Three-step isolation method for sensitive detection of enterovirus, rotavirus, hepatitis A virus, and small round structured viruses in water samples

Virus contamination and infectivity in beach environment: Focus on sand and stranded material

To assess the exposure of beachgoers to viruses, a study on seawater, sand, and beach-stranded material was carried out, searching for human viruses, fecal indicator organisms, and total fungi. Moreover, for the first time, the genome persistence and infectivity of two model viruses was studied in laboratory-spiked sand and seawater samples during a one-week experiment. Viral genome was detected in 13.6 % of the environmental samples, but it was not infectious (Human Adenovirus - HAdV, and enterovirus). Norovirus and SARS-CoV-2 were not detected. The most contaminated samples were from sand and close to riverine discharges. In lab-scale experiments, the infectivity of HAdV5 decreased by ~1.5-Log₁₀ in a week, the one of Human Coronavirus-229E disappeared in <3 h in sand. The genome of both viruses persisted throughout the experiment. Our results confirm viral contamination of the beach and suggest HAdV as an index pathogen for beach monitoring and quantitative risk assessment.

The occurrence and control of waterborne viruses in drinking water treatment: A review

As the coronavirus disease 2019 continues to spread globally, its culprit, the severe acute respiratory syndrome coronavirus 2 has been brought under scrutiny. In addition to inhalation transmission, the possible fecal-oral viral transmission via water/wastewater has also been brought under the spotlight, necessitating a timely global review on the current knowledge about waterborne viruses in drinking water treatment system - the very barrier that intercepts waterborne pathogens to terminal water users. In this article we reviewed the occurrence, concentration methods, and control strategies, also, treatment performance on waterborne viruses during drinking water treatment were summarized. Additionally, we emphasized the potential of applying the quantitative microbial risk assessment to guide drinking water treatment to mitigate the viral exposure risks, especially when the unregulated novel viral pathogens are of concern. This review paves road for better control of viruses at drinking water treatment plants to protect public health.

Fecal Source Tracking in A Wastewater Treatment and Reclamation System Using Multiple Waterborne Gastroenteritis Viruses

Gastroenteritis viruses in wastewater reclamation systems can pose a major threat to public health. In this study, multiple gastroenteritis viruses were detected from wastewater to estimate the viral contamination sources in a wastewater treatment and reclamation system installed in a suburb of Xi'an city, China. Reverse transcription plus nested or semi-nested PCR, followed by sequencing and phylogenetic analysis, were used for detection and genotyping of noroviruses and rotaviruses. As a result, 91.7% (22/24) of raw sewage samples, 70.8% (17/24) of the wastewater samples treated by anaerobic/anoxic/oxic (A²O) process and 62.5% (15/24) of lake water samples were positive for at least one of target gastroenteritis viruses while all samples collected from membrane bioreactor effluent after free chlorine disinfection were negative. Sequence analyses of the PCR products revealed that epidemiologically minor strains of norovirus GI (GI/14) and GII (GII/13) were frequently detected in the system. Considering virus concentration in the disinfected MBR effluent which is used as the source of lake water is below the detection limit, these results indicate that artificial lake may be contaminated from sources other than the wastewater reclamation system, which may include aerosols, and there is a possible norovirus infection risk by exposure through reclaimed water usage and by onshore winds transporting aerosols containing norovirus.

Persistent Norovirus Contamination of Groundwater Supplies in Two Waterborne Outbreaks

Microbiological contamination of groundwater supplies causes waterborne outbreaks worldwide. In this study, two waterborne outbreaks related to microbiological contamination of groundwater supplies are described. Analyses of pathogenic human enteric viruses (noroviruses and adenoviruses), fecal bacteria (Campylobacter spp. and Salmonella spp.), and indicator microbes (E. coli, coliform bacteria, intestinal enterococci, Clostridium perfringens, heterotrophic plate count, somatic and F-specific coliphages) were conducted in order to reveal the cause of the outbreaks and to examine the effectiveness of the implemented management measures. Moreover, the long-term persistence of noro- and adenovirus genomes was investigated. Noroviruses were detected in water samples from both outbreaks after the intrusion of wastewater into the drinking water sources. In the outbreak I, the removal efficiency of norovirus genome (3.0 log₁₀ removal) in the sand filter of onsite wastewater treatment system (OWTS) and during the transport through the soil into the groundwater well was lower than the removal efficiencies of E. coli, coliform bacteria, intestinal enterococci, and spores of C. perfringens (6.2, 6.0, > 5.9, and > 4.8 log₁₀ removals, respectively). In the outbreak II, cleaning of massively contaminated groundwater well and drinking water distribution network proved challenging, and noro- and adenovirus genomes were detected up to 3 months (108 days). The long-term persistence study showed that noro- and adenovirus genomes can remain detectable in the contaminated water samples up to 1277 and 1343 days, respectively. This study highlights the transport and survival properties of enteric viruses in the environment explaining their potency to cause waterborne outbreaks.

