
E. coli;
[95% Confidence
Limits]
NR
NR
1.19 (0.869);
[0.16,8.99]
NR
Enterococci;
[95% Confidence
Limits]
NR
0.73 (0.700);
[0.14,3.70]
0.87 (0.858);
[0.18,4.23]
1.06 (0.950);
[0.18,6.36]
Note: Data are from Wu et al. (2011).
Numbers in the table are the OR values followed by the ^-values in parentheses. OR values above 1 are in bold.
NR (not reported) indicates that the data were not included in the paper.
Pathogens and indicators are listed in alphabetical order.
Effects of human virus detection methods on associations between fecal indicators and
pathogens
As briefly described above in Section 2.3, there are currently numerous methods to detect human
viruses. These include culture methods, molecular methods, and a combination of the two (Fong
and Lipp, 2005). Similar to coliphage detection methods, each method has advantages and
disadvantages, which in turn affect the type of data collected, including both quantity and the
type(s) of virus(es) detected. An overview of the strengths and weaknesses of each enteric virus
detection method is shown below in Table 7. For example, according to Moce-Llivina et al.
(2005), genomic techniques used to detect human enteroviruses and other human viruses have
detection rates from 7 to 70% and are not always consistent with the values of other methods for
enumerating the same organisms. Reasons for the variability between PCR and culture-based
techniques are due in part to: (1) PCR does not distinguish between infectious and noninfectious
viruses (i.e., live and dead viruses); (2) the high sensitivity of PCR may contribute to artifacts,
which could result in false positives; and (3) natural inhibitors in the environment may reduce or
block PCR amplification resulting in false negatives or under-representation of infectious viruses
(Fong and Lipp, 2005; Moce-Llivina et al., 2005). It is important to keep in mind that differences
in enteric virus detection methods (see Table 7) combined with differences in coliphage
detection methods (see Table 3) may greatly affect the presence, absence and/or strength of
correlations found between coliphages and enteric viruses.
29
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Table 7. Comparison of common methods for the detection of pathogenic human enteric
viruses from environmental sources.
Method
Advantages
Disadvantages
Cell culture
• Provides quantitative data; and
• Infectivity can be determined.
Lengthy processing time (takes days to
weeks);
Relatively more expensive than PCR;
and
Not all viruses from environmental
samples can grow in cell culture (e.g.,
NoV).
PCR (RT-PCR)
• Rapid; •
• Can be quantitative (e.g., end point •
analysis); and
• Increased sensitivity and specificity •
compared to cell culture.
Usually qualitative;
Inhibitors may be present in the
environmental matrix; and
Infectivity cannot be determined3.
Nested PCR
(semi-/heminested)
• Increased sensitivity compared to •
conventional PCR; and •
• Can replace PCR confirmation
steps, such as hybridization. •
Qualitative only;
Inhibitors may be present in the
environmental matrix;
Potential risk of carryover
contamination when transferring PCR
products; and
Infectivity cannot be determined".
Multiplex PCR and Multiplex
RT-PCR
Several types, groups, or species of •
viruses can be detected in a single
reaction; and
Saves time and cost compared to •
PCR.
Difficult to achieve equal sensitivity
for all targeted virus species, groups, or
types;
May produce nonspecific amplification
in environmental samples);
Inhibitors may be present in the
environmental matrix; and
Infectivity cannot be determined3.
qPCR/RT-qPCR
Provides quantitative data;
Confirmation of PCR products is
not required (saves time); and
Can be done in a closed system,
which reduces risk of
contamination compared to nested
PCR.
The lower limit of quantification is
higher than the lower limit of detection,
so qPCR can be considered less
sensitive than presence/absence PCR;
Can be more affected by inhibitors
present in the environmental matrix
than culture methods; and
Infectivity cannot be determined".
ICC-PCR and ICC-RT-PCR
Improves detection of infectious
viral pathogens compared to
conventional cell culture;
Detects viruses that do not produce
cytoplasmic effects in cell culture;
and
Provides results in half the time
required for conventional cell
culture.
Less time-efficient and more costly
than direct PCR detection;
Carryover detection of DNA of
inactivated viruses inoculated onto
cultured cells is possible; and
Cannot be used for viruses that cannot
be cultured.
Note: Table modified from Table 2 in Fong and Lipp (2005).
a Can determine infectivity if conducted in combination with ICC. See row on ICC-PCR and ICC-RT-PCR in table
for more details.
30
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4.1.1 Coliphage - Virus Associations in Freshwater
In studies that evaluated the association between the occurrence of coliphages and viruses in
freshwater, results have varied. For example, Espinosa et al. (2009) found a strong association
between F-specific coliphages and enterovirus (p-value = 0.0182), but a weak relationship with
coliphages and rotavirus (p-value = 0.1502) and astrovirus (p-value = 0.4587) in high-altitude
surface water.
In a four-year study of surface source waters using 10 testing locations in the Netherlands,
Lodder et al. (2010) found a significant association between densities of coliphages (F-specific
and somatic) and enteroviruses, but not between coliphages and other viruses (NoV, rotavirus,
and reovirus) or between the other viruses (NoV, rotavirus, and reovirus). NoV and rotavirus
were detected in 45% and 48% of the samples, respectively. Infectious enterovirus and reovirus
were detected in approximately 80% of the tested samples. Somatic and F-specific coliphages
were detected in 100% and 97% of the samples, respectively. In the two samples where no F-
specific coliphages could be detected, enteroviruses were present, and in one sample and
rotavirus and NoV was also detected. Lodder et al. (2010) concluded that their results do not
support a role for coliphages as indicators of source water quality, however, they also conclude
that coliphages may be useful for determining treatment efficiencies.
Payment and Locas (2011) used 20 years of sampling data from their laboratory to examine the
association between pathogens and multiple microbial indicators, including coliphages, in
sewage, surface water, and groundwater. Although the authors review data for several water
types, coliphage associations with pathogens were investigated in groundwater. Their analysis of
242 samples from 25 municipal groundwater well sites indicated that somatic and F-specific
RNA coliphages were not predictive of virus presence or absence. This was due in part to the
low numbers of coliphages present in the samples and their infrequent detection (Payment and
Locas, 2011).
Viau et al. (201 Ib) found no significant association between the presence of F-specific
coliphages and adenovirus, enterovirus, NoV GI, and NoV Gil in tropical coastal streams.
Additionally, Hot et al. (2003) found no significant association between the density of somatic
coliphages and the presence of viral pathogens (RT-PCR detection of the genome of hepatitis A
virus, NoV GI and Gil, astrovirus, rotavirus, and infectious enteroviruses) in concentrated
surface river water samples. In the 68 samples taken over 12 months, genomic detection of
human pathogenic viruses was not statistically associated with the levels of somatic coliphages
in surface water (Hot et al., 2003). For more information on the detection methods used, see
Table 8 below.
4.1.2 Coliphage-Virus Associations in Saline or Brackish Water
The associations between coliphages and viruses in saline or brackish waters are also varied.
Jiang et al. (2001) found that in urban runoff- impacted coastal waters, the presence of human
adenovirus was significantly associated with the presence of F-specific coliphages (Jiang et al.,
2001). Moce-Llivina et al. (2005) found that in seawater samples at public beaches, somatic
coliphages were the best indicators of enteroviruses out of all of the indicators tested (F-specific
coliphages, total coliforms, fecal coliforms, and enterococci) as they were found in higher
31
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numbers than other fecal indicators, including F-specific coliphages, and their amounts were
indicative of enterovirus levels (Moce-Llivina et al., 2005). Similarly, Ballester et al. (2005)
found that in samples of marine water, both F-specific and somatic coliphages were significantly
associated with adenoviruses, and F-specific coliphages were also significantly associated with
rotavirus and enterovirus. Neither type of coliphage was significantly associated with the
presence of astroviruses (Ballester et al., 2005). The amounts of coliphages and viruses varied by
season. From seasonal and proximity data, it appeared that coliphages were more associated with
viral presence than E. coli and that F-specific coliphages had the highest association with viral
presence (Ballester et al., 2005).
In contrast, in a study of the occurrence and distribution of FIB (total coliform, fecal coliform,
and Enterococcus\ F-specific coliphages, human adenovirus, and enterovirus in freshwater
streams and an estuary, Jiang et al. (2007) found a strong association between the occurrence of
FIB and F-specific coliphages, but no association between the presence of F-specific coliphages
and human adenovirus or enterovirus. Jiang et al. (2007) found that the detection of human
viruses depends on a seasonal and freshwater-to-saltwater distribution pattern that was the
opposite of that of FIB and coliphages. For more information on the detection methods used, see
Table 8 below. Similarly, Boehm et al. (2009) did not find an association between the presence
of coliphages, including somatic and F-specific DNA and F-specific RNA coliphages, and
human enterovirus or adenovirus in marine waters in Avalon Beach, California (Boehm et al.,
2009).
A summary of the above papers, detection methods, and quantitative data (when available) are
presented below in Table 8. A systematic literature review was not conducted, so the studies
shown in Table 8 are only a subset of the studies that likely exist.
32
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Table 8. Summary table of coliphages - virus correlations in ambient water.
Study
Baggi et al.
(2001)
Jiang et al.
(2001)
Hot et al.
(2003)
Skraber et al.
(2004b)
Ballester et al.
(2005)
Water type
(Location)
Fresh
(Switzerland)
(upstream of
WWTP)
Marine
Coastal waters
impacted by
urban run-off
(Southern CA)
Fresh river
(France)
Fresh river
(France)
Marine
Coastal water
impacted by
WWTP
discharge
(Boston, MA)
Coliphage
Coliphages detected detection
method
Somatic coliphages ISO 10705-1
(means: 1.9 and 3-
logioPFUpermL)
F-specific coliphages
(range of means:
1.5-3-logioPFUper
mL)
Somatic coliphages EPA Method
(5.3-3,332 PFU per 1601
L)
F-specific
(5.5-300 PFU per L)
Somatic coliphages ISO 10705-2
(range of densities:
4xl02-1.6xl05PFU
perL)
Somatic coliphages ISO 10705-2
(Mean: 3.06-logio
PFU/100 mL)
Somatic and F- EPA Method
specific coliphages 1602
Viruses detected
Enteroviruses, rotaviruses, and
hepatitis A (41-44% of samples
positive)
Adenovirus
(880-7,500 genomes per L)
Cell culture: total culturable
enteroviruses (later determined
to be poliovirus type3)
Molecular methods: hepatitis A
virus (1 positive 768 total),
astrovirus (2/68), NoV GI (0
detects), No V Gil (1/68),
rotavirus (0 detects), and
enterovirus (2/68).
Enterovirus spp. and NoV Gil
(34 samples out of 90 (38%)
were positive for enterovirus
(13%) and/or NoV Gil (27%)
genome)
Human astrovirus,
enteroviruses, rotavirus, and
adenovirus types 40 and 41
Virus detection
method
RT-PCRplus
nested PCR
Nested PCR
Cell culture and
RT-PCR followed
by Southern Blot
Enterovirus spp.:
cell culture, ICC-
RT-PCR, and RT-
PCR
NoV Gil: RT-PCR
ICC-nPCR, ICC-
RT-nPCR
Occurrence findings
Coliphages associated with
viruses. FIB not associated with
viruses.
The presence of human
adenovirus was significantly
associated with F-specific
coliphages.
No significant association was
observed between the density
of somatic coliphages and the
presence of infectious
enteroviruses, or enterovirus
genomes.
The number of samples positive
for pathogenic viral genome
increased with increasing
densities of somatic coliphages.
The presence of enteric viruses
and adenovirus was
significantly associated with
the presence of F-specific
coliphages and somatic
coliphages. Only F-specific
coliphages were significantly
associated with the presence of
rotavirus and enterovirus.
33
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Study
Betancourt and
Rose (2005)
Moce-Llivina
et al. (2005)
Westrell et al.
(2006)
Jiang et al.
(2007)
Boehm et al.
(2009)
Espinosa et al.
(2009)
Water type
(Location)
Wetland and
proposed
sources for
wetland
restoration
(Florida, USA)
Marine
coastal water
impacted by
urban run-off
(Barcelona,
Spain)
Fresh
river impacted
by WWTP
(The
Netherlands)
Marine and fresh
coastal estuary
(Newport Bay,
CA)
Marine
sewage impacted
beach
(Avalon, CA)
Fresh
high-altitude
surface water
(Mexico City,
Mexico)
Coliphages detected
F-specific coliphages
(5 PFU per 100 mL
reported for one
wetland lake sample)
Somatic coliphages
(9-12,240 PFU per
100 mL)
F-specific coliphages
(0-84 PFU per 100
mL)
F-specific coliphages
In 2001:
Range: 6-7400 PFU
perL
In 2002-2003:
Peak: 5,100
Median: 1,300 PFU
perL
F-specific coliphages
F-specific DNA and
RNAcoliphages,
somatic coliphages
Not specified (but
likely F-specific
coliphages)
Coliphage
detection
method
Agar overlay
method and
enrichment
protocol
developed by B.
Yanko
ISO 10705-1
10705-2
ISO 10705-1
EPA Method
1601
Membrane
filtration
Double layer
culture (K12 Hfr
host)
Viruses detected
Enteric viruses (detected in
14/28 samples)
Culturable entero viruses (0-158
PFU per 10 L)
NoV
In 2001:
January peak: 240 PCR
detectable units per L
In 2002-2003:
Peak: 2,000-3,000
Mean: 12-1,700 PCR detectable
units per L
Adenovirus, enterovirus
Adenovirus, enterovirus
Enterovirus, rotavirus,
astrovirus
Virus detection
method
Cell culture
Cell culture
methods: standard
plaque assay,
double-layer plaque
assay, VIRADEN
method, RT-PCR,
andRT-nPCR
RT-PCR
RT-PCR
(enterovirus),
nested PCR
(adenovirus)
RT-PCR
(enterovirus),
nested PCR
(adenovirus)
RT-PCR
Occurrence findings
Not discussed by the authors
but low levels of occurrence in
the sample set indicate
association is unlikely.
Receiver operating
characteristic curves of
"numbers of enteroviruses in 10
L of seawater" indicated that
the numbers of somatic
coliphages (and enterococci)
most accurately predicted the
numbers of cultivable
enteroviruses.
Peaks in NoV did not coincide
with those of enteroviruses, F-
specific coliphages, or
turbidity.
The seasonal and freshwater-to-
saltwater distribution pattern of
human viruses is the opposite
of FIB and coliphages.
No association between
coliphages and adenovirus or
enterovirus.
Coliphages showed strong
association with enterovirus,
but weak association with other
enteric viruses.
34
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Study
Water type
(Location)
Coliphages detected
Coliphage
detection
method
Viruses detected
Virus detection
method
Occurrence findings
Lodder et al. Fresh
(2010) rivers
(The
Netherlands)
Somatic coliphages
(1.1 to 114,156 PFU
per L),
F-specific coliphages
(0.12 to 14,403 PFU
perL)
ISO 10705-1 Enterovirus (present in 75% of
ISO 10705-2 samples (range, 0.0033 to 5.2
PFU per L)
Reovirus (83% of samples
(0.0030 to 5.9 PFU per L),
Cell culture using
RT-PCR and ICC-
RT-PCR
A significant association was
observed between the densities
of the two coliphages and
enteroviruses.
Payment and Fresh
Locas (2011), groundwater
using data (Canada)
taken from
Locas et al.
(2007, 2008)
Somatic and F- EPA Methods Cell culture and
specific RNA 1601 and 1602 immunoperoxidase: total
coliphages culturable human enteric viruses
Molecular methods: NoV,
adenovirus types 40 and 41,
enteroviruses, and reoviruses
types 1, 2, and 3
Cell culture,
immunoperoxidase,
ICC-PCR, ICC-RT-
PCR, and RT-PCR
Somatic and F-specific RNA
coliphages were not predictive
of virus presence or absence.
Coliphages were present only
in low numbers and less
frequently than bacterial
indicators.
Viau et al. Fresh,brackish
(20lib), using and marine
data presented tropical coastal
in Viau et al. streams and
(2011 a) estuaries
(Hawaii)
F-specific coliphages
(present in 85/88
samples, logic mean
1.2 ±0.8 per 100
mL)
Membrane Adenovirus (present in 13/88
filtration and samples, 0.8 to 4.2 gene copies
double agar per 100 mL)
layer Enterovirus (5/88 samples, 0.4
to 4.8 gene copies per 100 mL)
NoV GI (19/88 samples, 1.2 to
1,441 gene copies per 100 mL)
NoV Gil (11/88 samples, 0.9 to
62.4 gene copies per 100 mL)
qPCR,
RT-qPCR
There were no associations
between occurrence of viruses
and fecal indicator densities
(including coliphages).
Love et al.
(2014)
Marine
recreational
beaches
F-specific coliphages
(median
concentrations at
both beaches 0.3
MPN per 100 mL)
Somatic coliphages
(median
concentrations were
4.9 and 3.1 MPN per
100 mL)
Modified
version of
modified version
of EPA Method
1601
Adenovirus (25.5% of water
samples at Doheny Beach
and in 9.3% at Avalon Beach
NoV (22.3% of water samples at
Doheny Beach and 0.7% at
Avalon Beach
Adenovirus: nested
PCR
NoV: nested RT-
PCR
The presence of F-specific
coliphages was positively
associated with the probability
of detecting adenovirus. NoV
was not significantly associated
with either type of coliphages.
35
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Study
Water type
(Location)
Coliphages detected
Coliphage
detection
method
Viruses detected
Virus detection
method
Occurrence findings
Rezaeinejad et Urbanized
al. (2014) catchment
waters
(freshwater) in
tropical
Singapore
F-specific coliphages EPA Method
(mean concentration 1602
= l.lx!02PFUper
100 mL)
Somatic coliphages
(mean concentration
= 2.2xl02PFUper
100 mL)
Adenovirus (mean = 9.4 x 101 Adenovirus: real
gene copies/L) time PCR
Astrovirus (mean = 2.9 x 102 Astrovirus,
gene copies/L) rotavirus, NoV GI
NoV Gil (mean = 3.7 x 102gene and Gil: real time
copies/L) RT-PCR
Rotavirus (mean = 2.5 x 102
gene copies/L)
F-specific coliphages were
positively associated with NoV
densities.
VTRADEN method = "virus adsorption enumeration" based on the direct enumeration of viruses adsorbed into nitrate-acetate cellulose membranes.
Note: Bacterial hosts for somatic coliphages include: WG5, CN13, E. coli 036; bacterial hosts for F-specific coliphages include: Stm WG49, E. coli FamP, K12
Hfr.
36
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5. Environmental Factors and Fate
The ability of coliphages (including different coliphage genogroups) and other enteric viruses to
survive in environmental media varies widely (Callahan et al., 1995; Reyes and Jiang, 2010;
Johczyk et al., 2011; Bertrand et al., 2012). As described previously, the effect of environmental
factors on coliphage survival is associated with morphology, where some specific structural
characteristics, such as tails, large capsids, and lack of an envelope have been shown to be
associated with greater resistance to external factors (Ackermann et al., 2004; Johczyk et al.,
2011). Researchers have investigated the survival of coliphages and enteric viruses under a
variety of environmental conditions. Studies have examined the effects of physical stress (e.g.,
temperatures and sunlight), biological antagonists (e.g., microbial predation and enzymatic
degradation), and chemical antagonists (e.g., disinfection). This section focuses on physical and
biological antagonists in natural aquatic environments, mechanisms of inactivation, and where
data are available, compares inactivation rates of somatic, F-specific and Bacteroides
bacteriophages to inactivation of human enteric viruses. Chemical treatment and other
disinfection methods are discussed in Section 6 (Wastewater Treatment).
