Waterborne Viruses and F-Specific Coliphages in Mixed-Use Watersheds: Microbial Associations, Host Specificities, and Affinities with Environmental/Land Use Factors

Occurrence of Hepatitis A Virus in Water Matrices: A Systematic Review and Meta-Analysis

Hepatitis A is a common form of viral hepatitis. It is usually transmitted through the ingestion of contaminated food and water. This systematic review was carried out to summarise the overall prevalence of Hepatitis A virus (HAV) in different water matrices: untreated and treated wastewater, surface water, groundwater, drinking water, and others (e.g., irrigation water and floodwater). The literature search was performed in four databases: PubMed, Web of Science, Global Index Medicus, and Excerpta Medica Database. Heterogeneity (I2) was assessed using the χ2 test on the Cochran Q statistic and H parameters. A total of 200 prevalence data from 144 articles were included in this meta-analysis. The overall prevalence of HAV in water matrices was 16.7% (95% CI: 13.4−20.3). The prevalence for individual matrix was as follows: 31.4% (95% CI: 23.0−40.4) untreated wastewater, 18.0% (95% CI: 9.5−28.2) treated wastewater, 15.0% (95% CI: 10.1−20.5) surface water, 2.3% (95% CI: 0.1−6.0) in groundwater, 0.3% (95% CI: 0.0−1.7) in drinking water, and 8.5% (95% CI: 3.1−15.6) in other matrices. The prevalence was higher in low-income economies (29.0%). Africa and Eastern Mediterranean were the regions with higher HAV prevalence values. This study showed a high heterogeneity (I2 > 75%) with a significant publication bias (p value Egger test < 0.001). The results of this review suggest that water matrices could be an important route of HAV transmission even in industrialized countries, despite the lower prevalence compared to less industrialized countries, and the availability of advanced water management systems. More effective water/wastewater treatment strategies are needed in developing countries to limit the environmental circulation of HAV.

Coliphages as viral indicators of sanitary significance for drinking water

Coliphages are virus that infect coliform bacteria and are used in aquatic systems for risk assessment for human enteric viruses. This mini-review appraises the types and sources of coliphage and their fate and behavior in source waters and engineered drinking water treatment systems. Somatic (cell wall infection) and F+ (male specific) coliphages are abundant in drinking water sources and are used as indicators of fecal contamination. Coliphage abundances do not consistently correlate to human enteric virus abundance, but they suitably reflect the risks of exposure to human enteric viruses. Coliphages have highly variable surface characteristics with respect to morphology, size, charge, isoelectric point, and hydrophobicity which together interact to govern partitioning and removal characteristics during water treatment. The groups somatic and F+ coliphages are valuable for investigating the virus elimination during water treatment steps and as indicators for viral water quality assessment. Strain level analyses (e.g., Qβ or GA-like) provide more information about specific sources of viral pollution but are impractical for routine monitoring. Consistent links between rapid online monitoring tools (e.g., turbidity, particle counters, and flow cytometry) and phages in drinking water have yet to be established but are recommended as a future area of research activity. This could enable the real-time monitoring of virus and improve the process understanding during transient operational events. Exciting future prospects for the use of coliphages in aquatic microbiology are also discussed based on current scientific evidence and practical needs.

Human Land-Use Impacts Viral Diversity and Abundance in a New Zealand River

Although water-borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land use on viral diversity and evolution in water systems such as rivers. We used metatranscriptomic sequencing to compare the diversity and abundance of viruses at sampling sites along a single river in New Zealand that differed in human land-use impacts, ranging from pristine to urban. From this, we identified 504 putative virus species, of which 97 per cent were novel. Many of the novel viruses were highly divergent and likely included a new subfamily within the Parvoviridae. We identified at least sixty-three virus species that may infect vertebrates—most likely fish and water birds—from the Astroviridae, Birnaviridae, Parvoviridae, and Picornaviridae. No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher diversity (327 virus species) than the farming (n = 150) and pristine sites (n = 119), and more viruses were shared between the urban and farming sites (n = 76) than between the pristine and farming or urban sites (n = 24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants, and fungi. We also identified viruses linked to agriculture and human impact at the river sampling sites in farming and urban areas that were not present at the native forest sites. Although based on a small sample size, our study suggests that human land use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanisation on water systems.

