Real-time PCR quantification of human adenoviruses in urban rivers indicates genome prevalence but low infectivity

Recombinant adenovirus as a model to evaluate the efficiency of free chlorine disinfection in filtered water samples

BACKGROUND

In Brazil, ordinance no. 2,914/2011 of the Ministry of Health requires the absence of total coliforms and Escherichia coli (E. coli) in treated water. However it is essential that water treatment is effective against all pathogens. Disinfection in Water Treatment Plants (WTP) is commonly performed with chlorine.

METHODS

The recombinant adenovirus (rAdV), which expresses green fluorescent protein (GFP) when cultivated in HEK 293A cells, was chosen as a model to evaluate the efficiency of chlorine for human adenovirus (HAdV) inactivation in filtered water samples from two WTPs: Lagoa do Peri (pH 6.9) and Morro dos Quadros (pH 6.5). Buffered demand free (BDF) water (pH 6.9 and 8.0) was used as control. The samples were previously submitted to physicochemical characterization, and bacteriological analysis. Two free chlorine concentrations and two temperatures were assayed for all samples (0.2 mg/L, 0.5 mg/L, and 15°C, and 20°C). Fluorescence microscopy (FM) was used to check viral infectivity in vitro and qPCR as a molecular method to determine viral genome copies. Real treated water samples from the WTP (at the output of WTP and the distribution network) were also evaluated for total coliforms, E. coli and HAdV.

RESULTS

The time required to inactivate 4log₁₀ of rAdV was less than 1 min, when analyzed by FM, except for BDF pH 8.0 (up to 2.5 min for 4log₁₀). The pH had a significant influence on the efficiency of disinfection. The qPCR assay was not able to provide information regarding rAdV inactivation. The data were modeled (Chick-Watson), and the observed Ct values were comparable with the values reported in the literature and smaller than the values recommended by the EPA. In the treated water samples, HAdV was detected in the distribution network of the WTP Morro dos Quadros (2.75 × 10(3) PFU/L).

CONCLUSION

The Chick-Watson model proved to have adjusted well to the experimental conditions used, and it was possible to prove that the adenoviruses were rapidly inactivated in the surface water treated with chlorine and that the recombinant adenovirus expressing GFP is a good model for this evaluation.

Applicability of integrated cell culture quantitative PCR (ICC-qPCR) for the detection of infectious adenovirus type 2 in UV disinfection studies

Practical difficulties of the traditional adenovirus infectivity assay such as intensive labor requirements and longer turnaround period limit the direct use of adenovirus as a testing microorganism for systematic, comprehensive disinfection studies. In this study, we attempted to validate the applicability of integrated cell culture quantitative PCR (ICC-qPCR) as an alternative to the traditional cell culture method with human adenovirus type 2 (HAdV2) in a low-pressure UV disinfection study and to further optimize the procedures of ICC-qPCR for 24-well plate format. The relatively high stability of the hexon gene of HAdV2 was observed after exposure to UV radiation, resulting in a maximum gene copy reduction of 0.5 log10 at 280 mJ cm(-2). Two-day post-inoculation incubation period and a maximum spiking level of 10(5) MPN mL(-1) were selected as optimum conditions of ICC-qPCR with the tested HAdV2. An approximate 1:1 correlation of virus quantities by the traditional and ICC-qPCR cell culture based methods suggested that ICC-qPCR is a satisfactory alternative for practical application in HAdV2 disinfection studies. ICC-qPCR results, coupled with a first-order kinetic model (i.e., the inactivation rate constant of 0.0232 cm(2) mJ(-1)), showed that an UV dose of 172 mJ cm(-2) achieved a 4-log inactivation credit for HAdV2. This estimate is comparable to other studies with HAdV2 and other adenovirus respiratory types. The newly optimized ICC-qPCR shows much promise for further study on its applicability of other slow replicating viruses in disinfection studies.

Physical lysis only (PLO) methods suitable as rapid sample pretreatment for qPCR assay

Quantitative PCR (qPCR) enables rapid and sensitive gene quantification and is widely used in genomics, such as biological, medical, environmental, and food sciences. However, sample pretreatment requires the use of conventional DNA extraction kits which are time-consuming and labor intensive. In this study, we investigated four physical lysis only (PLO) methods which are rapid and could serve as alternatives to conventional DNA extraction kits. These PLO methods are bead mill, heating, sonication, and freeze-thaw. Using ethidium bromide-based assay, their performance was evaluated and compared. The effects of cell debris and its removal were also investigated. Bead mill method without cell debris removal appeared to yield the best qPCR results among the four PLO methods. In addition, bead mill method also performed better than conventional DNA extraction kits. It is probably due to the substantial loss of DNA material during the extensive purification of the conventional DNA extraction kits. The bead mill method has been demonstrated to successfully quantify 10(2) to 10(7) copies of the PAH-RHDα gene of Pseudomonas putida.

Detection of pathogenic viruses in sewage provided early warnings of hepatitis A virus and norovirus outbreaks

Most persons infected with enterically transmitted viruses shed large amounts of virus in feces for days or weeks, both before and after onset of symptoms. Therefore, viruses causing gastroenteritis may be detected in wastewater, even if only a few persons are infected. In this study, the presence of eight pathogenic viruses (norovirus, astrovirus, rotavirus, adenovirus, Aichi virus, parechovirus, hepatitis A virus [HAV], and hepatitis E virus) was investigated in sewage to explore whether their identification could be used as an early warning of outbreaks. Samples of the untreated sewage were collected in proportion to flow at Ryaverket, Gothenburg, Sweden. Daily samples collected during every second week between January and May 2013 were pooled and analyzed for detection of viruses by concentration through adsorption to milk proteins and PCR. The largest amount of noroviruses was detected in sewage 2 to 3 weeks before most patients were diagnosed with this infection in Gothenburg. The other viruses were detected at lower levels. HAV was detected between weeks 5 and 13, and partial sequencing of the structural VP1protein identified three different strains. Two strains were involved in an ongoing outbreak in Scandinavia and were also identified in samples from patients with acute hepatitis A in Gothenburg during spring of 2013. The third strain was unique and was not detected in any patient sample. The method used may thus be a tool to detect incipient outbreaks of these viruses and provide early warning before the causative pathogens have been recognized in health care.