Evaluation of molecular- and culture-dependent MST markers to detect fecal contamination and indicate viral presence in good quality groundwater

Microbial contamination of groundwater represents a significant health risk to resource users. Culture-dependent Bacteroides phage and molecular-dependent Bacteroidales 16S rRNA assays are employed in microbial source tracking (MST) studies globally, however little is known regarding how these important groups relate to each other in the environment and which is more suitable to indicate the presence of waterborne fecal pollution and human enteric viruses. This study addresses this knowledge gap by examining 64 groundwater samples from sites with varying hydrogeological properties using a MST toolbox containing two bacteriophage groups (phage infecting GB-124 and ARABA-84), and two Bacteroidales 16S rRNA markers (Hf183 and BacR); those were compared to fecal indicator bacteria, somatic coliphage, Bacteroidales 16S rRNA marker AllBac, four human enteric viruses (norovirus GI and II, enterovirus and group A rotavirus) and supplementary hydrogeological/chemical data. Bacteroidales 16S rRNA indicators offered a more sensitive assessment of both human-specific and general fecal contamination than phage indicators, but may overestimate the risk from enteric viral pathogens. Comparison with hydrogeological and land use site characteristics as well as auxiliary microbiological and chemical data proved the plausibility of the MST findings. Sites representing karst aquifers were of significantly worse microbial quality than those with unconsolidated or fissured aquifers, highlighting the vulnerability of these hydrogeological settings.

A comparison of virus concentration methods for molecular detection and characterization of rotavirus in bivalve shellfish species

The objectives of this study were to develop a method for concentrating rotavirus, to assess the detection rate, and to characterize the genotype of naturally occurring rotavirus in bivalve shellfish species; including oysters (Saccostrea forskali), cockles (Anadara nodifera), and mussels (Perna viridis). The results demonstrated that an adsorption-twice elution-extraction method was less-time consuming method of concentrating the spiked rotavirus, yielding high sensitivity of 1.14 genome copies/g of digestive tissues from all three shellfish species, as detected using an RT-nested PCR. In seeding experiments, rotavirus as low as 1.39 genome copies was able to be detected in 4 g of digestive tissues or per sample. In the period of August 2011 to July 2012, of the 300 bivalve shellfish samples collected and tested, 24 (8.0%) were found to be contaminated with rotavirus, the figures being: oysters, 13/100 samples; mussels, 10/100 samples; and cockles, 1/100 samples. By DNA sequencing of the RT-nested PCR products and phylogenetic analysis, the rotaviruses detected were classified into G1, lineage II (4 samples); G3 (10 samples): lineage I (3 samples), lineage IIIc (3 samples), lineage IIId (3 samples), lineage IV (1 sample); G9 (6 samples); and G12, lineage III (1 sample). These findings suggest that this virus concentration method provides high sensitivity for the detection of rotavirus from the three bivalve shellfish species. The prevalence of rotavirus and the identified genotypes contribute to the molecular epidemiology of rotavirus in different shellfish species.

A simple and efficient method for detecting avian influenza virus in water samples

Waterborne transmission plays an essential role in the transmission and spread of avian influenza viruses. The abundance of influenza viruses in environmental water is usually extremely low and viruses or viral genomes can hardly be detected by conventional reverse transcription (RT-) PCR without concentration. In the present study, an electropositive filter membrane was used to concentrate influenza viruses from water sample, in addition, a glass fiber filter has been used prior to positive charged membrane for the prefiltration. Unlike the traditional adsorption-elution method, Trizol-LS reagent was used to lyse the viruses attached directly to the electropositive filter membrane and the influenza virus genomic RNA was extracted, followed by RT-PCR analysis. The method established in this study could improve the efficiency of the conventional RT-PCR technique used to detect the M, NP, and HA genes of influenza virus in natural water samples. This method could also reduce the time taken for the traditional adsorption-elution concentration procedure.

Genetic diversity of rotavirus strains circulating in environmental water and bivalve shellfish in Thailand

Rotavirus is a common cause of acute diarrhea in young children worldwide. This study investigated the prevalence and molecular characterization of rotavirus in environmental water and oyster samples in Thailand. A total of 114 water samples and 110 oyster samples were collected and tested for group A rotavirus using RT-nested PCR. Rotavirus genotype was identified by phylogenetic analysis of the VP7 genetic sequences. Group A rotavirus was detected in 21 water samples (18.4%) and six oyster samples (5.4%). Twenty five rotavirus strains were successfully sequenced and classified into four genotypes; G1, G2, G3, and G9. Rotavirus G1 (three strains), G2 (three strains), and G9 (two strains) demonstrated the genetic sequences similar to human strains (90%-99% nucleotide identity), whereas G3 (17 strains) was closely related to animal strains (84%-98% nucleotide identity). G1 strains belonged to lineages I (sub-lineage c) and II. G2 strains belonged to lineage II. G9 strains belonged to lineages III (sub-lineage b) and IV. G3 strains belonged to lineages I, III (sub-lineage c), and IV with a predominance of lineage I. The present study provides important information on the rotavirus strains circulating in the environment.