Human Fecal Contamination Corresponds to Changes in the Freshwater Bacterial Communities of a Large River Basin

Microbial water quality is generally monitored by culturable fecal indicator bacteria (FIB), which are intended to signal human health risk due to fecal pollution. However, FIB have limited utility in most urbanized watersheds as they do not discriminate among fecal pollution sources, tend to make up a small fraction of the total microbial community, and do not inform on pollution impacts on the native ecosystem. To move beyond these limitations, we assessed entire bacterial communities and investigated how bacterial diversity relates to traditional ecological and human health-relevant water quality indicators throughout the Milwaukee River Basin. Samples were collected from 16 sites on 5 days during the summer, including both wet and dry weather events, and were processed by 16S rRNA gene amplicon sequencing. Historical water quality at each sampling location, as opposed to upstream land use, was associated significantly with bacterial community alpha diversity. Source partitioning the sequence data was important for determining water quality relationships. Sewage-associated bacterial sequences were detected in all samples, and the relative abundance of sewage sequences was strongly associated with the human Bacteroides fecal marker. From this relationship, we developed a preliminary threshold for human sewage pollution when using bacterial community sequence data. Certain abundant freshwater bacterial sequences were also associated with human fecal pollution, suggesting their possible utility in water quality monitoring. This study sheds light on how bacterial community analysis can be used to supplement current water quality monitoring techniques to better understand interactions between ecological water quality and human health indicators. IMPORTANCE Surface waters in highly developed mixed-use watersheds are frequently impacted by a wide variety of pollutants, leading to a range of impairments that must be monitored and remediated. With advancing technologies, microbial community sequencing may soon become a feasible method for routine evaluation of the ecological quality and human health risk of a water body. In this study, we partnered with a local citizen science organization to evaluate the utility of microbial community sequencing for identifying pollution sources and ecological impairments in a large mixed-use watershed. We show that changes in microbial community diversity and composition are indicative of both long-term ecological impairments and short-term fecal pollution impacts. By source partitioning the sequence data, we also estimate a threshold target for human sewage pollution, which may be useful as a starting point for future development of sequencing-based water quality monitoring techniques.

Integrated analyses of fecal indicator bacteria, microbial source tracking markers, and pathogens for Southeast Asian beach water quality assessment

The degradation of coastal water quality from fecal pollution poses a health risk to visitors at recreational beaches. Fecal indicator bacteria (FIB) are a proxy for fecal pollution; however the accuracy of their representation of fecal pollution health risks at recreational beaches impacted by non-point sources is disputed due to non-human derivation. This study aimed to investigate the relationship between FIB and a range of culturable and molecular-based microbial source tracking (MST) markers and pathogenic bacteria, and physicochemical parameters and rainfall. Forty-two marine water samples were collected from seven sampling stations during six events at two tourist beaches in Thailand. Both beaches were contaminated with fecal pollution as evident from the GenBac3 marker at 88%-100% detection and up to 8.71 log₁₀ copies/100 mL. The human-specific MST marker human polyomaviruses JC and BK (HPyVs) at up to 4.33 log₁₀ copies/100 mL with 92%-94% positive detection indicated that human sewage was likely the main contamination source. CrAssphage showed lower frequencies and concentrations; its correlations with the FIB group (i.e., total coliforms, fecal coliforms, and enterococci) and GenBac3 diminished its use as a human-specific MST marker for coastal water. Human-specific culturable AIM06 and SR14 bacteriophages and general fecal indicator coliphages also showed less sensitivity than the human-specific molecular assays. The applicability of the GenBac3 endpoint PCR assay as a lower-cost prescreening step prior to the GenBac3 qPCR assay was supported by its 100% positive predictive value, but its limited negative predictive values required subsequent qPCR confirmation. Human enteric adenovirus and Vibrio cholerae were not found in any of the samples. The HPyVs related to Vibrio parahaemolyticus, Vibrio vulnificus, and 5-d rainfall records, all of which were more prevalent and concentrated during the wet season. More monitoring is therefore recommended during wet periods. Temporal differences but no spatial differences were observed, suggesting the need for a sentinel site at each beach for routine monitoring. The exceedance of FIB water quality standards did not indicate increased prevalence or concentrations of the HPyVs or Vibrio spp. pathogen group, so the utility of FIB as an indicator of health risks at tropical beaches maybe challenged. Accurate assessment of fecal pollution by incorporating MST markers could lead to developing a more effective water quality monitoring plan to better protect human health risks in tropical recreational beaches.