5.1. Temperature
Temperature is an important factor in viral ecology as it plays a fundamental role in attachment,
penetration, multiplication, occurrence, and viability (Sobsey and Meschke, 2003; Pradeep Ram
et al., 2005; Johczyk et al., 2011). Many studies have examined the effect of temperature on the
survival of different viruses in aquatic environments. Both enteric viruses and coliphages have
been reported to survive longer and occur more frequently at lower temperatures in natural
environments and decay more rapidly at higher temperatures (i.e., seawater, river, and
groundwater) (Long and Sobsey, 2004; Fong and Lipp, 2005). Below is a brief summary of the
evidence of the effects of temperature on human enteric virus and coliphage inactivation in
aquatic systems.
Bertrand et al. (2012) conducted a meta-analysis of the effects of temperature on the inactivation
of enteric viruses and bacteriophages in food and water. The study collected 658 data points from
76 published studies and analyzed the effects of virus type, matrix (simple or complex), and
temperature (<50 and >50°C) on virus survival. A simple matrix included: (1) synthetic media;
(2) drinking water; and (3) groundwater. A complex matrix included: (1) freshwater; (2) natural
seawater; (4) sewage; (4) soil; (5) dairy products; (6) food; and (7) urine (Bertrand et al., 2012).
The study determined that, overall, virus inactivation was faster at temperatures >50°C than at
temperatures <50°C and that virus inactivation was less sensitive to temperature change in
complex matrices than in simple matrices (Bertrand et al., 2012). The somatic coliphage OX174
was highly persistent under all temperatures and matrices tested.
Studies reported differences in survival among different F-specific coliphage groups across
temperature gradients. For example, Long and Sobsey (2004) reported that at 4°C, GI and Gil
F-specific RNA coliphages were detectable for over 100 days, GUI F-specific RNA coliphages
were detectable for 3 weeks, and GIV F-specific RNA coliphages were reduced to the limit of
detection after 10 days (Long and Sobsey, 2004). Of the F-specific DNA coliphages, all strains
were detectable after 110 days at 4°C (Long and Sobsey, 2004). The authors also noted that the
GI F-specific RNA coliphage MS2 and F-specific DNA coliphage Ml3 demonstrated a longer
37
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survival in environmental waters than other F-specific coliphage species (Long and Sobsey,
2004).
Temperature can also affect survival of somatic and Bacteroides bacteriophages in aquatic
systems. Lee and Sobsey (2011) estimated the temperature inactivation of four types of somatic
coliphages in laboratory tests using both reagent grade water and surface water. The authors
found that T4 (Myoviridae family), OX 174 (Microviridae family), and X (Siphoviridae family),
survived better than Tl (Siphoviridae family), and T7 (Podoviridae family), at low temperatures
(4°C) and high temperatures (25°C). Chung and Sobsey (1993) found that B. fragilis coliphages
survived comparable to or better than hepatitis A, poliovirus, and rotavirus (measured using cell
culture) in seawater exposed to low (5°C) and high (25°C) temperatures.
Reported comparisons between decay rates of F-specific RNA coliphages and human enteric
viruses, or proxies to human enteric viruses, indicate that decay rates of both vary by temperature
and water conditions. For example, in their two studies, Allwood et al. (2003, 2005) compared
the survival of GI F-specific RNA coliphage MS2, feline calicivirus (FCV), and E. coll at 4°C,
25°C, and 37°C in chlorinated and dechlorinated water. In dechlorinated water at 4°C and 25°C,
MS2 survived three times longer than both E. coli and FCV, whereas they had similar survival
rates at 37°C (Allwood et al., 2003).
Similarly, Romero et al. (2011) found that porcine rotavirus and GI F-specific RNA coliphage
MS2 had relatively low inactivation rate constants in the dark from 14 to 42°C, 10-fold increases
in inactivation rates at 50°C and between 10- and 60-fold increases in inactivation rates at 60°C.
In a similar experiment, Seo et al. (2012) compared the decay rates of murine NoV (MNV) and
GI F-specific RNA coliphage MS2 over a temperature range of 24 to 85°C. They found that
decay rate of MS2 was lower than MNV between 24°C and 60°C and that both were rapidly
inactivated by temperatures >60°C (Seo et al., 2012). For more details on the decay rates at
different temperatures, see Table 9 below.
Synergistic effects between temperature and other environmental factors
The importance of temperature as a determinant of coliphage survival has been found to vary
between freshwater and saltwater environments. For example, Reyes and Jiang (2010) noted that
temperature is more important in influencing coliphage occurrence in freshwater environments
than in saltwater environments (See Section 5.3 for more information on salinity). The
importance of temperature as a determinant of virus survival is also dependent on the presence of
sunlight. Romero et al. (2011) found that temperature played an important role in sunlight-
mediated inactivation. For example, degradation rates of both GI F-specific coliphage MS2 and
porcine rotavirus were higher for the same temperatures under different light conditions (full
solar spectrum and only UVA and visible light) as compared to in the dark (Romero et al., 2011)
(See Section 5.2 for more information on sunlight). Hurst et al. (1989) showed that temperature
effects on inactivation of enterovirus was dependent on the water sources used as the aqueous
phase in experiments.
Summary
38
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In summary, conclusions drawn in multiple studies indicate that the coliphages are equally
persistent to, or more persistent than enteric viruses. Bertrand et al. (2012) found that somatic
coliphage OX174 was highly persistent under all matrices and temperatures tested, and at higher
temperatures, somatic and F-specific coliphages were classified as the most persistent as
compared to enteric viruses. These data are consistent with the results of Allwood et al. (2003,
2005) and Seo et al. (2012). Combined, these data indicate that coliphages may be conservative
surrogates for the behavior of enteric viruses under a range of temperatures (meaning they
persist as long or longer than human viruses). Table 9 presents the decay rates of different types
of coliphages, other fecal indicators, and human viruses.
5.2. Sunlight
Sunlight is also an important factor leading to virus inactivation (Sobsey and Meschke, 2003;
Fong and Lipp, 2005; Johczyk et al., 2011). Sunlight that reaches Earth's surface is composed of
medium and long wavelength UV light [UVB (280 to 320 nm); UVA (320 to 400 nm)], visible
light (400 to 700 nm), and longer wavelengths (Love et al., 2010). There are three proposed
types of virus inactivation caused by the UV wavelengths in light: endogenous direct,
endogenous indirect, and exogenous indirect (Silverman et al., 2013). While UV radiation is
utilized in wastewater treatment processes, this application uses primarily UVC wavelengths
(which do not reach Earth's surface due to the ozone layer) and will be discussed in Section 6 on
wastewater treatment. This section will focus on inactivation of viruses due to natural or
simulated sunlight. Below is a brief summary of the evidence of the effects of sunlight on human
enteric viruses and coliphage inactivation in aquatic systems.
39
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Table 9. Comparison of mean exponential decay rates of coliphages, fecal indicators and human viruses in different media at
different temperatures.
„, , Allwood et al.
Study (2003)
Temperature 4°C 25°C 37°C
Organism
E. coli 0.30 0.40 0.77
FCV 0.32 0.44 1.15
GIF-specific RNA Q Q9 QU Q^
coliphage MS2
F-specific coliphages
Human adenovirus
Polioviras type 1
F-specific DNA
coliphages
GI F-specific RNA
coliphages
Gil F-specific RNA
coliphages
GUI F-specific RNA
coliphages
GIV F-specific RNA
coliphages
GV F-specific RNA
coliphages
Somatic coliphage Tl
Somatic coliphage T4
Somatic coliphage T7
Somatic coliphage
-------
Effects of sunlight on coliphage decay rates and decay rates of other fecal indicators
Love et al. (2010) found a correlation between the size of the genome and the inactivation rate of
environmental isolates of somatic coliphages in sunlight: Larger genomes were correlated with
higher inactivation rates. They also found that F-specific RNA coliphages were significantly
more resistant to sunlight inactivation than the F-specific DNA coliphages over an 8-hour period
(Love et al., 2010). Overall, they found that under full-spectrum-simulated sunlight, inactivation
rates varied more widely for ssDNA and dsDNA viruses than for ssRNA viruses, and that
differences in virus inactivation rate were not just a function of nucleic acid type, but also
genome length and morphology (Love et al., 2010).
Sinton et al. (1999) studied the inactivation rates of sewage-isolated somatic coliphages,
F-specific coliphages, B.fragilis bacteriophages, and fecal coliforms by solar radiation in
sewage-seawater mixtures. Overall, their data showed that sunlight conditions resulted in faster
decay rates of all indicators as compared to dark conditions and that, under all conditions,
somatic and F-specific coliphages had lower decay rates than B. fragilis bacteriophages and fecal
coliforms (Sinton et al., 1999). The authors also found that colder water resulted in slower decay
rates than warmer water under all light and dark conditions tested (Sinton et al., 1999).
In their follow-up study, Sinton et al. (2002) investigated the inactivation rates of waste
stabilization pond effluent isolated fecal coliforms, enterococci, E. coli, somatic coliphages, and
F-specific RNA coliphages by solar radiation in freshwater (Table 10 below). Overall, their data
showed that, for all indicators, sunlight conditions resulted in faster decay rates than dark
conditions and that under both light and dark conditions, somatic and F-specific RNA coliphages
had smaller decay rates than E. coli, enterococci, and fecal coliforms (Sinton et al., 2002). Sinton
et al. (2002) also found that F-specific RNA coliphages were inactivated by a wide range of
wavelengths, whereas somatic coliphages were mainly inactivated by UVB wavelengths (318
nm).
41
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Table 10. Mean exponential decay rates of coliphages and fecal indicators in fresh river
water contaminated with raw sewage or effluent under different light conditions.
Organism
Fecal coliforms
E. coli
Enterococci
Somatic coliphages
F-specific RNA
coliphages
Source of contamination
Wastewater effluent
Raw sewage
Wastewater effluent
Raw sewage
Wastewater effluent
Raw sewage
Wastewater effluent
Raw sewage
Wastewater effluent
Raw sewage
Dark
kD(/hour)a
0.02
0.01
0.02
0.02
0.02
0.01
0.01
0.00
0.01
0.00
Summer
Mm2/
0.09
0.28
0.08
0.29
0.28
0.14
0.08
0.10
0.07
0.08
Winter
|t/|T\b
0.08
0.22
0.07
0.24
0.11
0.14
0.05
0.09
0.05
0.07
Summer Winter
kL(/hour)a
0.26 0.14
0.70 0.30
0.25 0.11
0.70 0.33
0.77 0.16
0.36 0.18
0.20 0.08
0.28 0.14
0.17 0.08
0.18 0.12
Source: Sinton et al. (2002)
a The mean exponential decay rate, kD and kL, may be used in the exponential decay equation: Nt =
Alternatively, kD (decay in the dark) and kL (decay in the light) may be used in the base 10 exponential decay
equation as Nt = NolO"1^10'. Note that kL may be used only in equivalent solar insolation conditions as the study.
b The mean solar inactivation rate ks may be used in the exponential decay equation: Nt = N0es~kslt, where I is the
solar irradiance.
Effects of sunlight on decay rates of enteric viruses and coliphages
Individual enteric viruses and coliphages also have different levels of resistance to sunlight. For
example, Love et al. (2010) observed that in seawater under sunlit conditions, the decay rates of
adenovirus 2 and GI, Gil, GUI and GIV F-specific RNA coliphages were similar and slower than
the decay rates of F-specific DNA coliphages, somatic coliphages, and poliovirus type 3 (Love et
al., 2010). These results are consistent with field experiments under conditions of similar
sunlight intensity (Love, et al., 2010).
Romero et al. (2011) used both full spectrum sunlight and a combination of UVA and visible
light to determine the decay rates of GI F-specific RNA coliphage MS2 and porcine rotavirus at
temperatures ranging from 14 to 50°C (see Table 11 below). Under dark conditions, decay rates
were not detected for either virus between 14 and 42°C whereas at 50°C, low decay rates were
detected for both (Romero et al., 2011). Under full spectrum sunlight, the decay rates (K0bs) of
both viruses increased and those for GI F-specific RNA coliphage MS2 were below those of
porcine rotavirus (Romero et al., 2011). Under a combination of UVA and visible light, both
viruses had low, approximately constant degradation rates between 14 and 42°C, whereas at
50°C the rates increased slightly (Romero et al., 2011). The very low levels of degradation of
both MS2 and porcine rotavirus in the absence of UVB were consistent with previous studies
indicating that the majority of sunlight degradation of viruses in water is due to UVB light
(Sinton et al., 2002; Romero et al., 2011). These results are consistent with the findings of Fisher
et al. (2011) who found that in phosphate buffered saline, GI F-specific RNA coliphage MS2
was resistant to UVA but highly sensitive to UVB wavelengths.
42
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Silverman et al. (2013) compared the inactivation rates of poliovirus type 3, adenovirus type 2,
and GI F-specific RNA coliphages (MS2 and PRD1) under dark and full simulated sunlight
conditions in four different types of environmental water (seawater from two marine beaches,
river estuary water, coastal wetland, and coastal wetland collected near cattail plants) and in
phosphate-buffered saline (see Table 11). They found that all dark control inactivation rates were
less than those obtained from experiments conducted under full-spectrum simulated sunlight for
all three viruses in all five types of water (Silverman et al., 2013). Additionally, they found that
decay rates of GI F-specific RNA coliphages under full-spectrum simulated sunlight were
significantly below those of poliovirus type 3 in all five types of water and less than or equal to
those of adenovirus type 2. The authors conclude that GI F-specific RNA coliphages are a
conservative surrogate for predicting poliovirus type 3 and adenovirus type 2 decay in all five
types of water tested (Silverman et al., 2013).
Table 11. Comparison of mean exponential decay rates of coliphages and human viruses
under different light conditions.
_ , , ,_„.,.,.. Silverman
Romero et al. (2011) et al. (2013)"
Medium/ ^ ,,
T d'f
20 mg C/L of riverine natural organic material (full-spectrum sunlight)3 spectrum
sunlight
Microorganism 14°C 23-26°C 34°C 42°C 50°C Temperature
not provided
kD(/h)
MS2 ND
Rotavirus ND
Poliovirus (Type 3)
Adenovirus (Type2)
kL(/h) kD(/h) kL(/h) kD(/h) kL(/h) kD(/h) kL(/h) kD(/h) kL(/h) kD(/h)
4.00 ND 4.23 ND 4.49 ND 5.00 0.50 NS
7.31 ND 8.58 ND 8.63 ND 9.42 0.33
NS
NS
kL(/h)
0.10
0.08
0.11
ND = Nondetect
NS = Not significantly different from zero
empty cells = not reported
mg = milligrams
a The mean exponential decay rate kD and kL may be used in the exponential decay equation: Nt = No6'11.
Alternatively, kD (decay in the dark) and kL (decay in the light) may be used in the base 10 exponential decay
equation as Nt = NolO-1^10). Note that kL may be used only in equivalent solar insolation conditions as the study.
b The decay rates reported in Silverman et al. (2013) are from water collected from Tijuana River estuary (Imperial
Beach, California) at the end of the ebb tide.
Synergistic effects between sunlight and other environmental factors
Several studies have found synergy between sunlight and other environmental factors in the
inactivation rates of viruses, such as the presence of organic matter or particulate matter,
sunlight, and salinity. For example, inactivation of viruses may be greater in waters with organic
matter that produces reactive oxygen species (Kohn et al., 2007; Love et al., 2010; Romero et al.,
2011). However, the presence of flora, fauna, and dissolved and paniculate matter may also
increase viral survival by blocking or absorbing photons from passing through water (Bitton et
al., 1979; Romero et al., 2011). Please refer to Sections 5.4 and 5.5 for more information on
microbial activity and organics, respectively. The synergy between sunlight and temperature
appears to play a role in the inactivation of viruses. For example, Romero et al. (2011) concluded
that temperature is a critical factor in the sunlight-mediated inactivation of GI F-specific
43
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coliphage MS2. Please refer to Section 5.1 for more information on temperature. Differential
inactivation of coliphages by sunlight can also occur in saltwater versus freshwater. For example,
Sinton et al. (1999, 2002) found that salinity had a synergistic effect with sunlight. Specifically,
sunlight inactivation increased with increasing salinity. For more information on salinity please
see Section 5.3.
Summary
In summary, data indicated that human enteric viruses and coliphages have faster decay rates
under conditions of full sunlight as compared to in the dark (Sinton et al., 1999, 2002; Romero et
al., 2011). Reported decay rates varied by virus, amount and wavelengths of light (UVA, UVB),
temperature, and aquatic conditions (salt or freshwater), however, several studies indicated that
coliphage decay rate is generally lower than enteric virus or FIB decay rate in various sunlight
conditions (Sinton et al., 2002; Love et al., 2010; Romero et al., 2011; Silverman et al., 2013).
Thus, coliphages may be a conservative surrogate for predicting virus decay due to sunlight.
5.3. Salinity
The types and concentrations of salts found in natural waters differ depending on the type of
water. Generally, seawater is considered to be 35 parts per thousand salt. Chloride (Na) and
sodium (Cl) are the most prevalent ions and account for more than 85% of the salt content by
mass (Murray, 2004). Concentrations of these ions (Na and Cl) are significantly lower in
freshwaters, and vary depending on type and source of water (Murray, 2004).
Salts, or salinity, can influence viral survival in aquatic environments. Salinity can either
increase or decrease degradation rates of viruses depending on the type and concentration of salt,
the temperature, and the specific virus (Hurst and Gerba, 1980; Gutierrez et al., 2010; Mylon et
al., 2010; da Silva et al., 2011; Nguyen et al., 2011; Seo et al., 2012). It has been hypothesized
that monovalent salts provide strong steric and electrosteric stabilization of GI F-specific
coliphage MS2, whereas divalent salts have been found to cause MS2 aggregation (Mylon et al.,
2010; Nguyen et al., 2011). Similar results have been shown for rotavirus and NoV Gl.l
(Gutierrez et al., 2010; da Silva et al., 2011). Aggregation of viruses can make it difficult to
measure their infectivity, as plaque assays result in underestimates (e.g., a single PFU may be
comprised of clumps of virus particles). Additionally, osmotic shock through rapid changes in
osmotic pressure can trigger inactivation of coliphages via direct oxidization, which can cause
capsid degradation and dispersion, tail fragmentation, and release of viral nucleic acids into the
aquatic environment (Johczyk et al., 2011). This section will describe the effects of salinity on
viral degradation. Below is a brief summary of the evidence of the effects of salinity on human
enteric viruses and coliphage inactivation in aquatic environments.