Circulation of intergenotype recombinant noroviruses GII.9/GII.6 from 2006 to 2011 in central Greece

Noroviruses (NoVs) are members of the Caliciviridae family and are recognized as a worldwide cause of acute nonbacterial gastroenteritis. Based on the genetic analysis of the RdRp and capsid regions, human NoVs are divided into three genogroups (Gs), GI, GII, and GIV, which further segregate into distinct lineages called genotypes. In this study, in an attempt to discern the circulation of an intergenotypic recombinant GII.9/GII.6, which was previously reported by our group in central Greece, we investigated NoVs in raw sewages from 2006 to 2011 and compared the results with the viruses detected from clinical samples in the same area and in the same time period. Two specific primer pairs for NoVs were designed which amplified in a single PCR fragment from polymerase to capsid gene covering the widespread recombination point in ORF1/ORF2 junction. Based on the genetic analysis, recombinant NoV strains GII.9/GII.6 were identified. Fourteen out of 15 environmental and eight out of ten clinical samples that were used in the present study were positive, with both primer pairs, confirming that the intergenotypic recombinant GII.9/GII.6 was circulating in the population of central Greece from 2006 to 2011. The crossover point was identified to be within the overlapping region of ORF1/ORF2 (GII.9/GII.6, respectively) and was determined by Simplot at nucleotide position 5,032 bp.

Serial foodborne norovirus outbreaks associated with multiple genotypes

Noroviruses (NoV) have been recognized as an important pathogen associated with acute gastroenteritis worldwide during the past three decades. In the spring of 2012, a series of foodborne outbreaks in tourist groups were reported to Xiamen Center for Disease Control and Prevention, Xiamen, Fujian province, China. Among a total of 268 tourists in 7 groups, the prevalence rate of acute gastroenteritis was 16.0% (43/268). Twenty-three feces or anal swabs were collected for laboratory tests of causative agents, no bacterial pathogen was identified, while 22 of them were positive for NoV RNA. In addition, thirteen NoV fragments were recovered from positive specimens and sequenced, belonging to five genotypes such as GI.3, GI.4, GII.4, GII.6, and GII.14, respectively. However, NoV fragments obtained from locally infected patients showed distinct genotypes. Therefore, epidemiological investigation and laboratory analyses demonstrated that the serial foodborne NoV outbreaks in tourists were co-infection of multiple genotypes induced acute gastroenteritis linked to a restaurant.

Concentration and recovery of viruses from water: a comprehensive review

Enteric viruses are a cause of waterborne disease worldwide, and low numbers in drinking water can present a significant risk of infection. Because the numbers are often quite low, large volumes (100-1,000 L) of water are usually processed. The VIRADEL method using microporous filters is most commonly used today for this purpose. Negatively charged filters require the addition of multivalent salts and acidification of the water sample to effect virus adsorption, which can make large-volume sampling difficult. Positively charged filters require no preconditioning of samples, and are able to concentrate viruses from water over a greater pH range than electronegative filters. The most widely used electropositive filter is the Virosorb 1MDS; however, the Environmental Protection Agency has added the positively charged NanoCeram filters to their proposed Method 1615. Ultrafilters concentrate viruses based on size exclusion rather than electrokinetics, but are impractical for field sampling or processing of turbid water. Elution (recovery) of viruses from filters following concentration is performed with organic (e.g., beef extract) or inorganic solutions (e.g., sodium polyphosphates). Eluates are then reconcentrated to decrease the sample volume to enhance detection methods (e.g., cell culture infectivity assays and molecular detection techniques). While the majority of available filters have demonstrated high virus retention efficiencies, the methods to elute and reconcentrate viruses have met with varying degrees of success due to the biological variability of viruses present in water.

Detection method for avian influenza viruses in water

Recent events have shown that humans may become infected with some pathogenic avian influenza A viruses (AIV). Since soil and water, including lakes, rivers, and seashores, may be contaminated by AIV excreted by birds, effective methods are needed for monitoring water for emerging viruses. Combining water filtration with molecular methods such as PCR is a fast and effective way for detecting viruses. The objective of this study was to apply a convenient method for the detection of AIV in natural water samples. Distilled water and lake, river, and seawater were artificially contaminated with AIV (H5N3) and passed through a filter system. AIV was detected from filter membrane by real-time RT-PCR. The performance of Zetapor, SMWP, and Sartobind D5F membranes in recovering influenza viruses was first evaluated using contaminated distilled water. SWMP, which gave the highest virus recoveries, was then compared with a pre-filter combined GF/F filter membrane in a trial using natural water samples. In this study, the cellulose membrane SMWP was found to be practical for recovery of AIVs in water. Viral yields varied between 62.1 and 65.9% in distilled water and between 1 and 16.7% in natural water samples. The borosilicate glass membrane GF/F combined with pre-filter was also feasible in filtering natural water samples with viral yields from 1.98 to 7.33%. The methods described can be used for monitoring fresh and seawater samples for the presence of AIV and to determine the source of AIV transmission in an outbreak situation.