Human and bovine viruses in the Milwaukee River watershed: hydrologically relevant representation and relations with environmental variables

To examine the occurrence, hydrologic variability, and seasonal variability of human and bovine viruses in surface water, three stream locations were monitored in the Milwaukee River watershed in Wisconsin, USA, from February 2007 through June 2008. Monitoring sites included an urban subwatershed, a rural subwatershed, and the Milwaukee River at the mouth. To collect samples that characterize variability throughout changing hydrologic periods, a process control system was developed for unattended, large-volume (56-2800 L) filtration over extended durations. This system provided flow-weighted mean concentrations during runoff and extended (24-h) low-flow periods. Human viruses and bovine viruses were detected by real-time qPCR in 49% and 41% of samples (n=63), respectively. All human viruses analyzed were detected at least once including adenovirus (40% of samples), GI norovirus (10%), enterovirus (8%), rotavirus (6%), GII norovirus (1.6%) and hepatitis A virus (1.6%). Three of seven bovine viruses analyzed were detected including bovine polyomavirus (32%), bovine rotavirus (19%), and bovine viral diarrhea virus type 1 (5%). Human viruses were present in 63% of runoff samples resulting from precipitation and snowmelt, and 20% of low-flow samples. Maximum human virus concentrations exceeded 300 genomic copies/L. Bovine viruses were present in 46% of runoff samples resulting from precipitation and snowmelt and 14% of low-flow samples. The maximum bovine virus concentration was 11 genomic copies/L. Statistical modeling indicated that stream flow, precipitation, and season explained the variability of human viruses in the watershed, and hydrologic condition (runoff event or low-flow) and season explained the variability of the sum of human and bovine viruses; however, no model was identified that could explain the variability of bovine viruses alone. Understanding the factors that affect virus fate and transport in rivers will aid watershed management for minimizing human exposure and disease transmission.

Surveillance of enteric viruses and coliphages in a tropical urban catchment

An assessment of the occurrence and concentration of enteric viruses and coliphages was carried out in highly urbanized catchment waters in the tropical city-state of Singapore. Target enteric viruses in this study were noroviruses, adenoviruses, astroviruses and rotaviruses. In total, 65 water samples were collected from canals and the reservoir of the Marina catchment on a monthly basis over a period of a year. Quantitative PCR (qPCR) and single agar layer plaque assay (SAL) were used to enumerate target enteric viruses and coliphages in water samples, respectively. The most prevalent pathogen were noroviruses, detected in 37 samples (57%), particularly norovirus genogroup II (48%), with a mean concentration of 3.7 × 10(2) gene copies per liter. Rotavirus was the second most prevalent virus (40%) with a mean concentration of 2.5 × 10(2) GC/L. The mean concentrations of somatic and male-specific coliphages were 2.2 × 10(2) and 1.1 × 10(2) PFU/100 ml, respectively. The occurrence and concentration of each target virus and the ratio of somatic to male-specific coliphages varied at different sampling sites in the catchment. For sampling sites with higher frequency of occurrence and concentration of viruses, the ratio of somatic to male-specific coliphages was generally much lower than other sampling sites with lower incidences of enteric viruses. Overall, higher statistical correlation was observed between target enteric viruses than between enteric viruses and coliphages. However, male-specific coliphages were positively correlated with norovirus concentrations. A multi-level integrated surveillance system, which comprises the monitoring of bacterial indicators, coliphages and selected enteric viruses, could help to meet recreational and surface water quality criteria in a complex urbanized catchment.

Adenovirus-associated health risks for recreational activities in a multi-use coastal watershed based on site-specific quantitative microbial risk assessment

We used site-specific quantitative microbial risk assessment (QMRA) to assess the probability of adenovirus illness for three groups of swimmers: adults with primary contact, children with primary contact, and secondary contact regardless of age. Human enteroviruses and adenoviruses were monitored by qPCR in a multi-use watershed and Adenovirus type 40/41 was detected in 11% of 73 samples, ranging from 147 to 4117 genomes per liter. Enterovirus was detected only once (32 genomes per liter). Seven of eight virus detections occurred when E. coli concentrations were below the single sample maximum water quality criterion for contact recreation, and five of eight virus detections occurred when fecal coliforms were below the corresponding criterion. We employed dose-harmonization to convert viral genome measurements to TCID50 values needed for dose-response curves. The three scenarios considered different amounts of water ingestion and Monte Carlo simulation was used to account for the variability associated with the doses. The mean illness risk in children based on adenovirus measurements obtained over 11 months was estimated to be 3.5%, which is below the 3.6% risk considered tolerable by the current United States EPA recreational criteria for gastrointestinal illnesses (GI). The mean risks of GI illness for adults and secondary contact were 1.9% and 1.0%, respectively. These risks changed appreciably when different distributions were fitted to the data as determined by Monte Carlo simulations. In general, risk was at a maximum for the log-logistic distribution and lowest for the hockey stick distribution in all three selected scenarios. Also, under default assumptions, the risk was lowered considerably when assuming that only a small proportion of Adenovirus 40/41 (3%) was as infectious as Adenovirus type 4, compared to the assumption that all genomes were Adenovirus 4. In conclusion, site-specific QMRA on water-borne adenoviruses in this watershed provided a similar level of protection against public health risks as would be obtained by enumeration of fecal indicator bacteria under the new U.S. EPA guidelines.