Torque teno viruses in health and disease

Torque teno viruses (TTVs) are small, ubiquitous, viruses with a highly diverse, single-stranded, negative sense DNA genome and wide host range. They are detected at high rates in both healthy and diseased individuals and are considered a significant part of the mammalian virome. Similar to human TTVs, swine TTVs (TTSuVs) are epidemiologically linked to several coinfections including porcine circovirus types 2 and 3 and the porcine reproductive and respiratory disease syndrome virus. Experimental infection of gnotobiotic pigs with TTSuVs resulted in lesions in multiple organs and exacerbation of coinfections, making TTSuVs the only members of the Anelloviridae family with experimental evidence for pathogenicity. However, due to the lack of reliable cell culture and animal models, mechanistic studies on viral immunity and pathogenesis are limited. The objective of this review is to summarize the current status of knowledge regarding the biology, detection, pathogenesis and public health significance of TTSuVs, while identifying gaps in knowledge which limit the field.

Prevalence, levels and seasonal variations of human enteric viruses in six major rivers in Alberta, Canada

The prevalence and seasonal variation of 7 viruses in 6 major rivers in Alberta were assessed using a combination of qPCR, cell culture and integrated cell culture with qPCR (ICC-qPCR). Water samples were collected monthly from rivers at different sites upstream and downstream of major urban centers. Seven viruses including rotavirus, adenovirus, astrovirus, norovirus, sapovirus, JC virus and enterovirus, were detected in at least one of the water samples at each site using qPCR. Rotavirus was most common with concentration ranging from 2.3 to 4.5 log₁₀ genomic equivalent (GE) copies/L. Norovirus, sapovirus, astrovirus, adenoviruses and JC virus peaked during the winter (November to March). Viruses were most prevalent at the Bow River sampling site downstream of the City of Calgary, followed by the North Saskatchewan River site downstream of the City of Edmonton and the Red Deer River site downstream of the City of Red Deer. The detection rates and quantity of viruses had significant difference in the sampling sites between upstream and downstream of major urban centers (p < 0.001). 14% of the samples tested positive using viral culture indicating the presence of infectious viruses in river. Sequencing analysis identified human rotavirus in 75% of the samples collected from downstream versus 37% of the samples collected from upstream sites (p < 0.02). Multivariate binary regression showed that human activity in watersheds is a significant determinant of viruses in Alberta's Rivers. The discharge from wastewater treatment plants may be the possible sources of viral contamination. Seasonal coincidence of acute viral gastroenteritis outbreaks and monthly peak occurrence of enteric viruses in river water implies potential impact of waterborne viruses on human health.