Molecular techniques in ecohealth research toolkit: facilitating estimation of aggregate gastroenteritis burden in an irrigated periurban landscape

Assessment of microbial hazards associated with certain environmental matrices, livelihood strategies, and food handling practices are constrained by time-consuming conventional microbiological techniques that lead to health risk assessments of narrow geographic or time scope, often targeting very few pathogens. Health risk assessment based on one or few indicator organisms underestimates true disease burden due a number of coexisting causative pathogens. Here, we employed molecular techniques in a survey of Cryptosporidium parvum, Giardia lamblia, Campylobacter jejuni, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., Shigella spp., Vibrio cholera, and Rotavirus A densities in canal water with respect to seasonality and spatial distribution of point-nonpoint pollution sources. Three irrigational canals stretching across nearly a 150-km(2) periurban landscape, traditionally used for agricultural irrigation but function as vital part of municipal wastewater stabilization in recent years, were investigated. Compiled stochastic data (pathogen concentration, susceptible populations) and literature-obtained deterministic data (pathogen dose-response model parameter values) were used in estimating waterborne gastroenteritis burden. Exposure scenarios include swimming or fishing, consuming canal water-irrigated vegetables, and ingesting or inhaling water aerosols while working in canal water-irrigated fields. Estimated annual gastroenteritis burden due individual pathogens among the sampling points was -10.6log(10) to -2.2log(10) DALYs. Aggregated annual gastroenteritis burden due all the target pathogens per sampling point was -3.1log(10) to -1.9log(10) DALYs, far exceeding WHO acceptable limit of -6.0log(10) DALYs. The present approach will facilitate the comprehensive collection of surface water microbiological baseline data and setting of benchmarks for interventions aimed at reducing microbial hazards in similar landscapes worldwide.

Sequence analysis of human rotavirus strains: comparison of clinical isolates from Northern and Southern Italy

The surveillance and monitoring of rotavirus (RV)-related diseases, preferably through the establishment of sentinel surveillance sites, are essential for assessing the need for vaccination and the projected results of the vaccine in terms of reducing the burden of disease. The objective of the present study was to compare RV strains isolated in Northern (Ferrara) and Southern (Galatina-LE) Italy. During 2007-2008, 115 RV-positive stool samples were collected from children with diarrhea admitted to the hospitals of Ferrara and Galatina. The specimens were genotyped for VP7 (G-type) and VP4 (P-type) gene by reverse transcription (RT) and multiplex polymerase chain reaction (PCR). A subset of 21 RV strains was randomly selected and characterized by sequence analysis of the VP7 genes. In total, seven G/P combinations (G1P[8], G2P[4], G4P[8], G9P[8], G2P[8], G1P[9], and G2P[10]) were identified. Phylogenetic comparison of the VP7 encoding gene of selected strains showed that there was similarity among RV strains circulating in Northern and Southern Italy. The observation of nucleotide sequence diversity contributes to a better understanding of RV spreading and helps to characterize the various antigenic shifts that could have an impact on vaccine effectiveness.

Microbial contamination of groundwater at small community water supplies in Finland

The raw water quality and associations between the factors considered as threats to water safety were studied in 20 groundwater supplies in central Finland in 2002-2004. Faecal contaminations indicated by the appearance of Escherichia coli or intestinal enterococci were present in five small community water supplies, all these managed by local water cooperatives. Elevated concentrations of nutrients in raw water were linked with the presence of faecal bacteria. The presence of on-site technical hazards to water safety, such as inadequate well construction and maintenance enabling surface water to enter into the well and the insufficient depth of protective soil layers above the groundwater table, showed the vulnerability of the quality of groundwater used for drinking purposes. To minimize the risk of waterborne illnesses, the vulnerable water supplies need to be identified and appropriate prevention measures such as disinfection should be applied.

Environmental survey to assess viral contamination of air and surfaces in hospital settings

The presence of pathogenic viruses in healthcare settings represents a serious risk for both staff and patients. Direct viral detection in the environment poses significant technical problems and the indirect indicators currently in use suffer from serious limitations. The aim of this study was to monitor surfaces and air in hospital settings to reveal the presence of hepatitis C virus, human adenovirus, norovirus, human rotavirus and torque teno virus by nucleic acid assays, in parallel with measurements of total bacterial count and haemoglobin presence. In total, 114 surface and 62 air samples were collected. Bacterial contamination was very low (<1 cfu/cm²) on surfaces, whereas the ‘medium’ detected value in air was 282 cfu/m³. Overall, 19 (16.7%) surface samples tested positive for viral nucleic acids: one for norovirus, one for human adenovirus and 17 (14.9%) for torque teno virus (TTV). Only this latter virus was directly detected in 10 air samples (16.1%). Haemoglobin was found on two surfaces. No relationship was found between viral, biochemical or bacterial indicators. The data obtained confirm the difficulty of assessing viral contamination using bacterial indicators. The frequent detection of TTV suggests its possible use as an indicator for general viral contamination of the environment.

Rotavirus detection in environmental water samples by tangential flow ultrafiltration and RT-nested PCR

Environmental monitoring was conducted in Otranto (Italy), from January 2006 to April 2007, to monitor the circulation of rotaviruses in various water matrices (raw and treated sewage, surface waters and seawater) and to identify any correlation with the traditional bacteriological indices (faecal coliforms). The viruses were detected using tangential flow ultrafiltration and reverse transcriptase-nested polymerase chain reaction, whilst detection of feaecal coliform was performed according to standard methods. The results showed widespread viral contamination, particularly in spring, of the matrices tested, with the exception of seawater, which at all times tested negative for the presence of rotaviruses. The typing of the rotavirus strains identified the circulation in the studied area of only two genotypes: G1 (22%) and G2 (78%). The bacterial recoveries confirmed the presence of faecal pollution indicators in all examined samples, sometimes with high values. A very weak correlation was found between the presence of faecal coliforms and the circulation of rotaviruses in the environment. The presence of rotaviruses in the environmental water samples may constitute a potential health risk for the local population.