Effects of salinity on decay rates of coliphages
Sinton et al. (1999, 2002) found that salt water affected the decay rates of F-specific and somatic
coliphages under both dark and sunlight exposed conditions. Sinton et al. (1999) studied the
inactivation rates of sewage-isolated somatic coliphages and F-specific DNA and RNA
coliphages in sewage-seawater mixtures. Sinton et al. (2002) studied the inactivation rates of
somatic and F-specific RNA coliphages isolated from waste-stabilization pond effluent under
44
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both dark and sunlight exposed conditions in river water, simulated estuarine water (50% river
water, 50% seawater), and seawater. Under dark conditions, both somatic and F-specific
coliphages had lower decay rates in river water (somatic coliphages (kn = 0.008 h"1), F-specific
RNA coliphages (kn = 0.014 h"1)) than in sea water (somatic coliphages (kn = 0.044 h"1), F-
specific RNA coliphages (fo = 0.044 h"1) (Sinton et al., 1999, 2002). Degradation rates of
somatic coliphages increased 5.5 fold in salt water compared to river water under dark conditions
whereas F-specific RNA coliphages rates increased 3.1 fold under the same conditions. These
data indicate that somatic coliphages are less stable in seawater than F-specific RNA coliphages
under the tested conditions.
Somatic coliphages were more sensitive to salt water under sunlight conditions as well. For
example, Sinton et al. (2002) determined the degradation rates of somatic coliphages and F-
specific RNA coliphages isolated from waste-stabilization pond effluent under full sunlight
conditions in freshwater and 50:50 water and seawater. For somatic coliphages degradation rates
were ks = 0.079 m2 megajoules (MJ)"1 in river water, ks = 0.129 m2 MJ"1 in 50:50 water and ks =
0.184 m2 MJ"1 in sea water. Similarly, F-specific RNA coliphages rates were: ks = 0.086 m2 MJ"1
in river water, ks = 0.092 m2 MJ"1 in 50:50 water and ks = 0.123 m2 MJ"1 in sea water (Sinton et
al., 2002). Degradation rates of somatic coliphages increased 2.3 fold in salt water compared to
river water whereas F-specific RNA coliphages rates increased 1.4 fold under the same
conditions. These data indicate that somatic coliphages are more sensitive to salt water than F-
specific RNA coliphages under these conditions.
Overall, the authors concluded that as salinity increases, inactivation of coliphages increases as
well (Sinton et al., 2002). In particular, inactivation of F-specific RNA coliphages obtained from
sewage increased with salinity, but the trend in F-specific RNA coliphages obtained from
stabilization ponds was less pronounced (Sinton et al., 2002). These conclusions are in
agreement with those of Savichtcheva and Okabe (2006) who found that F-specific RNA
coliphages were more sensitive to sunlight inactivation at high salinity.
Seo et al. (2012) investigated the differences in tolerance of MNV and GI F-specific RNA
coliphage MS2 to different concentrations of NaCl (0.3, 1.3, 3.3, and 6.3% NaCl) at three
different temperatures, 24°C, 37°C, and 50°C. Their results show that there are complex
interactions between salt concentration and temperature for both of the viruses, with several
differences between the two. They found that MS2 was more resistant to NaCl than MNV at all
concentrations of NaCl and temperatures tested (Seo et al., 2012). At 24°C, MS2 did not show
any reduction in infectivity at any of the NaCl concentrations and at higher temperatures, NaCl
seem to have a protective effect (Table 12; Seo et al., 2012).
Hurst and Gerba (1980) compared the decay of poliovirus, echovirus, coxsackievirus and simian
rotavirus in estuarine and freshwater during two different years. Decay was quicker in estuarine
water relative to freshwater in one year, and decay was similar in the waters in the second years
suggesting factors other than salinity may have been contributing to viral decay.
45
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Synergistic effects between salinity and other environmental factors
Several studies have found synergy between salinity and other environmental factors in the
inactivation rates of viruses. For example, Seo et al. (2012) found an interaction between
temperature and salt concentration. Depending on the specific virus, incubation in high
concentrations of NaCl at high temperatures could either reduce virus infectivity (MNV) or
increase virus infectivity (GI F-specific RNA coliphage MS2) as compared to lower
concentrations of salt at the same temperature. The susceptibility of MNV to all concentrations
of NaCl increased rapidly at 37°C and 50°C, whereas at the same temperatures, GI F-specific
RNA coliphage MS2 was more stable at higher NaCl concentrations (1.3 to 6.3% NaCl) than at
low concentrations (0.3% NaCl) (Seo et al., 2012). The authors hypothesized that the high NaCl
concentration may "protect against thermally induced capsid opening or stabilize the viral
protein-RNA complex" (Seo et al., 2012). For more information on the effects of temperature on
virus degradation, see Section 5.1. Other studies have reported synergistic effects between salt
and natural organic and inorganic matter (Mylon et al., 2010). Mylon et al. (2010) found that GI
F-specific RNA coliphage MS2 aggregated at lower concentrations of Ca2+ in the presence of 10
mg/L Suwannee River organic matter (100 millimolar (mM) Ca2+) as compared to just Ca2+ (160
mM Ca2+). Lukasik et al. (2000) observed that mono-, di-, and trivalent salts (NaCl, MgCb, and
AlCb) either promoted or interfered with adsorption of GI F-specific RNA coliphage MS2,
somatic coliphage OX174, and poliovirus type 1 to different types of filters at different pH
levels. For more information on adsorption to organic and inorganic matter, please see Section
5.5 below.
Summary
In summary, both enteric viruses and coliphages are affected by salinity, the specific effects of
which vary depending on the type of virus and the type and concentration of salt, as well as
temperature. In terms of aggregation, multiple studies have found that monovalent cations are
either ineffective at, or are less effective at causing aggregation of coliphages (F-specific RNA
coliphage MS2) and enteric viruses (NoV GI. 1 and rotavirus) than divalent cations (Gutierrez et
al., 2010; Mylon et al., 2010; da Silva et al., 2011; Nguyen et al., 2011) and aggregation can
affect the number of PFUs measured in a sample. In terms of decay rates, Seo et al. (2012) found
that MS2 had lower decay rates than MNV at all NaCl concentrations tested (0.3 to 6.3%) at
three different temperatures (24°C, 37°C, and 50°C). Table 12 below shows the decay rates from
Seo etal. (2012).
46
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Table 12. Comparison of mean exponential decay rates of coliphages and MNV at different
concentrations of salt and at different temperatures.
°C NaCl%
0.3
-,4 1-3
3.3
6.3
0.3
1.3
3.3
6.3
0.3
1.3
3.3
6.3
MNV
1.17
3.03
2.96
2.73
2.54
4.44
4.11
4.11
61.40
72.08
122.80
118.42
Organism
GI F-specific coliphage MS2
k((H)
0.05
0.05
0.05
0.05
0.19
0.18
0.21
0.11
10.80
3.15
5.54
4.09
Source: Seoetal. (2012)
Higher k = faster decay
5.4. Predation and Enzymatic Degradation
Inactivation of viruses can occur via predation or release of virucidal agents from endogenous
microorganisms in environmental waters (Sobsey and Cooper, 1973; Fujioka et al., 1980; Ward
et al., 1986). Many bacteria produce proteolytic enzymes that are capable of inactivating viruses,
including human enteric viruses, by degradation of protein capsids (Bae and Schwab, 2008). In
seawater, virioplankton are postulated to be inactivated in part by enzymatic attack and predation
(Finiguerra et al., 2011). One study found that the presence/absence of microorganisms is a more
important factor than temperature on virus survival in groundwater (Wetz et al., 2004). Other
studies have shown that association with biofilms can also affect the inactivation of enteric
viruses and coliphages. Helmi et al. (2011) found that poliovirus, GI F-specific RNA coliphage
MS2, and somatic coliphage OX174 densities in drinking water biofilms decreased after 6 days
due to inactivation and detachment, but previous research has found that biofilms protect viruses
from inactivation (Skraber et al., 2007). While the effects of microbial antagonism and
enzymatic degradation on coliphages are not as well studied as the effects on human enteric
viruses, these processes are thought to inactivate them as well. For example, studies examining
coliphages in waste stabilization ponds have shown that while sunlight is the major cause of
inactivation, predation may also play a role (da Silva et al., 2008). Below is a brief summary of
the evidence of human enteric virus and coliphage predation- and enzymatic degradation-
mediated inactivation in aquatic systems.
Effects of predation and enzymatic degradation on decay rates of coliphages
In a study examining the role of aquatic plants in freshwater and salt water wetlands on the
survival of waterborne coliphages, Karim et al. (2008) found that the presence of wetland
vegetation significantly increased the inactivation of GI F-specific RNA coliphage MS2. The
authors hypothesized that the presence of aquatic plants may enhance rhizosphere bacterial
47
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populations, which increase coliphage inactivation due to the presence of metabolites or the
presence of proteolytic substances released by microbes or plants (Karim et al., 2008).
Finiguerra et al. (2011) investigated the light-independent mechanisms of inactivation of somatic
coliphage T4 (marine host: PWH3a) and coliphage PI (enteric host: E. coli B) in seawater. They
found that decay rates of both coliphages were reduced in particle-free seawater (<2 micrometers
[jim]) as compared to seawater containing nanoplankton (<10 jim) and the lowest decay rates
were found in ultra-filtered seawater (<10 kilodaltons [kDa]). The authors concluded that
inactivation of these coliphages is accelerated by naturally occurring particles, which include
living organisms and heat-labile colloids and macromolecules >10 kDa (Finiguerra et al., 2011).
Effects of predation and enzymatic degradation on decay rates of human viruses
A number of studies have examined the effect of microbial activity on enteric virus survival in
aquatic systems. Direct predation of enteric viruses can occur via engulfment or ingestion by
bacteria, protozoa, helminthes, and other aquatic organisms (Sobsey and Meschke, 2003).
Fujioka et al. (1980) demonstrated that inactivation of enteric viruses (poliovirus type 1,
coxsackievirus B4, and echovirus 7) in marine and estuarine waters is associated with the natural
microbial community. Microbial activity has also been shown to decrease persistence of
rotaviruses in raw and treated freshwaters (Raphael et al., 1985) and hepatitis A in mixed septic
tank effluent (Deng and Cliver, 1995). Toranzo et al. (1982) confirmed the ability of bacteria to
release virucidal agents by isolating marine bacteria that had marked activity against poliovirus
(net 2-logio inactivation or greater within 6 to 8 days), coxsackievirus B-5, and echovirus 6.
Sobsey and Cooper (1973) showed that microbial activity in waste stabilization pond water
contributed to poliovirus inactivation. Similarly, Herrmann et al. (1974) showed that
enteroviruses decayed more quickly in lake water compared to sterilized lake water. Ward et al.
(1986) also showed that proteolytic bacterial enzymes were responsible for echovirus
inactivation in freshwater.
Wetz et al. (2004) studied the inactivation rate of poliovirus in filtered natural seawater,
unfiltered natural seawater, artificial seawater, and deionized water at 22 and 30°C. They found
that the highest rates of virus inactivation occurred in unfiltered natural seawater at both
temperatures tested. Prior to spiking they exposed all of the water in their experiments to >14
hours of UV light (to kill the indigenous microorganisms). Because the indigenous
microorganisms were killed, the authors hypothesized that direct microbial inactivation of the
viruses was highly unlikely and degradation was likely caused by a release of cellular proteases,
nucleases, and other enzymes (Wetz et al., 2004).
Synergistic effects between predation and enzymatic degradation and other environmental
factors
Several studies have identified synergy between predation and enzymatic degradation and other
environmental factors in the inactivation rates of viruses. There is some evidence that when
viruses, including enteric viruses and coliphages, adsorb to particles, the associated particle may
offer them some protection from predation (Fong and Lipp, 2005; Weaver and Sinton, 2009;
Finiguerra et al., 2011). For more information on adsorption to organic and inorganic matter, see
48
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Section 5.5 below. There are also synergistic effects between enzymatic degradation and
temperature. For example, Wetz et al. (2004) found a synergistic effect between temperature and
enzymatic degradation of poliovirus in natural seawater, as degradation rates were higher at 30°C
than at 22°C. For more information on effects of temperature, see Section 5.1 above.
Summary
Microbial predation and enzymatic degradation are both important mechanisms of virus
inactivation in natural waters. Both predation and enzymatic degradation have been shown to
increase human virus degradation rates in freshwater, salt water, treated water and septic system
effluent (Fujioka et al., 1980; Toranzo et al., 1982; Raphael et al., 1985; Deng and Cliver, 1995;
Wetz et al., 2004). While there are fewer data for coliphages, there is some evidence that
microbial predation and enzymatic degradation do contribute to virus inactivation in natural
waters. Due to lack of data, it is not currently possible to compare degradation rates of enteric
viruses and coliphages by microbial predation or enzymatic degradation in natural waters.
5.5. Organic and Inorganic Matter
Aquatic environments contain both organic and inorganic matter. Inorganic matter consists of
materials made from nonbiological sources and do not contain carbon (except for CO2 and CFU).
These include metals, chemicals, sand, clay, salts, and ions. Natural organic matter consists of
materials that are made from biological sources and contain carbon. These include exudates from
organisms and the materials that are produced from their decay. Organic matter in water is a
diverse mixture of organic compounds ranging from macromolecules to low molecular-weight
compounds (USGS, 2013). Organic matter is capable of both attenuating light (thus decreasing
photoactivation rates) and producing reactive oxygen species (thus increasing photoactivation
rates) (Silverman et al., 2013). Depending on the absolute amount of sunlight that reaches the
virus and the amount of reactive oxygen species produced, the overall effect of organic matter
can either result in decreased or increased viral photoinactivation rates.
Viruses in the environment are often associated with particulate matter, which has a major effect
on persistence and transport in the environment (Gerba, 1984). For example, clay surface
exchange capacity and particle size and shape affect the virus-adsorption activity of a clay
(Carlson et al., 1968). Laboratory-based predictions suggest that as many as 99% of viruses in
coastal waters should be adsorbed to naturally occurring colloids and particles (Finiguerra et al.,
2011). If the resultant aggregate is dense and large, it can settle out of the water column
(Characklis et al., 2005; Shen et al., 2008). If the aggregate is less dense, viruses may remain
more mobile in the environment (Characklis et al., 2005).
The isoelectric point of the virus dictates its overall charge at a given pH, ionic strength, and
water chemistry and thus affects virus adsorption. For example, reoviruses adsorb primarily to
negatively charged sites on clay, while Tl and T7 coliphages adsorb to positively charged sites at
environmentally relevant pHs (Gerba, 1984). Stotsky et al. (1980) found that adsorption to clay
by reovirus (the family to which rotavirus belongs) and somatic coliphages (Tl and T7)
increased the persistence of the viruses in lake water (Stotsky et al., 1980, as cited in Sobsey and
Meschke, 2003).
49
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This section will focus on inactivation of viruses due to interactions with organic and inorganic
matter. Below is a brief summary of the evidence of the effects of organic and inorganic matter
on human enteric viruses and coliphage inactivation in aquatic systems.
Effect of organic and inorganic matter on decay rates of coliphages
Finiguerra et al. (2011) investigated the effects of paniculate, dissolved, and colloidal organic
and inorganic material in seawater on the inactivation rate of somatic coliphage T4. They
determined that a significant fraction of viral inactivation (39-65%) can be attributed to passive
sorption to living and inert planktonic particles (sterile debris was produced from cultivated
phytoplankton species; 0.2 to 10 um) (Finiguerra et al., 2011). The lowest decay rates were in
oxidized filtrate from a 10 kDa tangential filtration system. The authors identified virucidal
material between 10 kDa and 0.2 jim in size that is resistant to autoclaving. They concluded that
inorganic solutes may be the primary inactivating mechanism in the dissolved fraction
(Finiguerra et al., 2011).
Effects of organic and inorganic matter on decay rates of enteric viruses and coliphages
LaBelle and Gerba (1980) found that adsorption to marine sediment increased the time required
for 99% inactivation from 1 hour to greater than 4 days for poliovirus and from 1.4 days to
greater than 6 days for echovirus. Another study found that enteroviruses associated with marine
solids are infectious for longer (19 days) than unassociated enteroviruses in the water column (9
days) (Griffin et al., 2003). Shen et al. (2008) estimated somatic coliphage P22 inactivation rates
to be in the range 0.27 to 0.57 per day (0.12 to 0.25 logic per day) with the highest inactivation
rate found in samples with high suspended solids concentration, relatively low dissolved organic
carbon content, and sediment with high clay content.
Chung and Sobsey (1993) found both temperature- and sediment-dependent differences between
the decay rates of the five viruses tested: F-specific coliphages, B.fragilis phages, hepatitis A,
poliovirus, and rotavirus. The effect of sediment differed among the viruses. Sediment protected
poliovirus and human adenovirus at 5°C and 25°C and F-specific coliphages at 25°C, whereas it
accelerated inactivation of rotavirus at both temperatures. B.fragilis phage survival was not
affected by sediment at either temperature (Chung and Sobsey, 1993). Interestingly, at 5°C, all of
the viruses had increasing levels of association with the sediment fraction over a 60-day period,
except for hepatitis A, which had approximately constant rates over the entire period.
Association with the sediment did not correlate with inactivation rates (Chung and Sobsey,
1993). All five of the viruses tested had faster decay rates at 25°C than at 5°C (Chung and
Sobsey, 1993). Under the conditions tested, F-specific coliphages had similar decay rates to
poliovirus in sediment at 25°C and in seawater at 5°C, and rotavirus in sediment at 5°C (Chung
and Sobsey, 1993).
Silverman et al. (2013) found that the presence of photosensitizers (presumably colored
dissolved organic matter [CDOM]) in five different natural waters, had different effects on
human virus and bacteriophage photoinactivation in different waters exposed to full spectrum,
simulated sunlight. In four of the five natural waters, the inactivation rate of poliovirus type 3
was significantly slowed relative to a clear, buffered control. In one of the five natural waters,
50
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the inactivation of PRD-1 (which infects Salmonella LT2) was significantly slowed. In three of
five waters, adenovirus and GI F-specific coliphage MS2 inactivation was significantly faster
than the clear control buffer. The authors also examined inactivation rates in UVB-blocked
simulated sunlight to gain insight into the mechanisms of photoinactivation of the different
viruses. The authors concluded that exogenous mechanisms (reaction reactive species formed by
photosensitizers in the water column) contributed significantly to inactivation of the viruses other
than poliovirus type 3 for which endogenous processes are likely dominant.
Synergistic effects between organic and inorganic matter and other environmental factors
Several studies have found synergy between organic and inorganic matter and other
environmental factors in the inactivation rates of viruses. Sunlight has been shown to have
synergistic effects with CDOM present in the water matrix, the effects of which vary depending
on the type of virus, the amount of UVB attenuated by the CDOM, and the number and
concentration of damaging radicals produced (Silverman et al., 2013). Please see Section 5.1,
5.2, and 5.3 for more information sunlight, temperature, and salinity. Viral adsorption to
biofilms, sediment and organic matter can protect viruses from inactivation or expose viruses to
detrimental microbial activity. Please see Section 5.4 for more information on biofilms and
predation and degradation by microbes.
Summary
In summary, depending on the specific environmental conditions coliphages may be a
conservative surrogate for the inactivation of human enteric viruses. The presence of organic and
inorganic matter affects inactivation of enteric viruses and coliphages in aquatic systems. Both
organic and inorganic matter have been shown to either increase or decrease degradation rates,
depending on the type of the virus and the nature of the organic matter (Chung and Sobsey,
1993; Silverman et al., 2013). For example, several groups found that poliovirus, echovirus, and
enterovirus adsorption to sediment or solids decreased inactivation of the viruses (LaBelle and
Gerba, 1980; Griffin et al., 2003), whereas others have found that inactivation rates increased in
samples with high suspended solids and sediment with high clay content (Shen et al., 2008).