Detection of coliphages and human adenoviruses in a subtropical estuarine lake

Fecal indicator bacteria (FIB) have been used to assess fecal contamination in recreational water. However, enteric viruses have been shown to be more persistent in the environment and resistant to wastewater treatment than bacteria. Recently, U.S Environmental Protection Agency has proposed the use of coliphages as viral indicators to better protect against viral waterborne outbreaks. This study aimed to detect and determine correlation between coliphages (F-specific and somatic), fecal indicator bacteria (enterococci and fecal coliforms), and human enteric viruses (human adenovirus) in a subtropical brackish estuarine lake. Water samples were collected from 9 estuarine recreation sites on Lake Pontchartrain in southeast Louisiana. Water samples (n = 222, collected weekly) were analyzed for coliphages and fecal indicator bacteria using culture-based methods and large volume water samples (n = 54, collected monthly) were analyzed for human adenovirus using quantitative PCR. Somatic coliphage and F-specific coliphage were found in 93.7 and 65.2% of samples with geometric mean concentrations of 30 and 3 plaque forming units (PFU) per 100 mL, respectively. Enterococci, fecal coliforms, and adenovirus were found in all samples with geometric mean concentrations of 27 most probable number (MPN), 77 MPN, and 3.0 × 10⁴ gene copies per 100 mL, respectively. Watersheds in suburban areas exhibited significantly higher concentrations of coliphages and fecal indicator bacteria, indicating potential fecal contamination from septic systems. There was no significant correlation (p > 0.05) observed between the presence of adenoviruses and fecal indicator bacteria and coliphages. The presence of human adenovirus in Lake Pontchartrain poses a significant public health problem for both recreational use and seafood harvesting as it increases exposure risks. This study demonstrated the lack of relationship between fecal indicators and human viral pathogen in Lake Pontchartrain supporting an alternative microbial surveillance system such as direct pathogen detection.

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach

This study applied a 16S rRNA gene metabarcoding approach to characterize bacterial community compositional and functional attributes for surface water samples collected within, primarily, agriculturally dominated watersheds in Ontario and Québec, Canada. Compositional heterogeneity was best explained by stream order, season, and watercourse discharge. Generally, community diversity was higher at agriculturally dominated lower order streams, compared to larger stream order systems such as small to large rivers. However, during times of lower relative water flow and cumulative 2-day rainfall, modestly higher relative diversity was found in the larger watercourses. Bacterial community assemblages were more sensitive to environmental/land use changes in the smaller watercourses, relative to small-to-large river systems, where the proximity of the sampled water column to bacteria reservoirs in the sediments and adjacent terrestrial environment was greater. Stream discharge was the environmental variable most significantly correlated (all positive) with bacterial functional groups, such as C/N cycling and plant pathogens. Comparison of the community structural similarity via network analyses helped to discriminate sources of bacteria in freshwater derived from, for example, wastewater treatment plant effluent and intensity and type of agricultural land uses (e.g., intensive swine production vs. dairy dominated cash/livestock cropping systems). When using metabarcoding approaches, bacterial community composition and coexisting pattern rather than individual taxonomic lineages, were better indicators of environmental/land use conditions (e.g., upstream land use) and bacterial sources in watershed settings. Overall, monitoring changes and differences in aquatic microbial communities at regional and local watershed scales has promise for enhancing environmental footprinting and for better understanding nutrient cycling and ecological function of aquatic systems impacted by a multitude of stressors and land uses.

Tracking enteric viruses in green vegetables from central Argentina: potential association with viral contamination of irrigation waters

Consumption of green vegetable products is commonly viewed as a potential risk factor for infection with enteric viruses. The link between vegetable crops and fecally contaminated irrigation water establishes an environmental scenario that can result in a risk to human health. The aim of this work was to analyze the enteric viral quality in leafy green vegetables from Córdoba (Argentina) and its potential association with viral contamination of irrigation waters. During July-December 2012, vegetables were collected from peri-urban green farms (n = 19) and its corresponding urban river irrigation waters (n = 12). Also, urban sewage samples (n = 6) were collected to analyze the viral variants circulating in the community. Viruses were eluted and concentrated by polyethylene glycol precipitation and then were subject to Reverse Transcription Polymerase Chain Reaction to assess the genome presence of norovirus, rotavirus and human astrovirus. The concentrates were also inoculated in HEp-2 (Human Epidermoid carcinoma strain #2) cells to monitor the occurrence of infective enterovirus. The frequency of detection of the viral groups in sewage, irrigation water and crops was: norovirus 100%, 67% and 58%, rotavirus 100%, 75% and 5%, astrovirus 83%, 75% and 32% and infective enterovirus 50%, 33% and 79%, respectively. A similar profile in sewage, irrigation water and green vegetables was observed for norovirus genogroups (I and II) distribution as well as for rotavirus and astrovirus G-types. These results provide the first data for Argentina pointing out that green leafy vegetables are contaminated with a broad range of enteric viruses and that the irrigation water would be a source of contamination. The presence of viral genomes and infective particles in food that in general suffer minimal treatment before consumption underlines that green crops can act as potential sources of enteric virus transmission. Public intervention in the use of the river waters as irrigation source is needed.