Comparison of different concentration methods for the detection of hepatitis A virus and calicivirus from bottled natural mineral waters

Viral contamination of drinking water is frequently reported as the primary source of gastroenteritis or hepatitis outbreaks. The presence of viruses at low concentration levels in most environmental water poses major analytical problems when determining their concentration. To evaluate the efficiency of different recovery methods of viral RNA from bottled water, a comparison was made of 2 positively and 2 negatively charged membranes that were used for absorbing and releasing HAV virus particles during the filtration of viral spiked bottled water. All the 4 membranes, regardless of charge and pore size, had low level viral recovery. The results show that a considerable number of the virus particles passed through the pores of the membranes instead of being trapped by the electrostatic charges. Two different procedures were then compared using 1.5L polyethylene bottles spiked with 10-fold serial dilutions of HAV and FCV. The first procedure included an ultrafiltration-based method followed by MiniMag RNA extraction, and the second an ultracentrifugation-based method followed by RNA extraction using QIAamp viral RNA mini kit. The ultracentrifugation-based method resulted in a better recovery of HAV and FCV when compared to the ultrafiltration-based method.

A novel method for concentrating hepatitis A virus and caliciviruses from bottled water

Human enteric viruses are detected frequently in various types of environmental water samples, such as irrigation water, wastewater, recreational water, ground or subsurface water and even drinking water, constituting a primary source of gastroenteritis or hepatitis outbreaks. Only a few, but still infective number of viral particles are normally present in water samples, therefore an efficient virus concentration procedure is essential prior to molecular detection of the viral nucleic acid. In this study, a novel chromatographic technology, Convective Interaction Media (CIM) monolithic supports, were optimized and applied to the concentration of hepatitis A virus (HAV) and feline calicivirus (FCV), a surrogate of norovirus (NoV), from water samples. Two-step real-time RT-qPCR was used for quantitation of the virus concentration in the chromatographic fractions. Positively charged CIM QA (quaternary amine) monolithic columns were used for binding of HAV and FCV present in previously inoculated 1.5 l bottled water samples. Column bound viruses were eluted from the monolith using 1M NaCl to a final volume of 15 ml. Elution volume was concentrated further by ultracentrifugation. When the CIM/ultracentrifugation method was compared with another concentration method employing positively charged membranes and ultrafiltration, the recovery of HAV was improved by approximately 20%.

Detection of infectious rotavirus in naturally contaminated source waters for drinking water production

AIMS

To assess public health risks of rotavirus via drinking water consumption, a cell culture-PCR assay was developed and optimized for the detection of infectious environmental rotavirus strains in naturally contaminated source waters for drinking water production.

METHODS AND RESULTS

Infectious rotavirus concentrations were estimated by an optimized cell culture-PCR assay as most probable numbers by using the presence or absence of replicated virus in different sample volumes. Infectious rotavirus was detected in 11 of 12 source water samples in concentrations varying from 0.19 (0.01-0.87) to 8.3 (1.8-34.0) infectious PCR detectable units per litre (IPDU/l), which was not significantly different from the concentrations of infectious enterovirus in these samples.

CONCLUSIONS

In 55% of the samples, rotavirus genomes were 1000 to 10 000 times (3 log(10)-4 log(10)) more abundantly present than infectious rotavirus particles, whereas in the remaining 45% of the samples, rotavirus genomes were less than 1000 times (<3 log(10)) more abundantly present.

SIGNIFICANCE AND IMPACT OF THE STUDY

The broad variation observed in the ratios of rotavirus RNA and infectious particles demonstrates the importance of detecting infectious viruses instead of viral RNA for the purposes involving estimations of public health risks.

New electropositive filter for concentrating enteroviruses and noroviruses from large volumes of water

The U.S. Environmental Protection Agency's information collection rule requires the use of 1MDS electropositive filters for concentrating enteric viruses from water, but unfortunately, these filters are not cost-effective for routine viral monitoring. In this study, an inexpensive electropositive cartridge filter, the NanoCeram filter, was evaluated for its ability to concentrate enteroviruses and noroviruses from large volumes of water. Seeded viruses were concentrated using the adsorption-elution procedure. The mean percent retention of seeded polioviruses by NanoCeram filters was 84%. To optimize the elution procedure, six protocols, each comprising two successive elutions with various lengths of filter immersion, were evaluated. The highest virus recovery (77%) was obtained by immersing the filters in beef extract for 1 minute during the first elution and for 15 min during the second elution. The recovery efficiencies of poliovirus, coxsackievirus B5, and echovirus 7 from 100-liter samples of seeded tap water were 54%, 27%, and 32%, respectively. There was no significant difference in virus recovery from tap water with a pH range of 6 to 9.5 and a water flow rate range of 5.5 liters/min to 20 liters/min. Finally, poliovirus and Norwalk virus recoveries by NanoCeram filters were compared to those by 1MDS filters, using tap water and Ohio River water. Poliovirus and Norwalk virus recoveries by NanoCeram filters from tap and river water were similar to or higher than those by the 1MDS filters. These data suggest that NanoCeram filters can be used as an inexpensive alternative to 1MDS filters for routine viral monitoring of water.