An improved infectivity assay combining cell culture with real-time PCR for rapid quantification of human adenoviruses 41 and semi-quantification of human adenovirus in sewage

A protocol for the rapid detection and semi-quantification of human enteric adenovirus based on the quantification of viral mRNA during cell culture infectivity assay was developed. Infectivity assays for adenovirus incorporated cell culture and reverse transcription real-time PCR, where viral mRNA detection was used to monitor the progress of adenovirus infection (CC/mRNA qPCR). The cell line used was G293. This specific infectivity assay was calibrated against different initial concentrations of human adenovirus 41. In addition, the expression of the host's housekeeping (HK) gene, GAPDH, served as internal control for the mRNA assays for quality assurance of the mRNA extraction and reverse transcription steps. The concentrations of infectious human adenoviruses in different sewage samples were estimated semi-quantitatively using the CC/mRNA qPCR assay and calibration obtained for adenovirus 41. A linear relationship between concentrations of viral mRNA (hexon gene) and infectious units was observed between 10(7) to 10(1) infectious units per assay (R(2) = 0.97) in samples analyzed 3-5 days post infection. The expressions of host cell GAPDH gene were not significantly affected by infections with different concentrations of human adenovirus 41, and between virus positive and negative cell cultures (p > 0.1). The estimated concentrations of human adenoviruses in sewage samples ranged between 10(2) to 10(3) mRNA-IU/L. Most of the viruses detected in sewage samples were from human adenovirus species F. The CC/mRNA qPCR assay can be used for quantifying infectious human adenovirus 41, estimating the levels of human adenoviruses in sewage samples, and applied to other sample settings. The CC/mRNA qPCR protocol described here represents an improvement in the detection of human enteric adenoviruses by reducing incubation time (5 days); whereas the conventional cell culture method requires longer incubation periods (10-20 days). More importantly, this protocol can be used to more rapidly and semi-quantitatively estimate the levels of infectious human adenoviruses in environmental samples.

Evaluation and molecular characterization of human adenovirus in drinking water supplies: viral integrity and viability assays

Background

Human adenoviruses (HAdVs) are the second-leading cause of childhood gastroenteritis worldwide. This virus is commonly found in environmental waters and is very resistant to water disinfection and environmental stressors, especially UV light inactivation. Molecular techniques, such as PCR-based methods (Polymerase Chain Reaction), are commonly used to detect and identify viral contamination in water, although PCR alone does not allow the discrimination between infectious and non-infectious viral particles. A combination of cell culture and PCR has allowed detection of infectious viruses that grow slowly or fail to produce cytopathic effects (CPE) in cell culture. This study aimed to assess the integrity and viability of human adenovirus (HAdV) in environmental water and evaluate circulating strains by molecular characterization in three sites of the water supply in Florianópolis, Santa Catarina Island, Brazil: Peri Lagoon water, spring source water, and water from the public water supply system.

Methods

Water samples were collected, concentrated and HAdV quantified by real-time PCR. Viral integrity was evaluated by enzymatic assay (DNase I) and infectivity by plaque assay (PA) and integrated cell culture using transcribed mRNA (ICC-RT-qPCR). Samples containing particles of infectious HAdV were selected for sequencing and molecular characterization.

Results

The analyzed sites contained 83, 66 and 58% undamaged HAdV particles (defined as those in which the genetic material is protected by the viral capsid) at Peri Lagoon, spring source water and public supply system water, respectively. Of these, 66% of the particles (by PA) and 75% (by ICC-RT-qPCR) HAdV were shown to be infectious, due to being undamaged in Peri Lagoon, 33% (by PA) and 58% (by ICC-RT-qPCR) in spring source water and 8% (by PA) and 25% (by ICC-RT-qPCR) in the public water supply system. ICC-RT-qPCR, a very sensitive and rapid technique, was able to detect as low as 1 × 10² HAdV genome copies per milliliter of infectious viral particles in the environmental water samples. The molecular characterization studies indicated that HAdV-2 was the prevalent serotype.

Conclusions

These results indicate a lack of proper public health measures. We suggest that HAdV can be efficiently used as a marker of environmental and drinking water contamination and ICC-RT-qPCR demonstrated greater sensitivity and speed of detection of infectious viral particles compared to PA.

Quantification of human and animal viruses to differentiate the origin of the fecal contamination present in environmental samples

Many different viruses are excreted by humans and animals and are frequently detected in fecal contaminated waters causing public health concerns. Classical bacterial indicator such as E. coli and enterococci could fail to predict the risk for waterborne pathogens such as viruses. Moreover, the presence and levels of bacterial indicators do not always correlate with the presence and concentration of viruses, especially when these indicators are present in low concentrations. Our research group has proposed new viral indicators and methodologies for determining the presence of fecal pollution in environmental samples as well as for tracing the origin of this fecal contamination (microbial source tracking). In this paper, we examine to what extent have these indicators been applied by the scientific community. Recently, quantitative assays for quantification of poultry and ovine viruses have also been described. Overall, quantification by qPCR of human adenoviruses and human polyomavirus JC, porcine adenoviruses, bovine polyomaviruses, chicken/turkey parvoviruses, and ovine polyomaviruses is suggested as a toolbox for the identification of human, porcine, bovine, poultry, and ovine fecal pollution in environmental samples.

Identification of human and animal fecal contamination after rainfall in the Han River, Korea

We investigated the effect of rainfall on the levels and sources of microbial contamination in the Han River, Korea. Thirty-four samples were collected at two sampling sites located upstream and downstream in the river from July 2010 to February 2011. Various fecal indicator microorganisms, including total coliform, fecal coliform, Escherichia coli, Enterococcus spp., somatic and male-specific (F+) coliphage, and four major enteric viruses were analyzed. Rainfall was positively correlated with the levels of fecal coliform and norovirus at both sampling sites. Additionally, rainfall was positively correlated with the levels of total coliform, E. coli, Enterococcus spp., and F+ coliphage at the upstream site. To identify the source of fecal contamination, microbial source tracking (MST) was conducted using both male-specific (F+) RNA coliphage and the Enterococcus faecium esp gene as previously described. Our results clearly indicated that the majority of fecal contamination at the downstream Han River site was from a human source. At the upstream sampling site, contamination from human fecal matter was very limited; however, fecal contamination from non-point animal sources increased following rainfall. In conclusion, our data suggest that rainfall significantly affects the level and source of fecal contamination in the Han River, Korea.