Quantification of human adenovirus and norovirus in river water in the north-east of France

Human adenoviruses (HAdVs) are a major cause of infection and have been proposed as viral indicators of water quality. Human noroviruses (NoV) are the main cause of viral acute gastroenteritis. Quantitative data on the environmental prevalence of both viruses are needed. The genomes of HAdVs enteric adenovirus type 41 (HAdV41) and noroviruses of genogroups I and II (NoV GGI and GGII) were quantified over a 6-month period in a river located in north-eastern France. The samples were collected downstream from the discharge of a wastewater treatment plant. The viruses were concentrated using a glass wool method and the viral genomes were quantified using digital droplet PCR (ddPCR). All river water samples (15/15) were positive for the genomes of HAdVs, HAdV41, NoV GGI and NoV GGII. Concentrations of HAdVs, HAdV41 and NoV GII genomes were similar and HAdV41 represented ~ 80% of HAdVs. Infectious HAdVs were quantified in these samples using an integrated cell culture-quantitative PCR method (ICC-qPCR); they were detected in 93% (14/15) and quantified in 53% (8/15) of the samples. Thus, infectious HAdVs represented 0.3 to 12.2% of total HAdV particles detected by ddPCR. Infectious HAdV41 particles were found in 73% (11/15) of the samples. This common presence of pathogenic enteric viruses underlines the impact of wastewater discharge on quality of surface waters and may constitute a threat for human health. The relative abundance of genome of HAdV41 underlines the need for studies focusing on the specific detection of its infectious forms along water cycle.

Hiding in Plain Sight? It's Time to Investigate Other Possible Transmission Routes for Hepatitis E Virus (HEV) in Developed Countries

Historically in developed countries, reported hepatitis E cases were typically travellers returning from countries where hepatitis E virus (HEV) is endemic, but now there are increasing numbers of non-travel-related ("autochthonous") cases being reported. Data for HEV in New Zealand remain limited and the transmission routes unproven. We critically reviewed the scientific evidence supporting HEV transmission routes in other developed countries to inform how people in New Zealand may be exposed to this virus. A substantial body of indirect evidence shows domesticated pigs are a source of zoonotic human HEV infection, but there is an information bias towards this established reservoir. The increasing range of animals in which HEV has been detected makes it important to consider other possible animal reservoirs of HEV genotypes that can or could infect humans. Foodborne transmission of HEV from swine and deer products has been proven, and a large body of indirect evidence (e.g. food surveys, epidemiological studies and phylogenetic analyses) support pig products as vehicles of HEV infection. Scarce data from other foods suggest we are neglecting other potential sources of foodborne HEV infection. Moreover, other transmission routes are scarcely investigated in developed countries; the role of infected food handlers, person-to-person transmission via the faecal-oral route, and waterborne transmission from recreational contact or drinking untreated or inadequately treated water. People have become symptomatic after receiving transfusions of HEV-contaminated blood, but it is unclear how important this is in the overall hepatitis E disease burden. There is need for broader research efforts to support establishing risk-based controls.