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.

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.

Chapter 7 Global Supply of Virus-Safe Drinking Water

This chapter illustrates the recommendations and guidelines of the World Health Organization (WHO) concerning water, sanitation, and health. The recommendations and guidelines are evaluated in the light of disease caused by human pathogenic viruses. The guidelines outline a preventive management framework for safe drinking water. The framework includes health-based targets to assist national authorities who are normally responsible to set the targets for the protection of public health from risks by exposure to drinking water. Assessing the adequacy of systems, defining and monitoring control measures, and establishing management plans are the three components of the so-called water safety plans. Achievement of health-based targets may be verified by independent surveillance to assess the safety of the drinking water through additional verification or audit-based approaches. This framework for safe drinking water can be adapted according to environmental, social, economic, and cultural circumstances of drinking water provision on the national, regional, and local level. The chapter concludes that viruses could be considered as biocolloids with specific properties such as size, shape, structure, charge, composition, and genome. These viral characteristics determine their behavior in the environment, resistance to natural inactivation and treatment, and disinfection processes. For each (re-)emerging virus these properties may be known or could be assessed predicting the effectiveness of possible intervention measures for prevention of waterborne disease.

Attachment of enteric viruses to bottles

Storage of water that was deliberately contaminated with enteric viruses in polyethylene terephthalate (PET) bottles led to a rapid decrease of the apparent viral load, thereby hampering the development of samples for a collaborative evaluation of viral detection methods for bottled water. To determine if this decrease was due to spontaneous inactivation or to adhesion, an elution protocol was developed and combined with a rapid and sensitive real-time reverse transcription-PCR-based method to quantify adsorbed norovirus (NV), hepatitis A virus (HAV), and rotavirus (RV) on bottle walls. The NV retention on PET bottle walls after 20 and 62 days reached an average level of 85% and 95% of the recovered inoculum, respectively. HAV and RV also showed adsorption onto PET bottles, reaching 90% and 80%, respectively, after 20 days of storage. NV and RV attachment was demonstrated to be dependent on the presence of autochthonous flora, whereas HAV adsorption was independent of it. Application of the elution and viral detection protocol to 294 commercially available water bottles obtained from 25 different countries did not give any positive result, thereby providing further evidence that the sources used for this product are free from enteric viruses and support for the theory that bottled water is not a vehicle for viral diseases.

Development of a viral concentration method for bottled water stored in hydrophobic support

Several protocols have been described for the detection of genomes of enteric viruses from water using two-step procedures: membrane filtration and RT-PCR detection. However, these methods, when applied to bottled water, generally consider only the aqueous phase. Such procedures do not take into account the adhesion of viruses onto the hydrophobic container. Potential adhesion results in loss of viral concentration in the aqueous phase and consequently viral pollution is underestimated in such a system. A procedure based on the addition of surfactant to elute viruses followed by membrane concentration was developed to avoid this underestimation. Firstly, using poliovirus 1 as a model, this study demonstrated that the best solution to recover virus and/or viral genome is a mix of sodium dodecyl sulphate, a nonionic detergent and guanidine thiocyanate. Furthermore, temperature has a significant but low effect on elution. A positively charged 0.2 microm inorganic membrane composed of Alumina (Anodisc, Whatman) is also the best membrane to concentrate viral material before the detection by RT-PCR. Finally, the developed protocol gives significantly higher poliovirus 1 recovery rate than a reference protocol previously described (aqueous phase concentration on Zetapore). The difference can be explained by the recovery of the viruses adsorbed onto the water container.

Waterborne norovirus outbreaks

Noroviruses (NoVs) are the most common nonbacterial causative agents of waterborne outbreaks. Due to the mild and short-lived disease of gastroenteritis, even large epidemics may go unnoticed, since patients do not necessarily visit a doctor. NoVs have several means by which to survive both in the environment and in a population. The nonenveloped small virus retains its infectivity in the environment, and particularly in cold water, for a long time. Unlike most enteric viruses, it causes disease both in children and adults. A large number of genotypes combined with a small infective dose and short-term immunity guarantee efficient circulation of these viruses. The world of NoVs has been revealed to us predominantly by molecular methods. Having learned to detect these viruses first in patients, the emphasis is now in searching for methods sensitive enough to find them in environmental samples. In this review, the latest methods and their use in monitoring of these viruses are discussed.

Removal of noro- and enteroviruses, Giardia cysts, Cryptosporidium oocysts, and fecal indicators at four secondary wastewater treatment plants in Sweden

The aim of this study was to investigate variation in the occurrence and removal of enteroviruses, noroviruses, Giardia cysts, Cryptosporidium oocysts, and the most commonly used fecal indicators in four Swedish secondary wastewater treatment plants (WWTPs). Paired samples were taken from the inlet and outlet of each WWTP. (Oo)cysts and indicators were enumerated with standard methods and viruses with a reverse transcriptase polymerase chain reaction. Giardia cysts and enteroviruses were constantly detected (mean numbers were 10(3.31) cysts and 10(4.44) polymerase chain reaction (PCR) units L(-1), respectively). Oocysts were found in 5 out of 19 samples (mean number was 20 L(-1)). Noroviruses were found between November and February, with an average titer of 10(3.29( L(-1). Mean cyst removal was 2.6 log, while noroviruses and enteroviruses were removed by 0.9 and 1.3 log, respectively. There was no correlation between the removals of pathogens and indicators (p > 0.05). Coliphage removal resembled human viral removal better than did F-specific phage.