Quantitative detection and characterization of human adenoviruses in the Buffalo River in the Eastern Cape Province of South Africa

Buffalo River is an important water resource in the Eastern Cape Province of South Africa. Over a 1-year period (August 2010-July 2011), we assessed the prevalence of human adenoviruses (HAdVs) at a total of 6 sites on the river and three dams along its course. HAdVs were detected by real-time quantitative PCR in about 35 % of the samples with concentrations ranging from 1.2 × 10(1) genome copies (GC)/l to 4.71 × 10(3) GC/l. HAdVs were detected at 5 of the 6 sampling sites with the detection rate ranging from 8.3 % at Rooikrantz Dam to 92 % at Parkside. The HAdV concentrations across the sampling sites were as follows: Parkside (3.25 × 10(2)-4.71 × 10(3) GC/); King William's Town (1.02 × 10(2)-4.56 × 10(3) GC/l); and Eluxolzweni (1.17 × 10(2)-3.97 × 10(2) GC/l). Significantly (P < 0.05) higher concentrations were detected at the non-dam sites compared to the dam sites. A very low mean concentration of 1.86 × 10(1) HAdV GC/l was observed at Bridle Drift Dam. While HAdVs were detected only once at Rooikrantz Dam (1.74 × 10(1) GC/l), no HAdV was detected at Maden Dam. Epidemiologically important serotypes, Ad40/41, constituted 83.3 %, while Ad21 made up 16.7 % of the all HAdVs detected and were characterized by qualitative PCR. The Buffalo River presents a public health risk heightened by the presence of Ad 40/41 and Ad21. Our results make imperative the need for assessing water sources for viral contamination in the interest of public health. This work is a significant contribution to the molecular epidemiology of adenoviruses and to the best of our knowledge this is the first report on detection of enteric virus from surface waters in the Eastern Cape.

Assessment of the incidence of enteric adenovirus species and serotypes in surface waters in the eastern cape province of South Africa: Tyume River as a case study

TaqMan real-time PCR was used for the detection and quantitation of adenoviruses in Tyume River water samples over a 12-month period. A total of 72 samples were analysed, and 22 samples were positive for adenovirus. Of the positive samples, 18 were collected from downstream sampling points. Among the downstream sampling points, adenovirus detection rate increased with distance downstream, being 28%, 33%, and 39% for Alice, Drayini, and Manqulweni, respectively. The Alice sampling site had the highest concentrations of adenovirus ranging between 6.54 × 103 genome copies/L and 8.49 × 104 genome copies/L. The observed trend could have been expected considering the level of anthropogenic activities in areas along the lower stretch of Tyume River, with the major one being the effluent of treated and semi treated sewage from wastewater treatment facilities. Adenovirus detection was sporadic at most sampling sites. Multiplex conventional PCR was used for the detection of clinically important adenovirus species B, C, and F and their serotypes. Species C and F adenoviruses were detected in 77% and 18% of the samples, respectively. Most adenovirus positive samples were obtained from areas of increased population densities. The presence of adenoviruses may confirm the risk of its transmission to the human population.

New approaches for enhanced detection of enteroviruses from Hawaiian environmental waters

Health risks associated with sewage-contaminated recreational waters are of important public health concern. Reliable water monitoring systems are therefore crucial. Current recreational water quality criteria rely predominantly on the enumeration of bacterial indicators, while potentially dangerous viral pathogens often remain undetected. Human enteric viruses have been proposed as alternative indicators; however, their detection is often hindered by low viral concentrations present in the environment. Reported here are novel and effective laboratory protocols for viral concentration and highly sensitive and optimized RT-PCR for the efficient detection of enteroviruses, an important enteric virus subset, in Hawaiian environmental waters. Eighteen published enterovirus primer pairs were comparatively evaluated for detection sensitivity. The primer set exhibiting the lowest detection limit under optimized conditions, EQ-1/EQ-2, was validated in a field survey of 22 recreational bodies of water located around the island of Oahu, Hawaii. Eleven sites tested positive for enterovirus, indicating fecal contamination at these locations. As an additional means of viral concentration, shellfish were collected from 9 sample sites and subjected to dissection, RNA extraction, and subsequent RT-PCR. Shellfish tissue from 6 of 9 sites tested positive for enterovirus. The techniques implemented here are valuable resources to aid accurate reflection of microbial contamination in Hawaii’s environmental waters.

The impact of combined sewage overflows on the viral contamination of receiving waters

The contribution of combined sewer overflows (CSO) to the viral contamination of receiving waters was determined. Adenovirus concentrations were determined using the Primary Liver Carcinoma (PLC/PRF/5) cell line and confirmed by Polymerase Chain Reaction (PCR). Norovirus concentration was determined using the Most Probable Number (MPN) and Reverse Transcription-Polymerase Chain Reaction (RT-PCR). Seventy-five water samples were collected during dry weather and 50 samples were collected during wet weather. CSO events significantly increased the concentration of culturable viruses, adenoviruses, and noroviruses in the receiving waters (P < 0.01). During dry weather, 56% of samples were positive for total virus cytopathic effects (CPE), adenoviruses were detected in 41% of the positive cell cultures, and noroviruses in 6% of the concentrates by direct RT-PCR. During wet weather, 100% of the samples were positive by CPE, 84% for adenoviruses, and 40% in the concentrates for norovirus. Our results demonstrate that CSOs can contribute significant viral loading to receiving waters.