Virus Type-Specific Removal in a Full-Scale Membrane Bioreactor Treatment Process

We investigated removal of noroviruses, sapoviruses, and rotaviruses in a full-scale membrane bioreactor (MBR) plant by monitoring virus concentrations in wastewater samples during two gastroenteritis seasons and evaluating the adsorption of viruses to mixed liquor suspended solids (MLSS). Sapoviruses and rotaviruses were detected in 25% of MBR effluent samples with log reduction values of 3- and 2-logs in geometric mean concentrations, respectively, while noroviruses were detected in only 6% of the samples. We found that norovirus and sapovirus concentrations in the solid phase of mixed liquor samples were significantly higher than in the liquid phase (P < 0.01, t test), while the concentration of rotaviruses was similar in both phases. The efficiency of adsorption of the rotavirus G1P[8] strain to MLSS was significantly less than norovirus GI.1 and GII.4 and sapovirus GI.2 strains (P < 0.01, t test). Differences in the adsorption of viruses to MLSS may cause virus type-specific removal during the MBR treatment process as shown by this study.

Enteric Viruses in Surface Waters from Argentina: Molecular and Viable-Virus Detection

Water resources contaminated with wastewater are an important source for the dissemination of enteric viruses with an impact on the health of the population. The aim of the study was to assess the viral contamination of freshwater from a dam in Argentina by using infectious enterovirus detection, viral RNA amplification, and a genetic characterization of five enteric viruses associated with diarrhea and hepatitis. Enterovirus infectivity (iEV) was evaluated by cell culture and direct immunofluorescence. The detection of the viral genome of rotavirus (RV), human astrovirus (HAstV), norovirus (NoV), hepatitis A virus (HAV), and hepatitis E virus (HEV) was performed by reverse transcriptase PCR (RT-PCR). A total of 48 water samples from 4 monitoring points on the body of the dam from January to December 2012 and 66 water samples from 3 tourist beaches on the edge of the dam from October 2013 to October 2015 were collected monthly. During the first period, the overall viral frequency detection was 52.1% for group A RV, 50% for HAstV, 60.4% for NoV, 22.9% for HAV, 2.1% for HEV, and 64.6% for iEV. The overall frequency detection for the second sampling was 18.2% for RV and HAstV, 31.8% for NoV, 7.57% for HEV, and 66.7% for iEV. There was no detection of HAV during this period. The genotypes and genogroups detected through the study correlated with the most common genomic variants associated with human gastrointestinal and hepatitis illnesses. The results obtained could alert the health systems and environmental sanitation to make decisions for viral control and prevention in our environment.IMPORTANCE The study shows the impact of anthropic contamination of one of the most important tourist water resources in Argentina. This course of recreational water would be a favorable scenario for infection, as well as a reservoir for the enteric viruses, creating a risk for the population exposed to these waters. The results obtained could alert the health systems and environmental sanitation to make decisions for the control and prevention of viral diseases in this environment.

Identification of Factors Affecting Fecal Pollution in Beaver Lake Reservoir

Standard methods for the evaluation of recreational water quality rely on generic bacterial indicators such as . However, does not provide enough information to determine fecal source or public health risk. The stsudy objective was to determine factors influencing the presence of and host-specific markers (HSM) from upstream to downstream in Beaver Lake Reservoir (BLR). From February 2014 to September 2015, 420 base flow and rain event samples were collected from seven sites-two sites from streams (White River [WR] and War Eagle Creek) draining into BLR and five sites from within BLR. Each sample was analyzed for and by quantitative polymerase chain reaction for HSM related to human, bovine, and poultry. The data indicate that overall levels of were significantly greater in the WR and significantly lower at the most downstream sampling location in BLR. is more likely present during spring (adjusted odds ratio [aOR] = 1.86), at the WR sampling site (aOR = 3.39), or during a rain event (aOR = 2.73). Moreover, the HSM HumM2 is more likely present (aOR = 1.99) when is present. These same factors were associated with concentrations >126 most probable number 100 mL (aOR = 2.76-12.48), except the poultry marker CL was more likely associated (aOR = 3.81) than HumM2. This study revealed that both seasonal and locational factors are important variables for fecal pollution in BLR. Moreover, these same factors may apply to fecal pollution in manmade reservoirs within similar types of watersheds across the United States, as well as internationally.