While it is impossible to compare coliphages with all human enteric viruses under all conditions,
Silverman et al. (2013) found that GI F-specific coliphage MS2 was a conservative surrogate for
poliovirus type 3 and human adenovirus type 2 (i.e., GI F-specific coliphage MS2 had a slower
decay rate than the human viruses) in five environmental waters with varying levels of
photosensitizing molecules both in the dark and in full sunlight.
5.6. Environmental Factors Impacts Summary
Some studies have found that coliphages are more resistant to environmental stressors than
human viruses, but such findings are highly contextual and dictated by a host of local
environmental conditions. The inactivation kinetics of coliphages is also relative. In general,
temperature, pH, sunlight, CDOM and the association with solids are some of the most important
factors influencing survival of coliphages (Schaper et al., 2002b). Table 13 summarizes these
environmental factors and their mechanisms of inactivation for human enteric viruses and
coliphages.
51
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Table 13. Summary of environmental factors influencing viral inactivation in aquatic environments.
Effects
Factor
Coliphages
NoV and other
human enteric viruses
References
Conclusions
Physical
Temperature • Variable decay rates among
strains; wild isolates more stable
than laboratory strains.
• F-specific RNA coliphages are
more resistant to decay at low
temperatures than high
temperatures.
• Somatic coliphage 50°C in a variety of media.
Salinity and sunlight have synergistic
effects at temperatures ranging from
0°C to 100°C (but in general, coliphage
-------
Sunlight • Different viruses have different
decay rates under the same
sunlight conditions. Genome size
of somatic coliphages is
correlated with decay rate.
• F-specific RNA coliphages are
more resistant to sunlight than F-
specific DNA coliphages in clear
seawater.
• Inactivation rates vary more
widely for ssDNA and dsDNA
viruses than for ssRNA viruses
based on nucleic acid type,
genome length, and morphology.
Different viruses have different
decay rates under the same
sunlight conditions.
Poliovirus type 3 has faster
decay rates than human
adenovirus type 2 under full
sunlight in four different
environmental waters.
Virus inactivation rates are higher in
sunlight conditions than in the dark.
UVB wavelengths are the most
damaging.
Synergistic effects with temperature,
salinity, organic, and inorganic matter.
Direct damage to protein capsid and
genetic material and indirect
inactivation due to reactive oxygen
species and other free radicals.
In full sunlight in seawater, the decay
rates of human adenovirus type 2 and
F-specific coliphages (MS2, Fi, Q(3,
and Sp) are similar.
The decay rates of F-specific DNA
coliphage Ml3 and poliovirus type 3
are also similar.
Decay rates for porcine rotavirus are
two- to three-fold higher than decay
rates for GI F-specific RNA coliphage
MS2 when tested between 14°C and
42°C.
GI F-specific RNA coliphage MS2 is a
conservative surrogate for decay of
poliovirus type 3 and human
adenovirus type 2 in four types of
environmental water.
Bittonetal.,1979;
Sintonetal., 1999,
2002; Sobsey and
Meschke, 2003;
Duizeretal.,2004;
Fong and Lipp, 2005;
Love etal., 2010;
Jonczyketal.,2011;
Lee and Sobsey,
2011; Romero etal.,
2011; Silvermanet
al., 2013
53
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Chemical
Salinity
GI F-specific RNA coliphage
MS2 does not aggregate in high
concentrations of monovalent
cations but does aggregate in
high concentrations of divalent
cations.
Concentrations of 1.3 to 6.3%
NaCl were protective of GI F-
specific RNA coliphage MS2 at
37°C and 50°C.
Salt water compared to
freshwater affects the decay rate
of F-specific coliphages and
somatic coliphages under both
dark and sunlight-exposed
conditions.
F-specific coliphages are more
tolerant in salt water than in
freshwater in the dark.
Somatic coliphages are more
tolerant of salt water than
freshwater under sunlight
conditions.
NoV GI. 1 aggregates with both
mono- and divalent cations,
rotavirus aggregates with
divalent cations.
In seawater, FCV has an initial
reduction (due to salt content),
but retains infectivity over a
month.
Salinity either increases or decreases
degradation rates of viruses based on
type and concentration of salt and
specific virus.
Salinity can affect viral adsorption to
organic and inorganic matter.
There are synergistic effects with
salinity and temperature and organic
and inorganic matter.
At 24°C, 37°C, and 50°C, GI F-specific
RNA coliphage MS2 is more resistant
to 0.3-6.3% NaCl concentrations than
MNV.
Slomka and
Appleton, 1998;
Gutierrez etal., 2010;
Mylonetal., 2010;
da Silvaetal., 2011;
Nguyen etal., 2011;
Seo etal., 2012
54
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Organic and • 39 to 65% of viral inactivation of
Inorganic coliphage T4 due to living and
Matter inert planktonic particles 0.2
to 10 um.
• Both somatic and F-specific
coliphages adsorb to particles
<5 um in size.
• Somatic coliphages attach
preferentially to particles <2 um
in size.
• Sediment protects F-specific
coliphages at 25°C, but not at
higher temperatures.
• Under full sunlight in
environmental waters containing
CDOM, GI F-specific RNA
coliphage MS2 degradation is
dominated by exogenous
mechanisms.
• Adsorption to clay increases
persistence in lake water for
reovirus (the family to which
rotavirus belongs).
• Inactivation of poliovirus and
echovirus decreases with
adsorption to marine sediment.
• Enteroviruses are associated
with paniculate matter protected
from degradation.
• Sediment protects poliovirus and
human adenovirus at 5°C and
25°C.
• Sediment accelerates
inactivation of rotavirus at 5°C
and 25°C.
• Under full sunlight, in
environmental waters containing
CDOM, poliovirus type 3
degradation is dominated by
endogenous mechanisms, human
adenovirus type 2 degradation
dominated by exogenous
mechanisms.
• Organic and inorganic material impact
viral degradation rates.
• Organic matter either decreases or
increases viral deactivation rates.
• Viruses adsorb to suspended paniculate
matter.
• Synergistic effects among sunlight,
temperature, pH, and salinity.
• F-specific coliphage decay rates are
similar to poliovirus in sediment at
25°C and in seawater at 5°C, and
rotavirus in sediment at 5°C.
• MS2 is a conservative surrogate for
decay of poliovirus type 3 and human
adenovirus type 2 in different types of
environmental waters.
Chung and Sobsey,
1993; Griffinetal.,
2003; Sobsey and
Meschke, 2003;
Characklis et al.,
2005 ;Kohn etal.,
2007; Shen et al.,
2008; Finiguerra et
al., 2011; Romero et
al., 2011; Silverman
etal., 2013
Biological
Predation • Wetland vegetation increases
and inactivation of GI F-specific
Enzymatic RNA coliphage MS2.
Degradation . Somatic coliphage T4
(including inactivation in seawater is
biofilms) accelerated by naturally
occurring particles >10 kDa.
• Biofilms protect viruses from
inactivation: somatic coliphage
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6. Wastewater Treatment
Treated wastewater is a source of viruses in ambient water (Kageyama et al., 2003; da Silva et
al., 2007; Haramoto et al., 2007; Kitajima et al., 2009; Kuo et al., 2010; Simmons et al., 2011).
This section provides a broad overview of how coliphages, human enteric viruses, and FIB
behave during various wastewater treatment processes. This section does not evaluate
engineering technologies or provide specifics on treatment processes. Rather, the overall context
is to evaluate whether coliphages could be better than traditional FIB at indicating removal or
inactivation of human enteric viruses during wastewater treatment.
Coliphages have been considered useful microorganisms for evaluating wastewater treatment
efficacy (Duran et al., 2003; Lucena et al., 2004; Bitton, 2005). Because coliphages and human
enteric viruses have similar morphological and structural characteristics (see Section 2.2), often
co-occur in feces, and often share fate and transport characteristics (see Section 5.0), the
reduction of human enteric viruses and coliphages may follow similar patterns during wastewater
treatment depending on the method of pathogen removal (Havelaar et al., 1993; Turner and
Lewis, 1995; Rose et al., 2004). These shared attributes of viruses also suggest that coliphages
would be better indicators for human enteric viruses than traditional FIB in wastewater. This
section discusses coliphage behavior during wastewater treatment and compares it to other
enteric viruses (with a focus on NoV) and FIB.
Somatic coliphages have been reported to outnumber F-specific coliphages in both treated and
untreated wastewater sources (Grabow et al., 1993; Gantzer et al., 1998; Grabow, 2001; Aw and
Gin, 2010). The lower density of indigenous F-specific coliphages is a potential limitation of
their use as an indicator. The range of coliphage densities, specifically the lower end found in
influent is highly variable. For example, within the influent for six WWTPs, Rose et al. (2004)
found somatic and F-specific coliphages from 103 to 106 PFU per 100 mL (host strain ATTC
15597), and F-specific coliphages at 102 to 108 PFU per 100 mL (host strain ATTC 700891). In a
study of eight WWTPs in Canada that serve 20,000 to 60,000 people, Payment and Locas (2011)
found F-specific coliphages in influent in a range of 102 to 106 PFU per 100 mL. Because
bacteria in biological treatment systems are not in logarithmic growth, it is unlikely that F-
specific coliphages replicate during treatment (Rose et al., 2004).
Wastewater treatment processes are often categorized as primary, secondary, tertiary and
advanced treatment, and disinfection. There are a variety of different secondary treatment unit
processes that can produce different qualities of water. Tertiary treatment has different purposes
and definitions depending on the State, and outside the United States. Definitions can vary
widely. In addition, natural treatment systems, such as waste stabilization ponds, are commonly
used to provide treatment that is roughly similar to primary and secondary treatment. There are a
wide variety of technologies available for wastewater treatment, and almost all WWTPs in the
United States include secondary treatment and some type of disinfection. This section focuses on
the removal or inactivation of coliphages and enteric viruses during the various steps of
wastewater treatment.
It is important to understand that treatment efficacy depends on the quality of the effluent prior to
disinfection (particularly turbidity or UV transmittance), pH, temperature, the type of
56
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chlorination (free or combined), chlorine dose and contact time, UV dose, and a number of other
factors (Asano et al., 2007). Given the importance of the specifics of the treatment processes, it is
difficult to draw generalized conclusions from studies that do not provide adequate information
on the treatment specifics. For example, efficacy of chlorination depends on the type of
chlorination, the contact time, and the specific nature of the secondary treated water. Coliphages
can be resistant to some chlorination practices (Havelaar, 1987; Sobsey, 1989; Havelaar et al.,
1990; Yahya and Yanko, 1992; Nasser et al., 1993; Gantzer et al., 1998; Bitton, 2005; Harwood
et al., 2005), but sequential chlorination (the free chlorine portion) can provide up to 6-logio
removal (LACSD, 2013).
Ideally, to examine the question of how coliphages, FIB, and enteric viruses compare during
wastewater treatment, a study would include the following design attributes:
• enumeration of indigenous somatic and F-specific coliphages, FIB, and one or more
human viruses (not addition of a laboratory generated stock of virus);
• density in influent and effluent;
• calculated logic reduction values;
• detailed information on the treatment processes that were applied including information
on discharge requirements that would impact level of treatment; and
• full-scale wastewater treatment facilities (not pilot and bench scale studies).
Although most of the literature found for this review did not include all of the above attributes,
the studies that provided the most relevant information are discussed in more detail (Rose et al.,
2004; Harwood et al., 2005; Aw and Gin, 2010; Keegan et al., 2012). It is beyond the scope of
this review to conduct a meta-analysis for synthesizing data from the different studies, so each
study is discussed individually. Given that this is a broad, high-level review and treatment details
are lacking in most of the studies, the nuances of wastewater treatment diversity are not
discussed.
The Water Environment Research Foundation (WERF) conducted an evaluation of the reduction
of pathogens, FIB, and alternative indicators (including somatic and F-specific coliphages) at six
WWTPs that produced tertiary recycled water by collecting samples five times (approximately
once every 2 months) over the course of a year (Rose et al., 2004). Samples were obtained from
the WWTPs at various stages of the treatment process and the microorganism density was
evaluated by culture dependent methods. A comparison of the logic reductions of all coliphages
and enteroviruses across all facilities indicated that the combination of primary and biological
secondary treatment results in a ~2-logio reduction of coliphages and enteroviruses, filtration
results in a ~0.5-logio reduction of both coliphages and enteric viruses, and disinfection results in
a ~0.5-logio reduction of coliphages, and little to no reduction of enteroviruses (Rose et al.,
2004). The lower average reduction of enteric viruses from disinfection at all six plants was
concluded to be partially due to the fact that enteroviruses were below detection limits in 69% of
the samples, and samples with no detection were recorded as being at the detection limit (Rose et
al., 2004). Coliphages were closer in logic reductions to enteroviruses than traditional FIB.
Whereas coliphages and enteroviruses both had a cumulative reduction of ~3 to 4 logic, FIB had
a cumulative reduction of ~5 to 6- logic.
57
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The study found that the densities of coliphages and viruses in the influent samples from the
different WWTPs were not significantly different; whereas the densities in final effluent were
significantly different among WWTP (Rose et al., 2004). These data indicate that differences in
effluent densities were related to the treatment processes employed in each WWTP. Although no
correlation of the density of coliphages and enteroviruses was found, the authors suggest that it is
possible to predict the absence of enteroviruses based on coliphage levels. Levels less than 10
coliphage PFU per 100 mL (either F-specific coliphages, or F-specific combined with somatic
coliphages) were indicative of effluents with no detectable cultivatable enteroviruses (Rose et al.,
2004). While Rose et al. (2004) reported logic reductions, they did not provide detailed
information on the treatment processes.
Harwood et al. (2005) evaluated the same data reported in Rose et al. (2004). F-specific
coliphages were detected in 100% of the influent samples at densities ranging from 103 PFU per
100 mL to 108 PFU per 100 mL. Although enteroviruses were above detection limits in 31% of
the disinfected effluent samples, coliphages and enteroviruses co-occurred in only 13% of the
disinfected effluent samples. The authors reported a weakly significant relationship between the
presence or absence of enteroviruses and coliphages in disinfected wastewater effluent (Harwood
et al., 2005).
Aw and Gin (2010) reported that, when comparing raw sewage to secondary effluent at a plant in
Singapore (where wastewater is treated using activated sludge processes), on average, somatic
and F-specific coliphage densities were reduced by 2.4-logio and NoV GI and Gil were reduced
by ~2-logio. Specifically, somatic coliphages were reduced from 1.8 x io5 to 102 PFU per 100
mL, F-specific coliphages from 4.3 x IO4 to IO2 PFU per 100 mL, NoV GI from 3.2 x IO5 to 7.1
x IO3 gene copies per 100 mL and NoV Gil from 2.3 x IO5 to 5.2 x IO3 gene copies per 100 mL.
Coliphages were quantified by infectivity assays and NoV were quantified by qPCR
amplification. PCR amplification can amplify both infectious and noninfectious virus particles
and may therefore overestimate the number of infectious NoV particles. The authors found
significant correlation between levels of somatic coliphages and adenoviruses, and between F-
specific coliphages and NoV Gil in raw sewage samples (Aw and Gin, 2010).
Figure 1 shows example reductions for three WWTPs in Singapore (secondary effluent -
activated sludge). Somatic and F-specific coliphages had on average 2.4-logio reduction, and
were reduced at a similar rate as enteric viruses, adenovirus, and astrovirus. NoV reductions
were less, but assays were based on qPCR results evaluating both viable and nonviable NoV (Aw
and Gin, 2010).
58
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1,0 •
8
I01-
§.»••
I
•o
e
»
10'
S. 10
io'
10'
ds
m
u Raw is wags
o S=:cn;3"\< eff Lent
o CLte»5
Adercvims
NcrcvirusGI
Scrratic ccliphage ^-specific zcliphage
Virus tf pe
Figure 1. Comparison of coliphages and enteric viruses in raw sewage
and secondary effluent.
Somatic and F-specific coliphages (PFU per 100 mL) and enteric viruses
(gene copy number per 100 mL) isolated from raw sewage (n = 18) and
secondary effluent (n = 18). The box represents 50% of the data values. The
line across the inside of the box represents the median value, and the lines
extending from the box represent the 95% CIs. Outliers are represented by
circles. Hashed boxes are raw sewage, and open boxes are secondary effluent
(adapted from Aw and Gin, 2010).
Keegan et al. (2012) investigated the required chlorine and chloramine contact times for
inactivating enterovirus (Coxsackie B5) and adenovirus 2. Enterovirus and adenovirus 2 were
cultured and added separately to wastewater with varying turbidity levels (0.2, 2, 5, and 20
nephelometric turbidity unit [NTU]) and pH (7, 8, and 9) at 10°C. The spiked samples were
exposed to different chlorine/chloramine concentrations and contact times to determine the
contact times for up to 4-logio virus inactivation. Results demonstrated that increasing contact
times are needed with increased turbidity and increased pH. For both viruses, a 4-logio
inactivation was possible even at the highest turbidity tested (20 NTU). The authors indicated
that the results of the study will be used in the development of new wastewater disinfection
guidelines for Australia.
Regulatory agencies in Australia use coliphages as indicators for wastewater treatment efficacy.
When evaluating a WWTP, the South Australian and Victorian Departments of Health use
minimum removal values as defaults for each treatment process, unless it has been demonstrated
that a greater inactivation is achievable in the system (Keegan et al., 2012). Table 14 shows the
logio reductions for wastewater treatments used by the South Australian and Victorian
59
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Departments of Health. Note that coliphage removals are more similar to human virus removal
than E. coli or bacterial pathogen removal for many treatments.
Table 14. Logio removals of enteric viruses and indicator organisms.
Indicative Logio Removals"
Treatment
Primary treatment
Secondary treatment
Dual media filtration with
coagulation
Membrane filtration
Reverse osmosis
Lagoon storage
Chlorination
Ozo nation
UVC light
Viruses (including
adenoviruses, rotaviruses
and enteroviruses)
0-0.1
0.5-2.0
0.5-3.0
2.5->6.0
>6.0
1.0-4.0
1.0-3.0
3.0-6.0
>1.0 adenovirus
>3 .0 enterovirus, hepatitis
A virus
Coliphages
N/A
0.5-2.5
1.0-4.0
3.0->6.0
>6.0
1.0-4.0
0-2.5
2.0-6.0
3.0-6.0
E. coli
0-0.5
1.0-3.0
0-1.0
3.5->6.0
>6.0
1.0-5.0
2.0-6.0
2.0-6.0
2.0->4.0
Bacterial
pathogens
0-0.5
1.0-3.0
0-1.0
3.5->6.0
>6.0
1.0-5.0
2.0-6.0
2.0-6.0
2.0->4.0
Sources: Australian Guidelines for Water Recycling (2008) and Keegan et al. (2012)
a Reductions depend on specific features of the process, including detention times, pore size, filter depths, and
disinfectant. The default values are accumulated across the treatment train processes. Each row shows only the
reduction for that treatment step.
6.1. Primary Treatment
Primary treatment of wastewater involves settling of solids in settling tanks and results in
different reduction rates of different microbe groups. Viruses are too small to settle and are only
removed during primary treatment if they are attached to larger particles. The settling velocities
of individual bacteria and protozoan cysts are low compared to the retention time of
sedimentation tanks; thus, their removal is also enhanced by attachment to larger particles. As a
result, the removal efficiencies of microorganisms is a function of their association with
wastewater particles. Asano et al. (2007) report that typical removal is <0.1- to 0.3-logio for fecal
coliforms, 0.1- to 1.0-logio for Cryptosporidium,
-------
coliphages were reduced by 0.8-logio (SD = 0.4) and F-specific coliphages were reduced by 1.3-
logio (SD = 0.7) (Ottoson, 2005).