Terrestrial sources homogenize bacterial water quality during rainfall in two urbanized watersheds in Santa Barbara, CA

Microbiological contamination from runoff is a human health concern in urbanized coastal environments, but the contamination sources are often unknown. This study quantified fecal indicator bacteria and compared the distributions of human-specific genetic markers and bacterial community composition during dry and wet weather in urban creeks draining two neighboring watersheds in Santa Barbara, CA. In a prior study conducted during exclusively dry weather, the creeks were contaminated with human waste as indicated by elevated numbers of the human-specific Bacteroidales marker HF183 (Sercu et al. in Environ Sci Technol 43:293-298, 2009). During the storm, fecal indicator bacterial numbers and loads increased orders of magnitude above dry weather conditions. Moreover, bacterial community composition drastically changed during rainfall and differed from dry weather flow by (1) increased bacterial diversity, (2) reduced spatial heterogeneity within and between watersheds, and (3) clone library sequences more related to terrestrial than freshwater taxa. Finally, the spatial patterns of human-associated genetic markers (HF183 and Methanobrevibacter smithii nifH gene) changed during wet weather, and the contribution of surface soils to M. smithii nifH gene detection was suspected. The increased fecal indicator bacteria numbers during wet weather were likely associated with terrestrial sources, instead of human waste sources that dominated during dry weather flow.

Methods to detect infectious human enteric viruses in environmental water samples

Currently, a wide range of analytical methods is available for virus detection in environmental water samples. Molecular methods such as polymerase chain reaction (PCR) and quantitative real time PCR (qPCR) have the highest sensitivity and specificity to investigate virus contamination in water, so they are the most commonly used in environmental virology. Despite great sensitivity of PCR, the main limitation is the lack of the correlation between the detected viral genome and viral infectivity, which limits conclusions regarding the significance for public health. To provide information about the infectivity of the detected viruses, cultivation on animal cell culture is the gold standard. However, cell culture infectivity assays are laborious, time consuming and costly. Also, not all viruses are able to produce cytopathic effect and viruses such as human noroviruses have no available cell line for propagation. In this brief review, we present a summary and critical evaluation of different approaches that have been recently proposed to overcome limitations of the traditional cell culture assay and PCR assay such as integrated cell culture-PCR, detection of genome integrity, detection of capsid integrity, and measurement of oxidative damages on viral capsid protein. Techniques for rapid detection of infectious viruses such as fluorescence microscopy and automated flow cytometry have also been suggested to assess virus infectivity in water samples.

Swimmer risk of gastrointestinal illness from exposure to tropical coastal waters impacted by terrestrial dry-weather runoff

This study used molecular methods to measure concentrations of four enteric viruses (adenovirus, enterovirus, norovirus GI, and norovirus GII) and fecal source tracking markers (human, ruminant, and pig Bacteroidales) in land-based runoff from 22 tropical streams on O'ahu, Hawai'i. Each stream was sampled twice in the morning and afternoon during dry weather. Viruses and human Bacteroidales were widespread in the streams. Watershed septic tank densities were positively associated with higher occurrence of human Bacteroidales and norovirus. There were no associations between occurrence of viruses and fecal indicator concentrations. Virus concentrations and previously reported culturable Salmonella and Campylobacter were used as inputs to a quantitative microbial risk assessment (QMRA) model to estimate the risk of acquiring gastrointestinal (GI) illness from swimming in tropical marine waters adjacent to discharging streams. Monte Carlo methods were used to incorporate uncertainties in the dilution of stream discharge with seawater, swimmer ingestion volumes, pathogen concentrations, and dose-response parameters into the model. Median GI illness risk to swimmers from exposure to coastal waters adjacent to the 22 streams ranged from 0 to 21/1000. GI illness risks from viral exposures were generally orders of magnitude greater than bacterial exposures. Swimming adjacent to streams positive for norovirus or adenovirus resulted in the highest risks. The median risk adjacent to each stream was positively, significantly correlated to the concentration of Clostridium perfringens in the stream. Although a number of important assumptions were made to complete the QMRA, results suggest land-based runoff in the tropics as a potential source of GI illness risk, with pathogens coming from both human and nonhuman nonpoint sources including septic tanks.

Detection of poliovirus by ICC/qPCR in concentrated water samples has greater sensitivity and is less costly using BGM cells in suspension as compared to monolayers

The integrated cell culture quantitative reverse transcriptase PCR (ICC/qRT-PCR) method is used in our lab to detect enteroviruses in environmental waters. Typically we utilize monolayers of 3 cell lines; buffalo green monkey kidney (BGM), human colonic carcinoma (CACO-2) and African rhesus monkey kidney (MA104) with the intent of providing one or more permissive hosts to a wide range of enteroviruses. In this study the BGM cell line was used to compare poliovirus infectivity in conventional monolayer cultures to BGM cells in suspensions. Propagated virus was subsequently amplified by qRT-PCR. Our PCR data showed lower cycle threshold (Ct) values in the suspensions which corresponded to a higher rate of infectivity than that observed in the monolayers. The difference in Ct values was determined statistically significant by One-way ANOVA (0.000). Infecting BGM cells in suspensions required less hands-on time, less chance of contamination and was more cost effective than utilizing the conventional monolayer technique.

A new set of PCR assays for the identification of multiple human adenovirus species in environmental samples

AIMS

To assess human adenovirus (HAdV) diversity in environmental samples based on sequence comparisons of hexon gene fragments amplified using newly designed HAdV-specific polymerase chain reaction (PCR) assays.