Removal of viruses, parasitic protozoa and microbial indicators in conventional and membrane processes in a wastewater pilot plant

The aim of this study was to investigate variations in the occurrence and removal of enterovirus and norovirus genomes, Giardia cysts, Cryptosporidium oocysts and the most commonly used faecal indicators in a Swedish wastewater pilot plant. Paired samples were taken from the inlet and outlet of each treatment line: tertiary filtration, membrane bioreactor (MBR) and upflow anaerobic sludge blankets (UASB). (Oo)cysts and indicators were enumerated using standard methods and viruses using RT-PCR. Giardia cysts and enteroviruses were constantly detected, mean numbers 10(3.11) cysts and 10(4.0) PCR units L(-1), respectively. Oocysts were found in 5/19 samples, mean number 5 L(-1). Noroviruses were found in 6/7 influent samples, with an average titre of 10(3.28)L(-1), during winter, but only in 2/15 in the rest of the year (mean 200 L(-1)). MBR treatment removed indicators more efficiently than did the other two lines, with 5log removal of E. coli. Human virus genome removal did not differ between the MBR and tertiary treatment line. Microorganism removal in UASB was significantly lower for all the organisms studied. E. coli, enterococci and Cl. perfringens removal was correlated (p<0.05) with enterovirus genome removal, with R-values around 0.4. However, values for removal of indicators were more strongly correlated to each other. Removal of viruses based on enumeration using RT-PCR probably underestimates infectious virion removal.

Diagnosis of hepatitis a virus infection: a molecular approach

Current serologic tests provide the foundation for diagnosis of hepatitis A and hepatitis A virus (HAV) infection. Recent advances in methods to identify and characterize nucleic acid markers of viral infections have provided the foundation for the field of molecular epidemiology and increased our knowledge of the molecular biology and epidemiology of HAV. Although HAV is primarily shed in feces, there is a strong viremic phase during infection which has allowed easy access to virus isolates and the use of molecular markers to determine their genetic relatedness. Molecular epidemiologic studies have provided new information on the types and extent of HAV infection and transmission in the United States. In addition, these new diagnostic methods have provided tools for the rapid detection of food-borne HAV transmission and identification of the potential source of the food contamination.

Norovirus outbreaks from drinking water

As part of an intensified monitoring program for foodborne disease outbreaks in Finland, waterborne outbreaks were investigated for viruses. The diagnostic procedure included analysis of patients' stool samples by electron microscopy and reverse transcription-polymerase chain reaction (RT-PCR) for noroviruses and astroviruses. When these test results were positive for a virus, the water sample was analyzed. Virus concentration was based on positively charged filters from 1-L samples. Of the total 41 waterborne outbreaks reported during the observation period (1998-2003), samples from 28 outbreaks were available for analysis. As judged by RT-PCR results from patient samples, noroviruses caused 18 outbreaks. In 10 outbreaks, the water sample also yielded a norovirus. In all but 1 instance, the amplicon sequence was identical to that recovered from the patients. The ubiquity of waterborne norovirus outbreaks calls for measures to monitor water for viruses.

Association of the G4 rotavirus genotype with gastroenteritis in adults

Rotavirus is the most common etiological cause of acute viral gastroenteritis in infants and young children worldwide, yet its role in the adult population is less well understood. We have recently identified rotavirus as the causative agent of severe diarrhea in adults, specifically in two gastroenteritis outbreaks in separate care for the elderly homes. Strain typing has shown the continued presence of P[8]G1, the emergence of P[8]G9, and the reemergence of P[8]G4. A total of 26 community cases and 6 outbreak cases of rotavirus infection, positive via a molecular screening assay, were subsequently amplified using VP4 and VP7 specific primers (Con2/Con3 and 1A/1B primer sets, respectively). The age range of patients investigated was from <1 year to 89 years. The resulting PCR products were cloned into TOPO10 PCR IV vector and sequenced to give the P- and G-type accordingly. All sequence data were subjected to BLAST analysis. Three different rotavirus types P[8]G1, P[8]G4, and P[8]G9 were identified. Types P[8]G1 and P[8]G9 were identified as circulating within the community, whereas the third type P[8]G4 was identified only in an elderly care outbreak. The identification of G9 rotaviruses supports evidence of emergence of the genotype on a global scale.