6.2. Secondary Treatment
Secondary treatment of wastewater involves the use of a natural population of bacteria, such as
the mixed liquor floes in activated sludge treatment or the biofilm on trickling filters, to decrease
biochemical oxygen demand (BOD), organic material, and in some cases nutrients (depending on
the design). In activated sludge treatment, aeration is necessary to support the growth of the
aerobic heterotrophic bacteria that consume the soluble organic material in the wastewater.
Although secondary treatment is not designed to remove pathogens, removal of indicator
organisms and pathogens often occurs.
Secondary treatment results in different logic reduction values for different microorganisms and
depends on the specifics of the secondary treatment. In a widely used general resource book
(Water Reuse), Asano et al. (2007) report that the typical range of removal is 0 to 2-logio for
fecal coliforms, 1-logio for Cryptosporidium, 2-logio for Giardia, and 0- to 2-logio for enteric
viruses. In addition, Asano et al. (2007) report that secondary treatment using activated sludge
results in a mean reduction of 1.83-logio for GI F-specific RNA coliphage MS2. The Australian
Guidelines for Water Recycling report logio reduction ranges of 1- to 3-logio for E. coli, 0.5- to
2.5-logio for coliphages, and 0.5- to 2-logio for enteric viruses (NRMMC-EPHC-NHMRC,
2008). A study of WWTPs in Argentina, Colombia, France, and Spain found that secondary
treatment reduced somatic coliphages, Bacteroidesfragilis bacteriophages, and F-specific
coliphages between 1.0- to 1.6-logio units (Lucena et al., 2004). In a study of WWTPs in
Switzerland, Baggi et al. (2001) found that three WWTPs with mechanical, biological, and
chemical processes provided 0.6- to 0.8-logio reductions for F-specific and somatic coliphages.
A fourth WWTP with mechanical, biological, and chemical processes, plus sand filtration
provided 1- to 4.4-logio reductions for F-specific and somatic coliphages (Baggi et al., 2001).
While some coliphages and human virus removal occurs during secondary treatment, they are
still typically detectable in non-disinfected secondary effluent. Aw and Gin (2010) detected
somatic coliphages and F-specific coliphages along with adenoviruses, astroviruses, and NoVs in
100% of the secondary effluent samples tested (Figure 1). Somatic coliphages and F-specific
coliphages were present in secondary effluent at 100 PFU per 100 mL (Aw and Gin, 2010). In
six WWTPs secondary effluents, Rose et al. (2004) found that somatic and F-specific coliphages
ranged from 10 to 105 PFU per 100 mL, enterococci from 103 to 105 CFU per 100 mL, and
enteroviruses from 10 to 102 MPN per 100 mL. However, in 27% of the secondary effluent
samples, enteroviruses were below the detection limits. In five Australian WWTPs, Keegan et al.
(2012) found coliphages, adenoviruses, rotaviruses, reoviruses, NoV, and enteroviruses in
secondary effluent (Table 15).
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Table 15. Virus densities in secondary treated wastewater samples from five Australian
WWTPs.
Microorganism
Sample
location
Bolivar
Bolivar 2
Glenelg
Cairns
Brisbane
ACT
Adeno virus
genome/L
1.59 xlO5
9.3 x 106
2.8 xlO5
8.1 xlO5
1.7 xlO6
ND
Enterovirus
genome/L
0
0
0
ND
ND
ND
Reovirus
genome/L
3.7 xlO8
0
1.16xl08
ND
ND
ND
NoV
genome/L
2.7 x 105
2.0 x 103
2.3 x 104
ND
ND
4.0 x 103
Rotavirus
genome/L
1.63 x 104
>6.0 x 103
1.05 x 104
ND
ND
ND
F-specific
RNA
coliphages
PFU/L
5.0 xlO5
3.7 xlO4
5.0 xlO3
ND
ND
21
Source: Keegan et al. (2012)
Performed in triplicates with mean results shown in the table.
ND = not detected.
Some other studies also measured logic reduction values for coliphages and enteric viruses, but
did not provide enough information on treatment design and operations to understand how these
reductions might apply in other WWTPs. For example, Lodder and de Roda Husman (2005)
found that secondary treatment resulted in the reduction of 1.8-logio for NoV, 1.6-logio for F-
specific coliphages, and 1.1-logio for somatic coliphages. Ottoson et al. (2005) found that
secondary treatment mean reductions from multiple WWTPs in Sweden were 1.73-logio
(SD = 0.6) for F-specific coliphages and 1.04-logio (SD = 0.3) for somatic coliphages, which
were similar to reductions of enteroviruses 1.3-logio (SD = 0.7), and NoVs 0.89-logio (SD = 0.3).
FIB had higher logic reduction values; enterococci was reduced 2- logic (SD = 0.5) and E. coli
was reduced 2.3- logic (SD = 0.6) (Ottoson et al., 2005). Flannery et al. (2012) measured the
densities of FIB, F-specific coliphages, and NoV GI and Gil in both influent and final effluent at
a WWTP. Treatment included preliminary processing by screening and grit removal followed by
treatment with a conventional activated sludge system, including primary sedimentation,
aeration, and secondary clarification, but no further treatment details were provided. A
comparison of influent to secondary effluent found that mean culturable F-specific coliphage
densities were reduced by 2.13-logio, NoV GI gene copy densities were reduced by 0.8-logio,
NoV Gil gene copy densities were reduced by 0.92-logio, and E. coli densities were reduced by
1.49-logio (Flannery et al., 2012).
Appendix B is a compilation of studies that investigated coliphage and NoV densities before,
during, and/or after wastewater treatment. It includes mostly non-disinfected secondary effluent,
but some disinfected effluents are also included as noted in the table. The Appendix B
information is focused on NoV compared to coliphages, because of NoV s importance as an
enteric pathogen. NoV is the leading etiological agent of gastrointestinal illness in the United
States, and of an estimated 36.4 million cases of domestically acquired gastrointestinal illness,
NoV causes an estimated average of 20.8 million cases annually (Scallan et al., 2011).
Some of the studies reviewed in this section evaluated correlations between coliphages and
enteric viruses to determine the usefulness of coliphages as surrogates for human viral presence
in non-disinfected secondary effluent. Gantzer et al. (1998) showed a significant correlation
between the density of coliphages and infectious enteroviruses in secondary effluent and the
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correlation between the density of somatic coliphages and the presence of the enterovirus
genomes (p-value <0.0001). No enteroviruses were isolated in secondary effluent (without
disinfection) when the somatic coliphage density was between 100 and 10,000 PFU per L
(Gantzer et al., 1998). Although the treatment specifics were different, these results are similar to
those in Rose et al. (2004), who found that coliphage levels less than 10 PFU per 100 mL in final
disinfected effluent contained no detectable cultivatable enteric viruses (Rose et al., 2004). The
threshold level in the WERF study is based on tertiary disinfected effluent and not non-
disinfected secondary effluent (Rose et al., 2004). Ottoson et al. (2006) found there was no
significant correlation between the reduction of coliphages or FIB compared to viruses
(enteroviruses and NoV) in secondary treated wastewater. Flannery et al. (2012) also found no
correlation between the densities of E. coll and F-specific coliphages with either NoV GI or NoV
Gil levels in effluent wastewater (r < 0.07 in all instances).
6.3. Wastewater Treatment Ponds
Wastewater treatment ponds, also known as waste stabilization ponds or lagoons, are shallow
synthetic basins that treat sewage in a single or series of anaerobic, facultative or maturation
ponds. Aeration and encouragement of aquatic life are other possible features of wastewater
treatment ponds. Verbyla and Mihelcic (2015) analyzed virus removal data from 71 different
systems. They found weak to moderate correlation between virus removal and hydraulic
retention time. For each logic reduction of viruses a geometric mean of 14.5 days of retention
(95th percentile was 54 days of retention) was required. GI F-specific RNA coliphage MS2
coliphage is considered to be the best surrogate for studying sunlight disinfection in wastewater
treatment ponds. Inactivation of coliphages by solar radiation in lagoons and ponding systems
tends to be seasonal, with the most effective inactivation occurring in summer months (Davies-
Colley et al., 2005; Blatchley et al., 2007). Sunlight inactivation of viruses is discussed in
Section 5.2 and is compared to UVC inactivation in Section 6.5.4.
The open water wetland is similar to a maturation pond, but instead of having planktonic algae,
the algae are part of a biomat on the bottom of the pond. Silverman et al. (2015) found that
removals of F-specific and somatic coliphages were similar in a pilot-scale system. Based on
laboratory and modeling work, they determined that GI F-specific RNA coliphage MS2 was
inactivated more slowly than poliovirus under summer conditions, but more rapidly under winter
conditions. More research is needed to determine how the relative inactivation rates of
indigenous coliphages (F-specific and somatic coliphages) and other enteric viruses change
seasonally in open water wetlands.
6.4. Tertiary Treatment and Advanced Treatment
Tertiary treatment typically refers to particle removal processes (e.g., granular media filtration,
cloth filtration, or membrane filtration) that are employed before final disinfection. The amount
by which viruses (and other pathogens) are reduced by filtration varies depending on filter
characteristics, operating practices, microbial properties, including size, surface properties, and
degree of association with other microorganisms or particles, and water quality variables (Levine
et al., 2008). Tertiary treatment may also refer to chemical or biological nutrient removal
processes (e.g., targeting nitrogen and/or phosphorus), although these processes are sometimes
considered part of secondary treatment. Literature reports for treatment plants employing nutrient
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removal were included in Section 6.2. Advanced treatment trains, which can be applied to
filtered tertiary effluents, can be used to further purify water for indirect or direct potable reuse.
Advanced treatment typically involves advanced oxidation processes (AOPs) and dense
membranes (nanofiltration and reverse osmosis) that target the removal of pathogens and trace
organic contaminants (Leverenz et al., 2011; NRC, 2011; Gerrity et al., 2013). Membrane
processes are reviewed here. Disinfection processes, including UV, ozone, free chlorine,
combined chlorine, and AOPs are described in detail in Section 6.5.
Depth filtration involves the use of granular media (e.g., sand, anthracite, garnet, or activated
carbon) in single (mono-media) or layered configurations (multi-media). Microorganism removal
differs based on a variety of factors, including water quality, the type and size of granular media,
the filtration velocity, and the use of coagulant and/or polymer. Typical removals from depth
filtration are reported to be 0 to 1-logic for fecal coliforms, 0 to 3-logio for Cryptosporidium, 0-
to 3-logio for Giardia, 0- to 1-logio for enteric viruses and -0.14- to 2-logio for coliphages
(Rajala et al., 2003; Hijnen et al., 2004; Zanetti et al., 2006; Asano et al., 2007; Hijnen and
Medema, 2007). Asano et al. (2007) report that tertiary treatment using depth filtration results in
a mean reduction of 0.29-logio for GI F-specific RNA coliphage MS2, and Zanetti et al. (2006)
found that tertiary sand filtration resulted in a mean reduction of 0.31-logio for E. coli and 0.14-
logio for somatic coliphages.
Rajala et al. (2003) conducted both laboratory and pilot-scale experiments on rapid sand
filtration of wastewater effluent from WWTPs in Finland. In the laboratory experiment, the rapid
sand filtration reduced coliphages by 0.15- to 0.26-logio (30-46%) at a hydraulic load of 5
meters per hour and 0.13- to 0.27-logio (23-38%) at a hydraulic load of 10 meters per hour. In
the pilot experiments (hydraulic loads range 7.7 to 10 meters per hour), coliphages were reduced
by 0.66- to 1.5-logio (7-97%), depending on the plant (Rajala et al., 2003). Based on pilot-scale
filter studies on rapid depth filtration, Williams et al. (2007) found that the removal efficiency of
GI F-specific RNA coliphage MS2 (seeded into secondary effluent) was similar to that of E. coli
and total coliforms (~ 0.8 logic at a loading rate of 12.2 meters per hour). The removal efficiency
of MS2 was more sensitive to the coagulant dose, compared to the indicator bacteria. In an
experimental rapid sand filtration setup, virus size (based on OX174, MS2, and T4 coliphages)
was the only factor that influenced retention and the larger the virus, the greater the retention
(Aronino et al., 2009).
Levine et al. (2008) conducted experiments to examine pathogen reduction from sand filtration
of secondary effluent at five full-scale water reclamation facilities in the United States (three
plants using monomedium and two plants using dual media) at peak usage over the course of a
year. These are the same facilities that are reported in Rose et al. (2004). The average reductions
for all five plants ranged from 0.1- to 4.2-logio for fecal coliforms, 0.3- to 1.1-logio for infectious
Cryptosporidium, 0.7- to 1.5-logio for Giardia, 0.3- to 1.2-logio for culturable enteroviruses, 0.3-
to 1.3-logio for F-specific coliphages, and 0.2- to 0.8-logio for somatic and F-specific coliphages
(Levine et al., 2008). The authors found that the differences in average reduction rates between
plants were likely due to a combination of loading rates, chemical addition practices (chlorine
and coagulant), backwashing and post backwashing operating strategies, and the effectiveness of
upstream biological treatment and sedimentation (Levine et al., 2008). In general, logic
reductions of indicator bacteria (coliforms, enterococci, and Clostridium) was 2-to 9-fold greater
64
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than the logic reduction of pathogens, suggesting that monitoring with bacterial indicators may
over predict pathogen reductions. Rose et al. (2004) noted that shallow sand filters were more
effective than deep-bed dual-media or monomedia filters for removal of coliphages and viruses.
However, this result was affected by the fact that pre-disinfection (pre-chlorination) was used for
the shallow sand filter tests but not for the deep-bed filters.
Surface Filtration includes mechanical sieving of secondary effluent, through cloth, metal or
synthetic woven materials with a pore size of-10 to 30 jim. In comparative testing for 15- to
30-|im particles, surface filtration removed more particles than granular filtration over all particle
sizes tested (Olivier et al., 2003). Asano et al. (2007) reported average reductions for surface
filtration of 0- to 1-logio for coliform bacteria and 0- to 0.5-logio for enteric viruses. These
results are consistent with Levine et al. (2008), who found that cloth filtration of secondary
effluent at a full-scale water reclamation facility at peak usage over the course of a year resulted
in average reductions of 3-logio (range: 1.9 to 4.3) for fecal coliforms, 0.5-logio (range: 0.3 to
0.7) for infectious Cryptosporidium, 0.5-logio (range: -0.4 to 1.3) for Giardia, 0.5-logio (range:
0.3 to 0.8) for culturable enteric viruses, 0.6-logio (range: -0.1 to 1.8) for F-specific coliphages,
and 0.4-logio (range: -0.1 to 1) for somatic and F-specific coliphages.
Membrane filtration, a type of advanced treatment, involves forcing wastewater through a thin
membrane filtering under pressure. Membranes with different sized pores can be used, including
microfilters (>50 nm), ultrafilters (2 to 50 nm), nanofilters (<2 nm), and reverse osmosis
(polymer matrix without discrete pores; particles are excluded and uncharged molecules pass
through membrane by diffusion). In general, the smaller the pore size used, the greater the
reduction of pathogens and the higher the operating pressure (Asano et al., 2007). For example,
Asano et al. (2007) reported that typical removal of pathogens from microfiltration are 1- to 4-
logio for fecal coliforms, 1- to 4-logio for Cryptosporidium, 2- to 6-logio for Giardia, and 0- to 2-
logio for enteric viruses. Ultrafiltration results in removal of 3- to 6-logio for fecal coliforms, >6-
logio for protozoa, and 2- to 7-logio for viruses. Nanofiltration results in removal of 3- to 6-logio
for all types of bacteria, >6-logio for protozoa, and 3- to 5-logio for viruses. Reverse osmosis
results in reductions of 4- to 7-logio for fecal coliforms, 4- to 7-logio for Cryptosporidium, >7-
logio for Giardia, and 4- to 7-logio for enteric viruses (Asano et al., 2007).
Perfectly intact nanofiltration and reverse osmosis membranes should not allow passage of any
bacteria or viruses; however, leaks in seals, and membrane imperfections or damage to the
membranes could allow their passage. Thus, monitoring the integrity of membranes is critical to
ensuring high removal of microorganisms.
Juby (2003) found that microfiltration of screened primary effluent at a demonstration plant in
California resulted in typical reductions of 4.7-logiofor fecal coliforms and 1.7-logiofor
coliphages. Gomez et al. (2006) used secondary effluent from a WWTP in Spain to determine
pathogen reduction rates from microfiltration and ultrafiltration. They found that microfiltration
resulted in a 2.7-logio reduction in fecal coliform, the removal of E. coli below detectable limits,
and a 1.3-logio reduction of coliphages, whereas ultrafiltration resulted in a 4.7-logio reduction of
fecal coliform, the removal of E. coli below detectable limits, and a 3.5-logio reduction of
coliphages (Gomez et al., 2006).
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Membrane Bioreactors are a relatively new technology that combine an activated sludge
bioreactor with membrane filtration, which replaces both secondary and tertiary treatment.
Zhang and Farahbakhsh (2007) found that membrane bioreactor pilot plants achieved 5.8-logio
removal of coliphages. Whereas conventional activated sludge process followed by advanced
tertiary treatment (nitrifying rotating biological contactors, sand filtration, and chlorination),
achieved 5.5-logioremoval of coliphages. For membrane systems, coliphages appear to be better
indicators of microbial removal efficacy (especially viral removal) probably because the pore
size of most microfiltration and ultrafiltration membranes exclude fecal coliforms, but some
coliphages can still pass through the membrane pores (Zhang and Farahbakhsh, 2007). In a full-
scale membrane bioreactor study, Purnell et al. (2015) reported a 5.3-logio reduction in
indigenous somatic coliphages. Indigenous F-specific coliphages were less abundant and
demonstrated a 3.5-logio reduction. In 'spiking' experiments, suspended GI F-specific RNA
coliphage MS2 demonstrated a 2.25-logio reduction (Purnell et al., 2015).
6.5. Disinfection
Disinfection of secondary effluent can be achieved using physical (UVC radiation) and chemical
(chlorine, chloramines, and ozone) treatments. This section focuses on the physical and chemical
treatments of secondary effluent and the effects of these treatments on coliphages, FIB, and
enteric virus inactivation. Although solar radiation can also play a role in further disinfection of
secondary effluent by lagooning (Gomila et al., 2008), lagooning is not typically considered a
disinfection treatment (see Section 6.3). It is important to note that if ammonium levels are not
reported, it cannot be determined whether free chlorine or combined chlorine was present during
the disinfection step. This is important because many studies report on water samples from
secondary disinfected effluent, but there is wide variation in what secondary disinfected effluent
includes.
As mentioned previously, studies with water samples collected at full-scale WWTPs are
preferred. However, pilot scale and bench-scale studies are also included when full-scale data
were not available.
6.5.1 Free Chlorine
Chlorine (Cl~) is the most widely used wastewater disinfectant (Asano et al., 2007). Chlorine is
an efficient disinfectant for most enteric bacteria, but is generally less efficient against viruses,
protozoan cysts, and bacterial spores (Keegan et al., 2012). The effectiveness of chlorine is
impacted by disinfection dose, contact time, temperature, and water quality variables (pH,
turbidity, presence of ammonia and oxidant demand) (Rose et al., 2004; Asano et al., 2007). For
example, above pH 7, a 10 mg per L residual chlorine resulted in 4-logio reduction of F2
coliphages, whereas at low pH, as little as one-fifth of this chlorine achieved the same reduction
(Hajenian and Butler, 1980).