METHODS AND RESULTS

Six PCR primer sets were designed based on 56 aligned hexon sequences from NCBI GenBank to amplify different hexon gene sections (241-349 bp) of the six HAdV species. The amplified hexon genes from wastewater samples were cloned, sequenced, and compared with those in publicly accessible databases (i.e. NCBI GenBank) by using the Blast program. A total of 46 analysed positive clones were affiliated to five HAdV serotypes, i.e. 1, 2, 12, 31 and 41. Similarities between the cloned and database hexon sequences ranged from 95.9 to 100% (with an average of 98.1 +/- 1.0%).

CONCLUSION

The designed primers showed higher amplification efficiencies when compared with the existing assays. Using the new assays, HAdV species A, C, and F (serotypes 1, 2, 12, 31 and 41 in particular) were identified in the studied municipal wastewater.

SIGNIFICANCE AND IMPACT OF THE STUDY

The six PCR primer sets developed in this study can be used to efficiently amplify hexon gene fragments in HAdV. Multiple HAdV serotypes identified in the municipal wastewater provide new information about HAdV diversity in environmental samples.

Relationship between F-specific RNA phage genogroups, faecal pollution indicators and human adenoviruses in river water

Recent studies have shown the increasing interest of F-specific RNA phage genotyping to identify major sources of faecal contamination in waters. This study, conducted in a river located in an urbanized watershed with recognized anthropogenic influences, was aimed at evaluating the relevance of direct phage genotyping by real-time RT-PCR. One hundred percent of positive results were obtained with a 5 mL aliquot of river water (n=31). Phage distribution was modified after cultivation, since the ratio of the two most abundant genogroups (II and I) reached 1.51 log(10) by direct RT-PCR-based method versus 0.30 log(10) after cultivation (n=8). For the first time, positive correlations between the concentrations of genogroup II, bacterial indicators and human adenoviruses were observed, which may indicate a human faecal pollution. No correlation between genogroups II and I has been revealed. The concentration of genogroup I was only correlated with water turbidity, suggesting an animal pollution coming from upstream after rainfall events. Among the microbiological parameters studied, only genogroup II/genogroup I ratio shows variations occurring in the major sources of faecal pollution.

Eukaryotic viruses in wastewater samples from the United States

Human fecal matter contains a large number of viruses, and current bacterial indicators used for monitoring water quality do not correlate with the presence of pathogenic viruses. Adenoviruses and enteroviruses have often been used to identify fecal pollution in the environment; however, other viruses shed in fecal matter may more accurately detect fecal pollution. The purpose of this study was to develop a baseline understanding of the types of viruses found in raw sewage. PCR was used to detect adenoviruses, enteroviruses, hepatitis B viruses, herpesviruses, morbilliviruses, noroviruses, papillomaviruses, picobirnaviruses, reoviruses, and rotaviruses in raw sewage collected throughout the United States. Adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples and 25% and 33% of final effluent samples, respectively. Enteroviruses and noroviruses were detected in 75% and 58% of raw sewage samples, respectively, and both viral groups were found in 8% of final effluent samples. This study showed that adenoviruses, enteroviruses, noroviruses, and picobirnaviruses are widespread in raw sewage. Since adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples, they are potential markers of fecal contamination. Additionally, this research uncovered previously unknown sequence diversity in human picobirnaviruses. This baseline understanding of viruses in raw sewage will enable educated decisions to be made regarding the use of different viruses in water quality assessments.

UV disinfection of adenoviruses: molecular indications of DNA damage efficiency

Adenovirus is a focus of the water treatment community because of its resistance to standard, monochromatic low-pressure (LP) UV irradiation. Recent research has shown that polychromatic, medium-pressure (MP) UV sources are more effective than LP UV for disinfection of adenovirus when viral inactivation is measured using cell culture infectivity assays; however, UV-induced DNA damage may be repaired during cell culture infectivity assays, and this confounds interpretation of these results. Objectives of this work were to study adenoviral response to both LP and MP UV using (i) standard cell culture infectivity assays and (ii) a PCR assay to directly assess damage to the adenoviral genome without introducing the virus into cell culture. LP and MP UV dose response curves were determined for (i) log inactivation of the virus in cell culture and (ii) UV-induced lesions per kilobase of viral DNA as measured by the PCR assay. Results show that LP and MP UV are equally effective at damaging the genome; MP UV is more effective at inactivating adenovirus in cell culture. This work suggests that the higher disinfection efficacy of MP UV cannot be attributed to a difference in DNA damage induction. These results enhance our understanding of the fundamental mechanisms of UV disinfection of viruses-especially double-stranded DNA viruses that infect humans--and improve the ability of the water treatment community to protect public health.

A real-time polymerase chain reaction assay for quantitative detection of the human-specific enterococci surface protein marker in sewage and environmental waters

A real-time polymerase chain reaction (PCR) assay using SYBR Green I dye was developed to quantify the Enterococcus faecium enterococci surface protein (esp) marker in sewage (n = 16) and environmental waters (n = 16). The concentration of culturable enterococci in raw sewage samples ranged between 1.3 x 10(5) and 5.6 x 10(5) colony-forming units (cfu) per 100 ml. The real-time PCR detected 9.8 x 10(3)-3.8 x 10(4) gene copies of the esp marker per 100 ml of sewage. However, the concentration of culturable enterococci and the esp marker in secondary effluent was two orders of magnitude lower than raw sewage. Surface water samples were collected from a non-sewered catchment after storm events and the real-time PCR was applied to quantify the esp marker. Of the 16 samples tested, 6 (38%) were PCR-positive and the concentration of the esp marker ranged between 1.1 x 10(2) and 5.3 x 10(2) gene copies per 100 ml of water samples. The newly developed real-time PCR method was successfully used to quantify the esp marker in samples collected from sewage and environmental waters. The presence of the esp marker in water samples immediately after storm events not only indicated human faecal pollution but also provided evidence of the degree of human faecal pollution. To our knowledge, this is the first study that reports the use of a real-time PCR assay to quantify the esp marker in sewage and surface waters. Such study would provide valuable information for managers for the improved management of water quality.