Due to the highly reactive chemical nature of free chlorine (HOC1 and OC1"), in secondary
effluents containing ammonium, it rapidly combines with ammonium to form chloramines, a
form of combined chlorine (U.S. EPA, 2002; Tree et al., 2003; Asano et al., 2007). Disinfection
with free chlorine can be achieved in ammonium-containing effluents if "breakpoint"
chlorination is practiced, in which sufficient free chlorine is added to convert all ammonium to
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nitrogen. Free chlorine is a much stronger oxidant than combined chlorine, and is more effective
at inactivating pathogenic bacteria and coliphages than combined chlorine (Tyrrell et al., 1995;
Duran et al., 2003; Tree et al., 2003; Keegan et al., 2012). Combined chlorine will be discussed
in more detail in Section 6.5.2. It is important to note that both free chlorine and combined
chlorine can result in formation of hazardous disinfection byproducts such as trihalomethanes,
haloacetic acids, chlorite, and other hazardous compounds.
In a bench-scale study, Shin and Sobsey (2008) studied the inactivation of NoV by free chlorine
using molecular methods and compared its inactivation to F-specific RNA coliphage MS2 and
poliovirus type 1. F-specific RNA coliphage MS2 and poliovirus type 1 were measured using
both culture-based and molecular methods. The authors conducted experiments using 1 and 5 mg
per L free chlorine. Inactivation of NoV was similar to F-specific RNA coliphage MS2 and faster
than poliovirus type 1 when densities were measured using molecular methods. They also
showed that the CT (disinfectant concentration times contact time) required for NoV inactivation
was not significantly different from other viruses even though the molecular methods likely
overestimate the CT needed. Thus, the study authors concluded that chlorine is a useful
disinfectant for NoV.
If a study evaluates disinfected effluent, but does not report ammonium levels, it cannot be
determined whether free chlorine or combined chlorine was present. Of the six WWTPs
evaluated in Rose et al. (2004), four used chlorine disinfection, but only one of the WWTP had
ammonium levels that allowed for free chlorine. Rose et al. (2004) combined the data from the
four WWTPs and found that on average, 300 minutes of contact time with chlorine (or combined
chlorine) in secondary effluent resulted in a 3-logio reduction of enterococci, whereas 500
minutes of contact time were required for a 3-logic reduction of enteroviruses. Data from the
WWTP with free chlorine disinfection of nitrified and filtered effluent is show in Table 16. More
studies that compare chlorine inactivation of FIB, indigenous F-specific and somatic coliphages,
and enteric viruses in nitrified effluent are needed.
Table 16. Average (and percent positive) microorganism effluent densities in a WWTP with
free chlorine treatment of nitrified and filtered secondary wastewater.
Treatment
Influent
Filtered and
disinfected with
free chlorine
Total coliform
CFU/100 mL
3.41 xlO7
(100%)
11.3
(60%)
Enterococci
CFU/100 mL
7.36 xlO5
(100%)
0.2 detection
limit
(0%)
Microorganism
Somatic and F-
specific
coliphages
PFU/100 mL
2.84 xlO5
(100%)
10.4
(80%)
F-specific
coliphages
PFU/100 mL
3.14xl05
(100%)
10.4
(80%)
Enterovirus
MPN/100 mL
1.52 xlO4
(100%)
0.3
(80%)
Source: Rose et al. (2004)
Over a 13-month period water samples were taken at Easterly WWTP in Vacaville, California
and evaluated for FIB, F-specific coliphages, NoV, and other pathogens (Olivieri et al., 2012).
This WWTP has bar screens, grit removal, primary clarification, secondary treatment with
activated sludge, secondary clarification, nitrification, and chlorine disinfection and de-
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chlorination. Logic removal of fecal coliform through secondary disinfection was a median of
6.8-logio (range 6.1- to 8.4-logio; all non-detects were set at the detection limit). In finished
effluent, fecal coliforms were not detected in 50 of the 55 samples (<2 MPN per 100 mL
detection limit), and the remaining 5 were at the limit of detection. For enterococci, log removals
through secondary disinfection was a median of 5.8-logio (range 3.2- to 6.2-logio; all non-detects
were set at the detection limit). In finished effluent, enterococci were not detected in 22 of 32
samples (<1 MPN per 100 mL detection limit). The 10 detectable enterococci samples ranged
from 1 to 648.8 MPN per 100 mL. F-specific coliphages were detected in all 32 influent samples.
Densities ranged from 60 PFU per 100 mL to 13,000 PFU per mL, with a median of 2,750 PFU
per 100 mL. F-specific coliphages in the final disinfected and dechlorinated effluent were below
the detection limit (<1 PFU/100 mL) in all but two samples. One sample was at the detection
limit (1 PFU/100 mL), and the other sample was 2 PFU per 100 mL. The log removal of F-
specific coliphages had a median of 3.4-logio(range 1.8- to 4.1-logio). NoV were present in the
ten WWTP influent samples and not detected in eleven final disinfected and dechlorinated
effluent samples (Olivieri et al., 2012). This demonstrates that free chlorine applied to nitrified
effluent is quite effective at inactivating F-specific coliphages and NoV.
6.5.2 Combined Chlorine
As stated above, studies have shown that in secondary effluent with ammonium, the free chlorine
rapidly combines with the ammonium to form chloramines (Asano et al., 2007). Combined
chlorine compounds are less effective at inactivating microorganisms than free chlorine (Tyrrell
et al., 1995; Duran et al., 2003; Tree et al., 2003; Keegan et al., 2012).
Tree et al. (2003) studied the chlorine-mediated inactivation of both seeded (E. coli,
Enterococcus faecalis, GI F-specific RNA coliphage MS2, and poliovirus - all measured using
culture-based methods) and naturally occurring (E. coli, enterococci, F-specific coliphages, and
enterovirus - also using culture-based methods) bacterial and viral indicators in primary sewage
effluent. The inactivation rates of three applied doses of free chlorine (8, 16, and 30 mg per L)
were investigated in both seeded sterilized primary effluent and unsterilized primary effluent.
Although free chlorine was applied, Tree et al. (2003) found that the amount of free chlorine
available in effluent decreased rapidly within the first 5 minutes and then remained
approximately constant for the duration of the experiments (30 minutes). In both experiments,
the authors found that FIB (E. coli and enterococci) were inactivated more rapidly and at lower
doses than the viruses (F-specific coliphages, poliovirus, and enterovirus) and that chlorine dose
and time of exposure had significant effects on survival of all organisms tested in both
experiments (Table 17). BothE1. coli (laboratory-cultured and indigenous) and enterococci had
linear degradation rates and were completely inactivated over the course of the experiment at all
chlorine applications tested. In contrast, enteroviruses had biphasic degradation rates, with a
rapid initial rate, followed by a slower inactivation rate. F-specific RNA coliphages (both
laboratory-cultured and naturally occurring) only showed degradation for the first 5 minutes of
exposure after which no further degradation occurred. The authors suggest that the slower rate of
degradation for enteroviruses and lack of degradation of F-specific RNA coliphages after 5
minutes is likely due to the weaker effect of combined chlorine on viruses. The authors conclude
that F-specific RNA coliphages are a useful and conservative model surrogate for chlorine
inactivation of viruses in sewage (Tree et al., 2005).
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Table 17. Logio reduction of FIB, enteric virus, and F-specific coliphages in sewage matrix
due to chlorine (adapted from Tree et al., 2003).
Matrix Microorganism
Seeded into sterilized primary E. coll
sewage matrix
Enterococcus
Applied chlorine concentration
8mg/L
>5
(<5 min.)
1
(<5 min.)
16mg/L
>5
(<5 min.)
(<15 min.)
30mg/L
>5
(5 min.)
>5
(5 min.)
Poliovirus 1 <2 4
(after 30 min.) (after 30 min.) (after 30 min.)
Naturally occurring in raw
sewage (after primary
treatment)
F-specific RNA
coliphage MS2
Indigenous E. coll
Indigenous
Enterococcus
Indigenous
Enteroviruses
Indigenous F-
specific RNA
coliphages
(after 30 min.)
4
(5 min.)
>3
(15 min.)
(after 30 min.)
(after 30 min.)
(after 30 min.)
4-5
(5 min.)
>3
(5 min.)
(after 30 min.)*
(after 30 min.)
1
(after 30 min.)
5
(5 min.)
>3
(5 min.)
(after 5)*
(after 30 min.)
* Because these were naturally occurring level (so lower density than seeded samples), the detection limit was
reached after about a 1-logio reduction.
Note: Times in parenthesis indicate the duration of the chlorine treatment. Log reductions were estimated based on
graphical information.
Duran et al. (2003) determined chlorine-mediated inactivation rates of both spiked and naturally
occurring FIB, bacteriophages, and enteroviruses in secondary effluents. The authors found that
after secondary effluent was exposed to 10 mg per L chlorine at the WWTP, naturally occurring
FIB (E. coli and enterococci) were reduced at significantly higher rates than were naturally
occurring viruses (F-specific RNA coliphages, somatic coliphages, B. fragilis bacteriophages,
and enteroviruses). Specifically, mean reductions of naturally occurring microorganisms in
chlorinated secondary effluent were: 2.9-logio (SD = 2.5) for fecal coliforms, 2.0-logio (SD = 0.7)
for enterococci, 1.6-logio (SD = 0.6) for somatic coliphages, 0.6-logio (SD = 0.5) for F- specific
RNA coliphages, 0.3-logio (SD = 0.3) for B. fragilis bacteriophages, and 0.4-logio for
enteroviruses (no SD was given due the low number of positive samples) (Duran et al., 2003).
Chlorination of secondary effluent in the laboratory resulted in similar inactivation rates as those
found from chlorination at the WWTP (Duran et al., 2003). Both F-specific and somatic
coliphages were inactivated more efficiently than enteroviruses. However, coliphages were
closer to enterovirus logic reductions than FIB.
To determine if different types of viruses have different levels of resistance to chlorine, Duran et
al. (2003) spiked secondary effluent with several bacteriophages, the vaccine strain of poliovirus
type 1 Lsc 2a, and an enterovirus isolated from the environment, AR51101-1. The logic reduction
of bacteriophages and enteroviruses are presented in Table 18.
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Table 18. Logio reduction of bacteriophages and enteroviruses in spiked secondary effluent
after chlorination with 20 mg/L of chlorine.*
Phage or Virus
Enteroviruses
Somatic coliphages
F-specific RNA coliphage
Bacteriophages specific to B.
fragilis HSP40
Source: Duran et al. (2003)
*Concentration of free chlorine
AR51101-1
Poliovirus type 1
-------
order of resistance. However, it should be noted that adenoviruses seem to be more resistant to
combined chlorine than enterovirus (Irving and Smith, 1981; Cromeans et al., 2010).
Adenovirus-2 is one of the most resistant viruses to chloramines and adenovirus-2 has similar
resistance as adenovirus 40 and 41 (Keegan et al., 2012). Reovirus may be even more difficult to
remove than adenovirus and enteroviruses through secondary treatment processes (Irving and
Smith, 1981). Future studies that compare the behavior of coliphages to adenovirus would be
helpful for evaluating the utility of coliphages as indicators of the presence of viruses in
wastewater.
6.5.3 Ozone
Ozone is a highly reactive chemical that damages microorganisms and reacts with water to
produce hydroxyl radicals (OH") that oxidize organic pollutants (Paraskeva and Graham, 2002).
Like other disinfection processes, high doses of ozone can result in hazardous disinfection
byproduct formation such as bromate. Additionally ozone decomposition occurs faster at higher
temperatures and higher pH, which can alter disinfection efficacy (U.S. EPA, 1999). Viruses as,
a group, are the most sensitive microorganisms to ozone of all the microorganisms listed on
EPA's Contaminant Candidate List (U.S. EPA, 1998; Gerba et al., 2003).
Several studies have shown that in secondary effluent, ozone is more effective at inactivating
coliphages than FIB (Tyrrell et al., 1995; Gehr et al., 2003; Tanner et al., 2004). For example,
Gehr et al. (2003) found that a transferred ozone dose of 17 mg per L resulted in a 3-logio
reduction of F-specific RNA coliphages, whereas a transferred ozone dose of 30 to 50 mg per L
was required for a 2-logio reduction in fecal coliforms and resulted in less than a 1-logio
reduction in Clostridiumperfringem (Gehr et al., 2003). Tyrrell et al. (1995) found that
secondary sewage treated with a pulse of ozone [mean residual ozone concentrations of 0.30
ppm (SD = 0.08)] resulted in approximate mean reductions of 2.5-1 ogio for F-specific coliphages,
2.25-logio for somatic coliphages, 1.3-logio for fecal coliforms, 1.2-logio for enterococci, and
0.2-logio for C. perfringens. Lazarova et al. (1998) found that 5 minutes of contact time of a 5-
mg per L dose of ozone resulted in a 5-logio removal of F-specific RNA coliphage MS2.
Tanner et al. (2004) investigated the effects of ozone on poliovirus, F-specific RNA coliphage
MS2, Klebsiella terrigena, E. coli, heterotrophic plate count bacteria, fecal coliforms, and total
coliforms, either in secondary effluent or reverse osmosis treated water. In secondary effluent,
continuous ozone treatment for 1 minute resulted in an average inactivation of 2.5-1 ogio for
coliphages, and <1.5-logio reductions for total coliforms, fecal coliforms, and heterotrophic plate
count bacteria. In demand-free reverse osmosis treated water, the authors found that 1 minute in
0.2 mg ozone per L resulted in a >3-logio inactivation of poliovirus and 1 minute in 0.25 mg
ozone per L resulted in a 6-logio inactivation of F-specific RNA coliphage MS2. Tanner et al.
(2004) also found that increasing the concentration of ozone reverse osmosis treated water
resulted in increased inactivation of all indicator organisms tested (F-specific RNA coliphage
MS2, Klebsiella terrigena, andE. coli). Table 19 presents the highest logic reductions of each
indicator organism at a given ozone concentration.
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Table 19. Inactivation of FIB and F-specific RNA coliphage in ozone disinfected water.*
Indicator
F-specific RNA coliphage MS2
Klebsiella terrigena
E. coli
poliovirus
Logio inactivation
>5.41
4.71
4.15
>3
Ozone concentration (nig ozone/L)
0.22
0.25
0.25
0.2
Source: Tanner et al. (2004)
*Water was spiked after receiving RO treatment.
Finch and Fairbairn (1991) found that in demand-free phosphate buffer, 1.6-1 ogio units more
inactivation was observed with GI F-specific RNA coliphage MS2 than with poliovirus type 3.
The authors conclude that use of MS2 coliphage as a surrogate organism for studies of enteric
virus with ozone disinfection systems can overestimate the inactivation of enteric viruses. In
contrast, Shin and Sobsey (2003) documented the inactivation of MS2, Norwalk virus, and
poliovirus type 1 in the presence of ozone using infectivity assays (for MS2 and poliovirus type
1) and RT-PCR (all three viruses). Using a 0.37-mg per L dose of ozone at pH 7 and 5°C, the
authors found that the three viruses were inactivated approximately 3-logio within 5 minutes and
hence had similar inactivation behavior when detected using molecular methods. Inactivation
measured by infectivity of F-specific RNA coliphage MS2 and poliovirus type 1 agreed well
with their inactivation using molecular methods. Hall and Sobsey (1993) studied the decay of F-
specific RNA coliphage MS2 and hepatitis A virus in buffered water when exposed to ozone, as
well as ozone and hydrogen peroxide in series. They found that both F-specific RNA coliphage
MS2 and hepatitis A virus behaved similarly and were rapidly inactivated (up to 6-logio in 5
seconds) by two types of treatments.
6.5.4 UVC
In contrast to oxidative disinfection processes with chemicals like free chlorine and ozone, the
efficacy of UVC (hereafter referred to as UV) disinfection is not affected by conditions like
temperature, pH, and the presence and concentration of reactive organic matter (UV absorbance
by organic and inorganic matter can shield microorganisms from UV, but the reactive properties
of the organic matter don't affect the UV, as happens with chemical disinfectants) (Oppenheimer
et al., 1993; Hijnen et al., 2006). UV light is primarily absorbed by nucleic acids of
microorganisms, causing harmful photoproducts such as thymine dimers on the same nucleic
acid strand. If the damage is not repaired, replication is blocked, leading to subsequent
inactivation of microorganisms (Ko et al., 2005). UV inactivation of microorganisms, including
coliphages, is proportional to the UV fluence or dose, the product of the UV intensity and
exposure time. Unlike free and combined chlorine and ozone, UV does not produce harmful
disinfection byproducts (Oppenheimer et al., 1993). UVC has a shorter wavelength than UVA
and UVB. UVC is filtered by the atmosphere, so does not occur in sunlight that reaches the
surface of the earth. UVC is the most biologically damaging of the three UV wavelength classes
and can be created artificially with UVC bulbs for treatment of water. UVC wavelengths (100 to
280 nm), also called short-wave or germicidal UV, have been shown to result in a 1.09- to 2-
logio reduction of indicator bacteria and coliphages in secondary effluent (Rose et al., 2004).
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In general, coliphages have been found to be more resistant to UVC light than FIB. For example,
Gehr et al. (2003) demonstrated that GI F-specific RNA coliphage MS2 is more resistant to UV
inactivation than fecal coliforms in effluent. Tree et al. (2005) found that F-specific RNA
coliphage MS2 was more resistant to UV reduction than E. coli (4-logio reduction required 62.5
ml/cm2 for MS2 and 5.32 ml/cm2 for E. coif) in seeded, sterilized secondary effluent. Wilson et
al. (1992) found that the viruses GI F-specific coliphage MS2, rotavirus, poliovirus, and hepatitis
A were at least 7.1 times more resistant than the bacteria Klebsiella terrigena, Legionella
pneumophila, Salmonella typhi, Aeromonas hydrophila, E. coli, Campylobacter jejuni, Yersina
enterocolitica, Shigella dysenteriae, and Vibrio cholerae. In general, the bacteria tested were
three to ten times more susceptible to UV irradiation than the viruses (Wilson et al., 1992).
One of the six WWTPs studied in Rose et al. (2004) used UV disinfection. Table 20 shows the
densities of microorganisms in the filtered secondary effluent compared to the filtered secondary
effluent after UV disinfection.
Table 20. Average (and percent positive) microorganism densities in a WWTP with UV
treatment of filtered secondary effluent (n=5).
Treatment
Filtered
secondary
effluent
Filtered
secondary
effluent
disinfected with
UV with free
chlorine
Total coliform
CFU/100 mL
1.79 x 104
(100%)
11.9
(80%)
Enterococci
CFU/100 mL
5.8 xlO2
(100%)
4.38
(20%)
Microorganism
Somatic and F-
specific
coliphages
PFU/100 mL
1.14xl03
(100%)
10 detection
limit
(0%)
F-specific
coliphages
PFU/100 mL
1.41 xlO2
(100%)
10 detection
limit
(0%)
Enterovirus
MPN/100 mL
0.7
(40%)
0.5 detection
limit
(0%)
Source: Rose etal. (2004).
The National Water Research Institute (NWRI) and Water Research Foundation (WRF)
Ultraviolet Disinfection Guidelines for Drinking Water and Water Reuse provided information
on logic inactivation of viruses and FIB. They indicated that water is essentially "pathogen-free"
if a 5-logio poliovirus reduction and a 7-day median total coliform density of 2.2 MPN per 100
mL is achieved. When media filtration is employed, effluent quality can vary, and particulate
matter may shield pathogens from UV light to various degrees. In these cases, a reduction
equivalent dose of 100 ml (millijoules) per square centimeter (cm2) is typically adequate to
inactivate total coliform to less than 2.2 MPN per 100 mL. The report also indicated a 5-logio
reduction of poliovirus can be achieved with a UV dose of 50 mJ/cm2 based on laboratory
studies, however the 100 ml per cm2 dose is recommended to account for effluent variability.
When using membrane filtration or ultrafiltration prior to UV treatment, the impact of particles is
normally eliminated. In this situation, the Ultraviolet Disinfection Guidelines for Drinking Water
and Water Reuse noted that a 5-logio reduction in poliovirus can be achieved with a UV dose of
50 mJ/cm2, and a design UV dose of 80 ml per cm2 is suggested to account for variability in the
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effluent quality for membrane filtration or ultrafiltration. When using reverse osmosis for
filtration, a reduction of at least 2-logio for viruses can be achieved through the reverse osmosis
process, and the additional 3-logio reduction required for poliovirus can be achieved with a UV
dose of about 30 ml per cm2. Therefore, to account for variability in the effluent quality for
reverse osmosis the design UV dose of 50 ml per cm2 is recommended (NWRI-WRF, 2012).
UV disinfection efficiency of secondary effluent is influenced by hydraulic properties of the
reactor and wastewater characteristics, such as initial density of microbes, UV absorbance, and
the concentration and characteristics of suspended solids (Koivunen, 2007; NWRI-WRF, 2012).
For example, organic humic acid floe particles shielded viral surrogates (F-specific RNA
coliphage MS2 and somatic coliphage T4) from UV light to a greater degree than inorganic
kaolin clay floe particles of similar size (diameters <2 mm) (Templeton et al., 2005). However,
humic acid floe particles also caused a greater reduction in logic inactivation virus than larger
activated sludge particles, which suggests that particulate chemical composition (e.g., UV
absorbing content) and size may be important factors in the survival of particle-associated
viruses during UV disinfection (Templeton et al., 2005). Because the study did not include
human viruses, more data are needed to know whether these results extend to human viruses.
Table 21 presents the estimated rate constants from a study on UV inactivation of F-specific
RNA coliphage MS2 (NWRI-WRF 2012).
Table 21. UVC inactivation of F-specific RNA coliphage MS2.
Dose
(mJ/cm2)
0
20
40
60
80
100
120
140
Source: NWRI-WRF
Surviving density
(PFU/mL)
1.00 xlO7
1.12xl06
6.76 x 104
1.95 xlO4
4.37 xlO3
1.20 xlO3
7.08 xlO1
1.48 xlO1
(2012)
Log survival
(log PFU/mL)
7.0
6.05
4.83
4.29
3.64
3.08
1.85
1.17
Logio inactivation
(log PFU/mL)
0.0
0.95
2.17
2.71
3.36
3.92
5.15
5.83
Different types of somatic coliphages have different levels of resistance to UV light. For
example, Lee and Sobsey (2011) estimated the UV inactivation of five types of somatic
coliphages (Tl, T4, T7 OX174, X) representing the four families (Microviridae (OX174),
Myoviridae (T4), Podoviridae (t7) and Siphoviridae (X, Tl)) in laboratory tests using both
reagent-grade water and surface water. Using regression analysis, the authors predicted the UV
doses (ml per cm2) for a 4-logio inactivation of each of the somatic coliphages to be (in order of
most to least resistant): 24 for X, 18 for OX 174, 12 for T7, 11 for Tl, and 4 for T4. Note that
these doses are lower than what is recommended for treatment plants. Based on these results, the
authors concluded that different somatic coliphage families can have very different inactivation
rates and that OX174 and X are the most resistant to UV radiation. In addition, different
wavelengths have different efficacy at coliphage attenuation. For example, GI F-specific RNA
coliphage MS2 was three times more sensitive to wavelengths near 214-nm compared to the
254-nm output of low-pressure lamps in simulated drinking water (Mamane-Gravetz et al.,
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2005). There is also evidence that laboratory propagated F-specific RNA coliphage MS2 is
inactivated by UV at a rate that is twice that of indigenous F-specific coliphages (Oppenheimer
et al., 1993). This highlights the importance of data evaluating indigenous coliphages.
Nuanualsuwan et al. (2002) evaluated coliphages and other virus inactivation in a phosphate-
buffered solution and UV light treatment. The UV dose (ml/cm2) required for 1-logio
inactivation was 47.85 for FCV, 36.50 for hepatitis A virus, 24.10 for poliovirus type 1, 23.04
for GI F-specific RNA coliphage MS2, and 15.48 for somatic coliphage OX174 (Nuanualsuwan
et al., 2002). The coliphages were slightly more sensitive to UV compared to the human viruses.
In contrast, other studies have found that coliphages are more resistant to UV than human
viruses. For example, Wiedenmann et al. (1993) found that in a sodium chloride solution, to
achieve 4-logio inactivation, a three-times higher UV dose was required for GI F-specific RNA
coliphage MS2 compared to hepatitis A virus. Havelaar (1987) found that, in secondary effluent,
F-specific coliphages are more resistant to UV treatment than coxsackievirus, rotavirus, and
poliovirus. Similarly, Tree et al. (2005) found that UV reduction of F-specific RNA coliphage
MS2 was less than that of poliovirus and FCV (a surrogate for NoV) in seeded, sterilized
secondary effluent. To achieve a 4-logio reduction, doses (ml per cm2) of 62.5 for GI F-specific
RNA coliphage MS2, 27.51 for poliovirus, and 19.04 for FCV were required. In bench-scale
experiments Wilson et al. (1992) found that GI F-specific coliphage MS2 was 1.9 times more
resistant to UV irradiation that the viruses, rotavirus, poliovirus, and hepatitis A.
Human adenoviruses are more resistant to UV light than other waterborne (enteric) viruses with
single and ds RNA genomes. The human adenovirus genome is comprised of dsDNA, which
affords the virus the ability to use host cell repair enzymes to repair damage in the DNA caused
by UV light (Hijnen et al., 2006). In contrast, viral genomes that are single stranded DNA cannot
be repaired in host cells because there is no second strand to serve as a template for replication of
the nucleic acid. Viral genomes made of RNA are not repaired efficiently because mammalian
hosts do not have sufficient repair mechanisms for RNA (Eischeid et al., 2011). Thompson et al.
(2003) conducted a pilot-scale study to examine the effects of UV disinfection on viruses in
wastewater. In seeded tertiary treated wastewater, 4-logio inactivation of poliovirus type 1
required 35 ml per cm2, GI F-specific RNA coliphage MS2 required 100 ml per cm2, and human
adenovirus (types 15 and 2) required 170 ml per cm2. In a buffered demand-free water 4-logio
inactivation of FCV required 36 ml per cm2, GI F-specific RNA coliphage MS2 required 119 ml
per cm2, and human adenovirus-40 would have required 226 ml per cm2 (extrapolated value, 4-
logio reduction was not achieved) (Thurston-Enriquez et al., 2003).
6.5.5 UVA and UVB
Solar radiation, which consists of UVA/UVB in addition to longer wavelengths, can also be used
as a disinfection method. Wastewater treatment ponds (see Section 6.3) can be used to treat
sewage or to further treat secondary effluent. For example, Davies-Colley et al. (2005)
constructed an outdoor (exposed to solar radiation) advanced pond system to determine the solar
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inactivation of somatic and F-specific RNA coliphages and E. coli in secondary effluent.7 Tests
were conducted in both the summer and winter to determine effects of seasonal variation in solar
radiation intensity. Somatic coliphages showed a 2.2-logio reduction in summer and a 0.45-logio
reduction in winter, whereas E. coli had a greater than 4-logio removal in both seasons.
Reductions of F-specific RNA coliphages were not reported due to low native coliphage
densities in the influent. The authors found that solar radiation within the UVB range
(represented by measurements at 311 nm) was responsible for somatic coliphage inactivation,
whereas F-specific RNA coliphages were hypothesized to be inactivated by both UVA and UVB
(Davies-Colley et al., 2005). These results are consistent with Sinton et al. (2002), who found
that under a variety of conditions, F-specific RNA coliphages were inactivated by a wide range
of wavelengths, whereas somatic coliphages were mainly inactivated by UVB wavelengths (less
than 318 nm). Davies-Colley et al. (2005) concluded that the advanced pond system is efficient
at removing coliphages mainly during the summer (or in the tropics), but not in the winter due to
decreased intensity of solar radiation.
Gomila et al. (2008) compared inactivation of coliphages and enteric viruses in secondary
effluent that was treated by UVC radiation (laminar flow through four banks of eight lamps of
87.5 Watts [W] each) or treated in a sunlit aerobic lagooning system with a residence time of 60
days. Inactivation of somatic coliphages, F-specific coliphages, and enteroviruses was greater in
a lagooning system compared to UVC treatment, as shown in Table 22. Using either a UVC
radiation step in a treatment facility or solar radiation in a lagooning system yielded a greater or
equal inactivation of coliphages as compared to enteric viruses. Costan-Longares et al. (2008)
investigated the logio inactivation of enteroviruses between secondary effluent and different
types of tertiary treatment at WWTPs in Spain. The authors found a greater than 2-logio
reduction in enteric virus density from secondary treatment after lagooning (Costan-Longares et
al., 2008).
Table 22. Logio reduction in coliphages and enteric viruses in secondary
effluent after lagooning in sunlight or UVC treatment.
Microorganism Logio reduction (lagooning) Logio reduction (UVC treatment)
Somatic coliphages 0.8 0.5
F-specific coliphages 1.6 0.5
Enteroviruses 0.7 0.5
Source: Gomila et al. (2008)
To compare the effects of UV wavelengths present in sunlight on both coliphages and enteric
viruses, Lee and Ko (2013) exposed F-specific RNA coliphages MS2 and MNV, to UVA and
UVB lamps. For all experiments, viruses were suspended in either saline solution or groundwater
and viral densities were measured by EPA Method 1602 (MS2) or plaque assays (MNV). UVA
irradiation resulted in a negligible effect on both F-specific RNA coliphages MS2 and MNV
across the dose range tested (0 to 1500 ml per cm2). In contrast, MNV was found to be
significantly more susceptible to UVB than MS2; exposure to 376 ml per cm2 UVB resulted in a
7 Sewage from the Ruakura Research Centre, near Hamilton, New Zealand fed into the advanced pond system. The
F-specific coliphage level was consistently low in the Ruakura sewage, so primary treated sewage from Hamilton
City was "spiked" into the pond system.
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4-logio reduction of MNV whereas 909 ml per cm2 UVB was required for the same reduction of
F-specific RNA coliphage MS2 (Lee and Ko, 2013). Duizer et al. (2004) found that caliciviruses
(enteric canine calicivirus no. 48 and respiratory FCV F9) were more susceptible to UVB than
coliphages as <50 ml per cm2 UVB resulted in a 4-logio reduction of both viruses (as determined
by cell culture) when suspended in buffer.
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7. Conclusions
This review provides background information relevant to the use of coliphages, specifically
somatic and F-specific coliphages, as indicators of fecal contamination. The following is a
summary of the major conclusions of this review.
Methods. Coliphage enumeration methods are adequate for water quality monitoring. EPA
Method 1601 may be the most useful. Rapid methods are possible and MST methods for
coliphage are under development. The ability to measure both somatic and F-specific coliphages
on a single host may be useful, but needs validation (Rose et al., 2004; Guzman et al., 2008).
EPA is currently evaluating a membrane filtration culture method and may also evaluate an
ultrafiltration culture method for use in coliphage enumeration. The intralaboratory (single
laboratory) method validation study is underway.
Epidemiological studies. This review summarizes eight epidemiological studies that evaluated
the relationship of coliphages and gastrointestinal illness from exposure to recreational water.
Five of the eight studies found a statistically significant relationship between F-specific
coliphages and illness levels (Lee et al., 1997; Colford et al., 2005, 2007; Wiedenmann et al.,
2006; Wade et al., 2010; Griffith et al., personal communication, 2015). One of the studies found
a statistically significant increase in RR of GE in bathers when somatic coliphage levels were
above the NOAEL of 10 PFU per 100 mL (Wiedenmann et al., 2006).
Occurrence in the Environment. Some studies have reported an association between the
presence of coliphages and human viruses, while other studies have found no association
between their presence in environmental waters. The results are strongly influenced by the
environments in which the studies are conducted. For example, an association between indicators
and pathogens has more often been reported for brackish and saline water than for freshwater.
There is evidence that coliphage and F-specific coliphage densities are more strongly associated
with pathogens than other traditional indicators (E. coli, enterococci, and fecal coliforms).
Environmental Fate. Coliphages might be reasonable surrogates for enteric viruses in the
environment. Human viruses and coliphages both decay faster at temperatures above 50°C
compared to lower temperatures. Human viruses and coliphages both decay faster in sunlight
than in the dark and are most stable near neutral pH (~6 to 9), but can also survive in lower pH
environments (i.e., in the gastrointestinal tract of warm-blooded animals). The effect of salinity
is equivocal and some studies have shown increased and others decreased inactivation in higher
salinity waters. In fresh, treated, septic, and salt water, predation and environmental factors (e.g.,
temperature, sunlight, pH) have been shown to increase degradation of both coliphages and
enteric viruses. Organic and inorganic matter affect inactivation—both have been shown to
increase or decrease decay rates, depending on the virus and the nature of the composition of the
organic or inorganic matter. There are synergistic or antagonistic interactions between all these
environmental stressors.
Wastewater treatment. For primary and secondary treatment, the removal efficiencies of FIB,
F-specific coliphages, somatic coliphages, and enteric viruses are not substantially different.
Disinfection is the key step in wastewater treatment for microbial inactivation. Although
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disinfection efficacies vary depending on the details of the treatment process, and the
characteristics of the incoming water at each step, some general conclusions are possible. UVC
and ozone are most effective at virus inactivation, followed by free chlorine. Combined chlorine
is not as effective at virus inactivation as the other disinfection treatments. For free chlorine
(chlorination of nitrified effluents), there are insufficient data to draw conclusions about the
relative inactivation efficiencies of FIB, indigenous F-specific coliphages, indigenous somatic
coliphages, and enteric viruses. For combined chlorine (non-breakpoint chlorination of un-
nitrified effluents), F-specific coliphages and enteric viruses are more resistant to inactivation
than FIB. In laboratory studies of UVC disinfection, coliphages and enteric viruses are generally
more resistant to inactivation compared to FIB. However, the inactivation rates of individual
strains of F-specific and somatic coliphages, as well as enteric viruses, are variable. For example,
adenovirus is highly resistant to UVC. With the exception of ozone, F-specific and somatic
coliphages overall are likely to be more conservative indicators than FIB in water treated by
most disinfectants.
Overall. Table 23 compares coliphage attributes against the currently recommended indicators
of fecal contamination, E. coli and enterococci. Each indicator/method combination is
summarized and compared against indicator attributes described in Section 1.3. While some of
the same limitations exist, coliphages are likely a better indicator of viruses in fecal
contamination than the current FIB (i.e., enterococci andE. coli).
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Table 23. Attributes of fecal contamination indicators.
Indicator
Attribute
Enterococci
(e.g. EPA Method 1600)
E. coli
(e.g. EPA Method 1603)
Coliphages
(e.g. EPA Method 1602)
Intestinal microflora of warm-
blooded animals
Yes
Yes
Yes
Present when pathogens are
present and absent in
uncontaminated samples
Present when fecal
pathogens are present, but
may also be present in
nonfecally contaminated
ambient water.
Present when fecal Present when fecal pathogens are
pathogens are present, but present, but is likely absent in
may also be present in nonfecally contaminated ambient
nonfecally contaminated water.
ambient water.
Not indicative of viruses in Not indicative of viruses
WWTP effluent. in WWTP effluent.
Better surrogate for viruses than
enterococci or E. coli in WWTP
effluent.
Present in greater numbers Depends on source3
than the pathogen (in this case,
human viruses)
Depends on source3
In most cases
Equally resistant as pathogens
(in this case viruses) to
environmental factors
Not as resistant as viruses Not as resistant as viruses Under most conditions
Equally resistant as pathogens
(in this case viruses) to
disinfection in water and
WWTPs
Not as resistant as viruses
(except for ozone).
Not as resistant as viruses
(except for ozone).
Under most conditions.
However, adenovirus is more
resistant than coliphages and
other enteric viruses to UV
inactivation.
Should not multiply in the Can multiply in the
environment
environment
Can multiply in the
environment
Not likely enough to affect
criteria levels
Detectable by means of easy,
rapid, and inexpensive
methods
Yes, but need EPA Method Yes, but EPA method is
1611 for rapid
enumeration. Other easy
and rapid methods are
available.
not considered rapid
(requires overnight
incubation). Other easy
and rapid methods are
available.
Yes, but Method 1601 needs
validation for quantification.
Other easy and rapid methods are
available.
Indicator organism should be
nonpathogenic
Generally nonpathogenicb Generally nonpathogenic.0 Nonpathogenic
Demonstrated association with
illness from epidemiological
studies
Yes
Yes
Yes
Specific to a fecal source or
identifiable as to source of
origin
Not EPA Method 1600, but Not EPA Method 1603,
MST methods being but MST methods being
developed. developed.
Not EPA Method 1602, but MST
methods being developed.
a In raw sewage FIB are present in greater numbers than pathogens. Viruses are less vulnerable to treatment processes
than bacteria, so could survive treatment in greater numbers than bacteria.
b Enterococci can be pathogenic or antibiotic resistant in some settings, like hospitals, but generally not in ambient water.
0 Enterohemorrhagic E. coli, specifically O157:H7, grows poorly at 44°C and is often negative for beta-glucuronidase, so
is not detected by Method 1603 (Degnan and Standridge, 2006). Other pathogenic strains could be detected by EPA
Method 1603.
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8. References
Abdelzaher, A.M., Wright, M.E., Ortega, C., Rasem Hasan, A., Shibata, T., Solo-Gabrieie, H.-
M., Kish, J., Withum, K., He, G., Elmir, S.M., Bonilla, J.A., Bonilla, T.D., Palmer, C.J., Scott,
T.M., Lukasik, J., Harwood, V.J., McQuaig, S., Sinigalliano, C.D., Gidley, M.L., Wanless, D.,
Piano, L.R., Garza, A.C., Zhu, X., Stewart, J.R., Dickerson, J.W., Yampara-Iquise, H., Carson,
C., Fleisher, J.M., Fleming, L.E. 2011. Daily measures of microbes and human health at a non-
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APPENDIX A: Literature Search Strategy and Summary of Literature Search Results
The literature search strategy consisted of a number of combined approaches. The following
'synopsis of information' and search terms were used to search online databases, including
PubMed. To supplement these searches, individual authors used free search engines on the
internet to find articles pertaining to specific information needed. The titles of literature cited in
specific reports, books, review articles, and conference proceedings were evaluated for
relevance.