New tools for the study and direct surveillance of viral pathogens in water

Half a century ago scientists attempted the detection of poliovirus in water. Since then other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection. However, most viral outbreaks are restricted to norovirus and hepatitis A virus, making them the main targets in water. The inclusion of virus analysis in regulatory standards for viruses in water samples must overcome several shortcomings such as the technical difficulties and high costs of virus monitoring, the lack of harmonised and standardised assays and the challenge posed by the ever-changing nature of viruses. However, new tools are nowadays available for the study and direct surveillance of viral pathogens in water that may contribute to fulfil these requirements.

Occurrence of human adenoviruses at two recreational beaches of the great lakes

Human adenoviruses (HAdVs) have been related to several waterborne diseases such as acute gastroenteritis, conjunctivitis, and respiratory illness, and it has been shown that an important human exposure pathway is through recreational waters. However, HAdV occurrence at recreational freshwater beaches has not been previously investigated. In this study, a total of 58 water samples were collected from two recreational beaches on Lake Michigan (i.e., Silver Beach and Washington Park Beach) during the summer of 2004. Occurrences of HAdVs in these lake samples were determined using two hexon-based real-time PCR assays (one for monitoring all 51 serotypes of HAdVs and another for specifically detecting F species HAdVs, i.e., serotypes 40 and 41) and compared to an integrated cell culture (ICC) PCR method. The real-time PCR results showed that 8 of 30 Silver Beach samples and 6 of 28 Washington Park Beach samples contained HAdVs, and F species HAdVs were detected in three of these positive samples. The concentrations of HAdVs ranged from (1.7 +/- 0.7) x 10(1) to (3.4 +/- 0.8) x 10(2) and from (7 +/- 2) x 10(0) to (3.8 +/- 0.3) x 10(3) virus particles/liter for Silver Beach and Washington Park Beach, respectively. F species HAdVs were detected at levels ranging from (4.8 +/- 0.8) x 10(1) to (4.6 +/- 1.5) x 10(2) virus particles/liter. Approximately 60% of the ICC-PCR analyses agreed with the real-time PCR results. This study revealed the occurrence of HAdVs at Lake Michigan recreational beaches. Given the potential health risks, further assessment regarding sources, virus transport, and survival is needed to improve the safety of the region.

Detection of murine norovirus 1 by using plaque assay, transfection assay, and real-time reverse transcription-PCR before and after heat exposure

The correlation between the detection of murine norovirus 1 RNA by real-time reverse transcription-PCR and the infectivity by plaque assay before and after heat exposure (80 degrees C) was examined. No correlation was found in the current study. Moreover, heat inactivation had a much stronger detrimental effect on virus infectivity than on the integrity of the viral genome.

Molecular detection of hepatitis A virus in urban sewage in Rio de Janeiro, Brazil

AIMS

A one-year survey was conducted to examine hepatitis A virus (HAV) prevalence, distribution of genotypes and their relationship to bacterial indicators in raw and treated sewage samples.

METHODS AND RESULTS

Fifty sewage samples (raw = 25 and treated = 25) were collected twice monthly from one sewage treatment plant in Rio de Janeiro. Virus concentration was performed by adsorption to an electronegative membrane followed by ultrafiltration. Viral RNA was detected by nested reverse transcriptase-polymerase chain reaction (RT-PCR) and real-time PCR and positive products were directly sequenced. Total and faecal coliform concentrations were also determined. By nested RT-PCR, HAV RNA was detected in 16/50 (32%) and eight (16%) of them were found in treated sewage samples. By real-time PCR, HAV RNA was detected in 46/50 (92%) samples and 24 were from treated sewage. Phylogenetic analyses classified nine isolates (56%) as subgenotype IA and seven (44%) as IB.

CONCLUSIONS

Real-time PCR was more sensitive than nested RT-PCR; the presence of subgenotypes IA and IB was described and bacterial indicators cannot be used to predict HAV presence in sewage.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results demonstrated that HAV still remains in the environment after sewage treatment and could play an important role in maintaining the endemicity of HAV infection.

Chapter 9 The Detection of Waterborne Viruses

Viruses in water are usually present in concentrations too low for detection by direct analysis. Virological investigation of water samples is always a multi-stage process involving concentration of viruses present followed by an appropriate detection procedure. There are several approaches to detection of viruses. Part or all of the concentrate may be inoculated into cell cultures to detect infectious cytopathogenic virus, and if this is done in a quantitative fashion the virus can be enumerated, the count being reported as plaque-forming units, the tissue culture infectious dose, or most probable number units. The virus may be isolated and identified from the cell cultures. Viruses that multiply without producing an identifiable cytopathic effect in culture may sometimes be detected by immunoperoxidase or immunofluorescence staining. The concentrate may also be analyzed by molecular biological procedures (usually polymerase chain reaction (PCR) or real-time-PCR). The problem then is that such techniques do not usually detect the infectious virus, and novel approaches have been made recently to meet this challenge.

Fecal source tracking, the indicator paradigm, and managing water quality

Fecal source tracking is used because standard methods of measuring fecal contamination in water by enumerating fecal indicator bacteria (FIB) do not identify the sources of the contamination. This paper presents a critical review of source tracking with emphasis on the extent to which methods have been tested (especially in comparison with other methods and/or with blind samples), when methods are applicable, their shortcomings, and their usefulness in predicting public health risk or pathogen occurrence. In addition, the paper discusses the broader question of whether fecal source tracking and fecal indicator monitoring is the best approach to regulate water quality and protect human health. Many fecal source-tracking methods have only been tested against sewage or fecal samples or isolates in laboratory studies (proof of concept testing) and/or applied in field studies where the "real" answer is not known, so their comparative performance and accuracy cannot be assessed. For source tracking to be quantitative, stability of ratios between host-specific markers in the environment must be established. In addition, research is needed on the correlation between host-specific markers and pathogens, and survival of markers after waste treatments. As a result of the exclusive emphasis on FIB in legislation, monitoring has concentrated on FIB and lost sight of pathogens. A more rational approach to regulating water quality would start with available epidemiological data to identify pathogens of concern in a particular water body, and then use targeted pathogen monitoring coupled with targeted fecal source tracking to control them. Baseline monitoring of indicators would become just one tool among many.

Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution

Advances in microbial source tracking (MST) have largely been driven by the need to comply with water quality standards based on traditional indicator bacteria. Recently, a number of culture-independent, and library-independent methods based on polymerase chain reaction (PCR) have been gaining popularity among source trackers. However, only a limited number of these methods have been successfully used in field applications, primarily due to the fact that many of them are still being developed. In this critical outlook, we examine different viewpoints associated with the practical use of MST to identify critical research gaps, propose a priority-based timeline to address them, and outline emerging technologies that will likely impact the future of source tracking. We propose that it is necessary to consider each of these aspects in order to advance towards a unifying framework in source identification, so that fecal pollution monitoring can be reliably used for comprehensive environmental microbial monitoring, to develop risk assessment models, and to implement and validate adequate management practices.

Microbial source tracking in a small southern California urban watershed indicates wild animals and growth as the source of fecal bacteria

Three independent microbial source tracking (MST) methods were applied to a small urban subwatershed in Orange County, California. Fifty-seven water samples collected over summer 2002 were analyzed for human adenovirus and enterovirus. Enterococci and E. coli were isolated for antibiotic resistance analysis (ARA) and for PCR identification of human- and animal-specific toxin genes, respectively. All water samples were PCR negative for human enteroviruses and E. coli human-specific toxin gene. E. coli toxin markers revealed the presence of toxin genes specific to bird, rabbit, and cow. Enterococci ARA results supported this conclusion and indicated that fecal bacteria from bird and wild animal feces as well as soil were the predominant source found in the watershed. An E. coli, isolated from the watershed and inoculated back into the heat-sterilized storm drain water, increased 4 log units within 6 days. Collectively, these results suggest that bird and wild animal feces, soil amendments, and/or fecal coliform growth in the storm drain are the major contributors to the fecal bacterial pollution in downstream areas. However, human adenoviruses were detected on two occasions. Fecal bacterial concentrations were not elevated on these two occasions, suggesting that the elevated levels of fecal indicator bacteria in this small watershed could be unrelated to the source of human adenovirus.

Chapter 1 Overview of Health-Related Water Virology

Viruses are a major cause of waterborne and water-related diseases. Extreme examples include the outbreak of hepatitis A and of viral gastroenteritis in Shanghai caused by shellfish harvested from a sewage-polluted estuary. Viruses predominantly associated with waterborne transmission are members of the group of enteric viruses that primarily infect cells of the gastrointestinal tract, and are excreted in the faeces of infected individuals. The viruses concerned are highly host specific, which implies that their presence in water environments is sound evidence of human faecal pollution. In some cases different strains of a viral species, or even different species of a viral genus, may infect animals. The extent of the host specificity of enteric viruses is such that it is used as a valuable tool to distinguish between faecal pollution of human and animal origin, or to identify the origin of faecal pollution. The hepatitis E virus may be the only meaningful exception to this rule, having strains that seem to infect both humans and certain animals, complying with the definition of a zoonosis. The potential risk of infection associated with respiratory viruses such as influenza and severe acute respiratory syndrome in water environments cannot be ignored. However, there is sound reason to believe that treatment and disinfection processes recommended for the acceptable control of enteric viruses will also accommodate enveloped viruses with a substantial safety margin.

Human adenoviruses in water: occurrence and health implications: a critical review

Adenoviruses are important human pathogens that are responsible for both enteric illnesses and respiratory and eye infections. Recently, these viruses have been found to be prevalent in rivers, coastal waters, swimming pool waters, and drinking water supplies worldwide. United Sates Environmental Protection Agency (USEPA) listed adenovirus as one of nine microorganisms on the Contamination Candidate List for drinking water because their survival characteristic during water treatment is not yet fully understood. Adenoviruses have been found to be significantly more stable than fecal indicator bacteria and other enteric viruses during UV treatment. Adenovirus infection may be caused by consumption of contaminated water or inhalation of aerosolized droplets during water recreation. The goal of this review is to summarize the state of technology for adenovirus detection in natural and drinking waters and the human health risk imposed by this emerging pathogen. The occurrence of these viruses in natural and treated waters is summarized from worldwide reports.

Development of real-time RT-PCR methods for specific detection of F-specific RNA bacteriophage genogroups: application to urban raw wastewater

F-specific RNA bacteriophages have been classified into four genogroups (GI, GII, GIII and GIV). It was suggested that two of these genogroups are more frequent in human excreta (GII and GIII) and the two other (GI and GIV) are specific for animal excreta. Real-time RT-PCR methods using TaqMan MGB probe were developed to detect the four genogroups. Primers and probes of each specific RT-PCR were designed to target all sequenced bacteriophages belonging to one genogroup, without cross-reactivity with other genogroups. These four methods showed detection limits ranging between 0.01 and 10 PFU/mL and PCR efficiencies ranging between 87 and 95%. The newly methods were tested in urban raw wastewater. Genogroups I and II were detected in all samples (n=7); GIII in six samples and GIV was never detected. GI was predominant in one sample, in which the quantity of Cryptosporidium and Giardia was, respectively, three and eight times higher than the mean values. Because GI is mainly observed in animals, it was hypothesized that this increase was due to an animal input. The use of F-specific RNA phage genotyping to estimate the origin of faecal pollution requires appropriate validation. In this context, real-time RT-PCR will undoubtedly be useful.