Synopsis of information gathered during the 2012 literature search:
• Evaluate the use of bacteriophage as indicators of fecal contamination or wastewater
treatment efficacy
• Determine the sources and persistence of bacteriophage in the environment
• Evaluate the correlation between bacteriophage occurrence and pathogens and traditional
fecal indicator bacteria (FIB) in wastewater
• Evaluate properties that affect fate and transport of viruses and bacteriophage
• Describe the different methods used for detection and analysis of bacteriophage
concentrations, particularly in recreational waters
• Evaluate the environmental factors (e.g., organics, temperature, pH, UV/sunlight,
predation, salinity, porosity, etc.) affecting viral and coliphage degradation
• Compare degradation in WWTP for bacteriophage and enteric viruses (i.e., primary,
secondary, and tertiary disinfection)
Initial Literature Search Strategy Conducted by Professional Librarian
Database: PubMed
Dates: 1985-present (Search conducted on July 5, 2012)
Language: No restrictions
Retrieve: Titles and year
Results Format: Microsoft Word; EndNote
Interested in international and domestic journals and government reports.
Search terms:
Set 1: bacteriophage OR coliphage
AND
Set 2: Water OR illness OR health OR risk
Search Results from PubMed
The PubMed search resulted in approximately 2,400 records after removing duplicates. These
titles were reviewed for relevance based on the outline for the literature review and the synopsis
above. From the database of titles, 391 articles were sorted as "yes" and 81 were sorted as
"maybe." Because this number of titles was still large, 125 "top" articles were selected. The 125
articles were retrieved by the EPA librarian and sent to the contractor (ICF International). The
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125 articles were the starting place for the literature review. Additional targeted literature
searches were required to obtain more complete information on specific topics.
HECD Resources
HECD has developed a robust library of references on waterborne pathogens. These resources
were included in the resources for this project. Primary authors had access to the HECD library
ofPDFs.
Supplemental Searches by Primary Authors
Primary Author 1:
Search Engine: Google Scholar (http://scholar.google.com/)
Search terms:
Bacteriophage AND temperature
Bacteriophage AND pH
Bacteriophage AND sunlight
Bacteriophage AND UVA
Bacteriophage AND UVB
Bacteriophage AND organic matter
Bacteriophage AND sediment
Bacteriophage AND predation
Bacteriophage AND degradation
Bacteriophage AND biofilms
Bacteriophage AND morphology AND survival
Enterovirus
Enterovirus
Enterovirus
Enterovirus
Enterovirus
Enterovirus
Enterovirus
Enterovirus
Enterovirus
Enterovirus
AND temperature
ANDpH
AND sunlight
AND UVA
AND UVB
AND organic matter
AND sediment
AND predation
AND degradation
AND biofilms
Primary Author 2:
Number of Records Considered:
20
20
20
10
10
20
20
20
20
15
25
20
20
20
10
10
20
20
20
20
15
Date
9-20-12
9-20-12
9-20-12
Search
Engine
PubMed
PubMed
PubMed
Search Terms
reviews for fecal source tracking
reviews for coliphages as viral
indicators
reviews for microbial indicators and
pathogens
# of Titles
Reviewed
20
20
20
# of Articles
retrieved
2
2
2
111
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9-20-12
9-20-12
9-25-12
9-25-12
9-25-12
9-25-12
9-26-12
9-27-12
9-27-12
9-27-12
10-1-12
Google
Google
PubMed
Google
Scholar
Google
Scholar
Google
Scholar
Google
Scholar
Google
Scholar
Google
Scholar
Google
Scholar
PubMed
coliphage environment fecal
contamination
coliphage indicator environment
Policies and practices for beach
monitoring
coliphage detection in fresh water
coliphage presence in environment
review
alternative indicators of fecal
pollution
Bacteriophage in the environment
environmental detection coliphage
coliphages environment
fecal source tracking
coliphage source tracking
20
20
40
20
20
20
20
40
40
40
30
2
2
2
2
2
2
4
4
4
4
2
The document was undergoing internal EPA review and external peer review throughout 2013-
2014. Additional supplemental searches were conducted to address EPA internal and external
peer reviewer comments. Ultimately, over 2,500 titles were reviewed for inclusion in the
literature review. There are 342 citations in the final document.
The Quality Assurance Project Plan includes Information Decision Criteria for selection of cited
references. The relevant Information Decision Criteria for this project from the Quality
Assurance Project Plan includes:
1. More recent references were preferred over older references, unless the older reference
was particularly notable, important, or widely cited.
2. Accessibility - References needed to be obtained within project time and budget
constraints.
3. English language was required.
4. Scientific, peer-reviewed publications were preferred, along with others references that
presented a balanced and objective tone. Government publications such as federal
regulations, state regulations, standards, permits, guidance documents, and other
government publications were acceptable.
5. The reference related to the scope of the information sought. In this case a document
outline was available.
6. Geographic relevance - Data collected in the U.S was preferred, but data from other
countries was also relevant.
112
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7. For a given topic, a literature review citation may have been used in lieu of listing
numerous primary research articles cited in the literature review. This was done when
the additional detail provided by the primary citations was not needed.
8. If a particular point was already in the document and a citation was already provided,
additional citations backing up this same point were not added. Redundant articles were
not necessarily cited.
9. Information provided through personal communication (phone, email) was used only
when another more widely obtainable source was not available for the same
information. Information obtained through personal communication needed to be
highly relevant.
10. Books citations were acceptable, but sources that could be more easily obtained were
preferred. Book citations were preferred when the book is an important resource in the
field.
11. Newspaper articles were not searched or cited.
12. Websites were not cited as primary sources of information. URLs are provided for
some of the references.
13. Information and references that presented alternative points of view or conclusions to
the mainstream view were given equal considerations to consensus or majority
viewpoints. Both alternative and majority viewpoints and conclusions had to provide
justification based on facts, employ accepted methodologies, and be grounded in the
scientific method.
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APPENDIX B: Coliphage and NoV Densities during Wastewater Treatment
Table A illustrates how coliphage reduction compares to NoV reduction during wastewater treatment. To be included in Table A, the
study has to include quantitative norovirus data, quantitative coliphage data, and water samples from raw sewage or effluent. The
studies are listed in chronological order by year of publication.
Table A. Coliphage and NoV densities during wastewater treatment.
Organism
NoV
(RT-qPCR)
F-specific
bacteriophages
(ISO 10705-1)
Somatic
coliphages
(ISO 10705-2)
NoVGI
(RT-qPCR)
NoV Gil
(RT-qPCR)
F-specific
coliphages
(ISO 10705-1)
NoV
(RT-qPCR)
F-specific
coliphages
(ISO 10705-1)
Influent (raw) Effluent
Mean 2 x 105 NRa
PCR detectable
unit per L
Mean 106 NRa
PFUperL
Mean 106 NRa
PFUperL
0.17-260 copies NR
per mL (range)
2.4-1900 copies NR
per mL (range)
NR NR
Mean 3. 29 ±0.26 NR
(<2.9-3.65)logio
MPN PCR units
perL
NR NR
Log
reduction
(logio)
1.8
1.6
1.1
2.27 ± 0.67
3.69 ±1.21
2.81 ±0.77
0.89 ±0.26
(0.39->1.3)
1.73 ±0.59
(0.74-2.63)
Treatment Location Reference
Non-disinfected activated Netherlands Lodder and de
sludge secondary Roda
treatment (preceded by Husman, 2005
primary and phosphorus
removal);
No design/operational
information provided to
understand secondary
treatment or performance.
Activated sludge Tokyo, Japan Haramoto et
secondary treatment and al, 2006
chlorination;
No design/operational
information provided to
understand secondary
treatment or performance;
no information if this is
free chlorine, combined
chlorine, ammonia
concentration.
Non-disinfected chemical Sweden Ottosonetal.,
precipitation and activated 2006
sludge (1 plant filtered the
effluent and 1 plant
provided additional
nitrogen removal);
114
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Organism
Somatic
coliphages
(ISO 10705-2)
Somatic
coliphages
(ISO 10705-2)
Somatic
coliphages
(EPA Method
1602)
F-specific
coliphages
(EPA Method
1602)
NoVGI
(RT- qPCR)
NoV Gil
(RT-qPCR)
Somatic
coliphages (EPA
Method 1602)
F-specific
coliphages (EPA
Method 1602)
NoV GI (qRT-
PCR)
Influent (raw)
NR
Mean 2.9 x 106
(± 2 x 106) PFU
permL
Mean 1.8 x 105
PFU per 100 mL
Mean 4.3 x 104
PFU per mL
Mean 3. 2 x 105
copies per 100
mL
Mean 2.3 x 105
copies per 100
mL
Range 9.1 x 104
to 4.5 x 105 PFU
per 100 mL
Range 3.1 x 105
to 2.2 x 107 PFU
per 100 mL
Range 230 c to
2.2 x 103 GC per
L
Effluent
NR
Mean 2.5 x 104(±2.9 x
104) PFU per mL
Mean 102 PFU per 100
mL
Mean 102 PFU per 100
mL
Mean 7.1 x 103 copies
per 100 mL
Mean 5.2 x 103 copies
per 100 mL
Range 3 to 63 PFU per
100 mL
Range <1 to 37 PFU
per 100 mL
Range<2.7tol.8cGC
perL
Log
reduction
(logio)
1.04 ±0.32
(0.61-1.86)
Mean 2. 16 ±
0.42
2.4
2.4
~2b
~2b
NR
NR
NR
Treatment
No design/operational
information provided to
understand secondary
treatment or performance.
Activated sludge
secondary treatment and
chlorination;
No design/operational
information provided to
understand secondary
treatment or performance;
no information if this is
free chlorine, combined
chlorine, ammonia
concentration.
Non-disinfected activated
sludge secondary
treatment;
No design/operational
information provided to
understand secondary
treatment or performance.
Conventional secondary
treatment with chlorine
disinfection. No
design/operational
information provided to
understand secondary
treatment or performance.
Location Reference
Italy Carducci et
al., 2009
Singapore Aw and Gin,
2010
Ohio, United Francy et al.
States 2011
115
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Organism
Somatic
coliphages (EPA
Method 1602)
F-specific
coliphages (EPA
Method 1602)
NoV GI (qRT-
PCR)
Somatic
coliphages (EPA
Method 1602)
F-specific
coliphages (EPA
Method 1602)
NoV GI (qRT-
PCR)
Somatic
coliphages
(EPA Method
1602)
F-specific
coliphages
(EPA Method
1602)
NoV (qPCR,
qRT-PCR)
Somatic
coliphages
(EPA Method
1602)
F-specific
coliphages
(EPA Method
1602)
Influent (raw)
Range 2.4 x 104
to 3.0 x 106PFU
per 100 mL
Range 3.8 x 104
to 2.1 x 105PFU
per 100 mL
Range <560 to
<8.3 x 103 GC
perL
Range 2.6 x 104
to 2.2 x 106PFU
per 100 mL
Range 3.8 x 104
to 1.9 x 106PFU
per 100 mL
Range 49 c to 1.8
x 104GCperL
Range 2.6 x 104
to 2.2 x 106PFU
per 100 mL
Range 3.8 x 104
to 1.9 x 106PFU
per 100 mL
Range 49 c to 1.8
x 104GCperL
Range 2.4 x 104
to 3.0 x 106PFU
per 100 mL
Range l.lx 104
to 2.1 x 105PFU
per 100 mL
Effluent
AlKlPFUper lOOmL
AlKlPFUperlOOmL
Range <36 to <67 GC
perL
Range <1 to 1.1 x 103
PFU per 100 mL
Range <1 to 19 PFU
per 100 mL
Range <1.5 to <130 GC
perL
Range <1 to 8 PFU per
100 mL
Range <1 to 2 PFU per
100 mL
Range<1.5to<53 GC
perL
<1 PFU per 100 mL
<1 PFU per 100 mL
Log
reduction
(logio)
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
Treatment Location Reference
Conventional tertiary
treatment (sand filtration)
with UV disinfection. No
design/operational
information provided to
understand secondary
treatment or performance.
Membrane bioreactor
(Kubota® Membrane
Systems by Ovivo MBR)
with UV disinfection. No
design/operational
information provided to
understand secondary
treatment or performance.
Two medium-sized Ohio, United Francy et al,
Kubota™ (Osaka, Japan) States 2012
system microfiltration
membrane bioreactors
with UV disinfection. No
design/operational
information provided to
understand secondary
treatment or performance.
One small-sized
conventional secondary
plant with tertiary
treatment and UV
disinfection. No
design/operational
information provided to
116
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Organism
NoV (qPCR,
qRT-PCR)
Somatic
coliphages
(EPA Method
1602)
F-specific
coliphages
(EPA Method
1602)
NoV (qPCR,
qRT-PCR)
F-specific RNA
coliphages
(double agar
layer)
Somatic
coliphages
(double agar
layer)
NoV
(RT-qPCR)
NoVGI
(RT-qPCR)
NoV Gil
(RT-qPCR)
F-specific
coliphages
(ISO 10705-1)
Somatic
coliphages (ISO
10705-2)
Influent (raw)
Range <5.6 x 102
to <8.3 x 103 GC
perL
Range 9.1 x 104
to 4.5 x 105 PFU
per 100 mL
Range 3.1 x 105
to 2.2 x 107 PFU
per 100 mL
Range 2.3 x I02c
to 1.5 x 103 GC
perL
NR
NR
NR
Mean 3. 32 ±0.64
(range 2.05-4.76)
logio density
Mean 3. 55 ±0.89
(range 1.81-5.34)
logic density
Mean 5.54 ±0.51
(range 3.87-6.82)
logio density
Mean 7. 10 ±
0.40-logio PFU
perL
Effluent
Range <36 to <67 GC
perL
Range 3 to 63 PFU per
100 mL
Range <1 to 37 PFU
per 100 mL
Range<1.8cto<2.7
GCperL
Means 5 x 103 to 5 x
105 PFU perL
Means 9 x I04to 1.67 x
105 PFU perL
Means ND to 2.7 x 105
genomes per L
Mean 2.53 ±0.57
(range 1.26-4.06) logio
density
Mean 2.63 ±0.71
(range 1.51-4.08) logio
density
Mean 3.41 ±0.77
(range 2.00-5.84) logio
density
Mean4.99±0.53-logio
PFU per L
Log
reduction
(logio)
NR
NR
NR
NR
NR
NR
NR
0.80 ±0.49
0.92 ±0.76
2.13 ±0.76
2.11 ±0.40
Treatment
understand secondary
treatment or performance.
One medium-sized
conventional secondary
plant with chlorine
disinfection. No
design/operational
information provided to
understand secondary
treatment or performance.
Secondary treated
wastewater (2 WWTPs)d
Secondary treated
wastewater (5 WWTPs)
Non-disinfected activated
sludge secondary
treatment;
No design/operational
information provided to
understand secondary
treatment or performance.
Rainy days: Activated
sludge, chlorination. No
design/operational
Location Reference
Australia Keegan et al.,
2012
Ireland Flannery et
al., 2012
Italy Carducci and
Verani, 2013
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Organism
NoV
(RT-qPCR)
Somatic
coliphages (ISO
10705-2)
NoV
(RT-qPCR)
F-specific RNA
coliphages (ISO
10705-1)
F-specific RNA
coliphage (RT-
qPCR)
NoV Gil (RT-
qPCR)
F-specific RNA
coliphages (ISO
10705-1)
NoV GI (qPCR)
NoV Gil (qPCR)
Somatic
coliphages (ISO
10705-2.2)
F-specific
coliphages (ISO
10705-1)
Influent (raw)
Mean 5. 83 ±
2.87-logio GC
perL
Mean 7.22 ±
0.40-logio PFU
perL
Mean 5. 92 ±
2.86-logio GC
perL
Mean5.26-logio
PFU per 100 mL
Mean5.11-logio
GC per 100 mL
Mean3.87-logio
GC per 100 mL
Range 5.9 x 104
to 7.5 x 105 PFU
perL
Range 2.9 x 103
to 1.4 x 106GC
perL
Range 6.0 x 104
to 1.4 x 107 GC
perL
Mean 4. 9 x 103
PFU per mL
Mean 3. 6 x 103
PFU per mL
Effluent
Mean5.80±2.75-logio
GCperL
Mean 5.00 ±0.56-logio
PFU perL
Mean 6.04 ±2.94-logio
GCperL
Mean 2.96-logio PFU
per 100 mL
Mean4.57-logioGC
per 100 mL
Mean3.61-logioGC
per 100 mL
Range 1.5 x 103to2.5 x
104 PFU perL
Range 5.6 x 103 to 9.2
x 104 GCperL
Range ND to 2.0 x 105
GCperL
Range <0. 01 to 2. 5 x
104 PFU per mL
Range <0.01 to 1.8 x
104PFUpermL
Log
reduction
(logio)
0.02 ±0.61
2.21 ±0.46
-0.11 ±0.34
NR
NR
NR
NR
NR
NR
Range of
Mean
Reduction
0.6 ±0.6 to
5.2 ±1.2
Range of
Mean
Reduction
0.7 ±0.6 to
5. 3 ±1.3
Treatment Location
information provided to
understand secondary
treatment or performance.
Dry days: Activated
sludge, chlorination. No
design/operational
information provided to
understand secondary
treatment or performance.
Screening and grit United States
removal, phosphate
removal through ferric
sulfate, secondary
treatment, UV
disinfection. No
design/operational
information provided to
understand secondary
treatment or performance.
Primary sedimentation. Fjellfoten,
Influent data includes Norway
samples taken when
treatment was interrupted.
No design/operational
information provided to
understand secondary
treatment or performance.
Raw municipal post- Kuopio,
screen wastewater influent Finland
and effluent from three
pilot-scale sand filters
with different filter
material and grain size
designs and one with a
separate phosphorous
removal unit. No
design/operational
Reference
Flannery et al.
2013
Grendahl-
Rosado et al.
2014
Kauppinen et
al. 2014
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Organism
NoV GI (RT-
PCR)
NoV Gil (RT-
PCR)
Influent (raw)
Mean 80 GC per
mL
Mean 2.3 x 104
GC per mL
Effluent
Range <0. 5 to 1.5 x 103
GC per mL
Range <0.4 to 1.1 x 104
GC per mL
Log
reduction
(logio)
Range of
Mean
Reduction
0.6 ±0.6 to
2.2 ±0.8
Range of
Mean
Reduction
0.5 ±0.2 to
4.0 ±0.6
Treatment Location Reference
information provided to
understand treatment or
performance.
Density units are as reported in the cited reference.
NR = not reported (in some cases effluent or influent densities were not reported, but logic reduction was reported); Stm WG49 = Salmonella
enterica serovar Typhimurium WG49 (host); ND = Not detected; GC = genome copies
a PFU reported in graphical format for influent, digester, high rate pond, algal settling pond, and maturation pond
b Estimated from figure
0 Reported as estimated value extrapolated at the low end. PCR threshold cycles were past the upper limit of the standard curve.
d Information from Table 3.6 and 3.7 in Keegan et al. (2012). The Bolivar WWTP consists of primary treatment (screening, grit removal,
sedimentation), activated sludge, lagoon (16 day retention), chlorination (or dissolved air flotation and chlorination); collected undisinfected
samples from the lagoon influent (thus secondary effluent), lagoon effluent, and post dissolved air flotation prior to chlorination. Two Melbourne
WWTPs were tested: MW1 - primary settling, ASP (not defined); MW2 - anaerobic digestion (not defined), ASP (not defined), and lagoon
polishing (26 days). This study was done for a very specific focus related to water recycling.
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