Isolation and detection of enterovirus RNA from large-volume water samples by using the NucliSens miniMAG system and real-time nucleic acid sequence-based amplification

Concentration of water samples is a prerequisite for the detection of the low virus levels that are present in water and may present a public health hazard. The aim of this study was to develop a rapid, standardized molecular method for the detection of enteroviruses in large-volume surface water samples, using a concentration method suitable for the detection of infectious viruses as well as virus RNA. Concentration of water was achieved by a conventional filter adsorption-elution method and ultrafiltration, resulting in a 10,000-fold concentration of the sample. Isolation of virus RNA by a silica-based RNA extraction method was compared with the nonmagnetic and magnetic NucliSens RNA isolation methods. By using the silica-based RNA extraction method in two out of five samples, enterovirus RNA was detected, whereas four out of five samples were positive following RNA isolation with magnetic silica beads. Moreover, estimated RNA levels increased at least 100 to 500 times. Furthermore, we compared enterovirus detection by an in-house reverse transcription (RT)-PCR with a novel commercially available real-time nucleic acid sequence-based amplification (NASBA) assay. We found that the rapid real-time NASBA assay was slightly less sensitive than our in-house RT-PCR. The advantages, however, of a commercial real-time NASBA assay, like the presence of an internal control RNA, standardization, and enormous decrease in turnaround time, makes it an attractive alternative to RT-PCR.

Detection and quantification of hepatitis A virus in seawater via real-time RT-PCR

A real-time RT-PCR method utilizing SYBR Green chemistry was developed to detect and enumerate hepatitis A virus (HAV) in ocean water. Ocean water samples were taken at the Tijuana River mouth (Tijuana, Mexico) and Imperial Beach pier (1.4 km north of the Tijuana River mouth in San Diego, California) following four separate rain events. A total of eight samples were collected, one from each location, each consisting of 4 l of ocean water. Using conventional RT-PCR and primers based on the conserved sequence at the VP3-VP1 genes of HAV, a 247 bp cDNA was amplified from six out of eight rain event water samples. HAV cDNA (confirmed by sequence analysis) was cloned into a TOPO vector (Invitrogen, Carlsbad, CA), and four primer sets were designed for application in SYBR Green real-time RT-PCR. The water samples were shown to contain inhibitors that affected real-time RT-PCR amplifications, however diluting the cDNA solution enabled successful amplification. Using real-time RT-PCR, HAV could be detected in all eight samples. Depending on the rain event, the viral load in these samples varied from 90 to 3523 copies of HAV/L of ocean water near the mouth of the Tijuana River, and 347 to 2656 copies/l near the Imperial Beach pier. The sensitivity, quantitative ability and the high throughput nature of SYBR Green real-time RT-PCR will be useful in monitoring HAV contamination in seawater.

Application of cation-coated filter method to detection of noroviruses, enteroviruses, adenoviruses, and torque teno viruses in the Tamagawa River in Japan

The occurrence of human enteric viruses in surface water in the Tamagawa River, Japan, was surveyed for 1 year, from April 2003 to March 2004. Sixty-four samples were collected from six sites along the river, and 500 ml of the sample was concentrated using the cation-coated filter method, which was developed in our previous study. This method showed recovery yields of 56% +/- 32% (n = 37) for surface water samples inoculated with polioviruses. More than one kind of tested virus was detected in 43 (67%) of 64 samples by TaqMan PCR. Noroviruses and adenoviruses were detected in a high positive ratio; 34 (53%), 28 (44%), and 29 (45%) of 64 samples were positive for norovirus genotype 1 and genotype 2 and adenoviruses, respectively. The mean concentrations of norovirus genotype 1 or genotype 2 determined by real-time PCR were 0.087 and 0.61 genome/ml, respectively, showing much higher values in winter (0.21 genome/ml for genotype 1 and 2.3 genomes/ml for genotype 2). Enteroviruses were detected by both direct PCR (6 of 64 samples; 9%) and cell culture PCR (2 of 64 samples; 3%). Torque teno viruses, emerging hepatitis viruses, were also isolated in three samples (5%). The concentration of total coliforms and the presence of F-specific phages showed a high correlation with the presence of viruses, which suggested that the simultaneous use of total coliforms and F-specific phages as indicators of surface water may work to monitor viral contamination.

Presence of noroviruses and other enteric viruses in sewage and surface waters in The Netherlands

Since virus concentrations in drinking waters are generally below the detection limit, the infectious risk from drinking water consumption requires assessment from the virus concentrations in source waters and removal efficiency of treatment processes. In this study, we estimated from reverse transcription-PCR on 10-fold serially diluted RNA that noroviruses, the most prevalent waterborne gastroenteritis agents, were present at 4 (0.2 to 38) to 4,900 (303 to 4.6 x 10(4)) PCR-detectable units (PDU) per liter of river water (ranges are given in parentheses). These virus concentrations are still high compared with 896 to 7,499 PDU/liter of treated sewage and 5,111 to 850,000 PDU/liter in raw sewage. Sequencing analyses designated human norovirus GGII.4 Lordsdale as the most prevalent strain in the sampling period 1998 to 1999 in both sewage and surface waters. Other GGII strains were also very abundant, indicating that the majority of the virus contamination was derived from urban sewage, although very divergent strains and one animal strain were also detected in the surface and sewage waters. Rotaviruses were also detected in two large rivers (the Maas and the Waal) at 57 to 5,386 PDU/liter. The high virus concentrations determined by PCR may in part be explained by the detection of virus RNA instead of infectious particles. Indeed, reoviruses and enteroviruses that can be cultured were present at much lower levels, of 0.3 to 1 and 2 to 10 PFU/liter, respectively. Assuming 1% of the noroviruses and rotaviruses to be infectious, a much higher disease burden than for other viruses can be expected, not only because of the higher levels but also because of these viruses' higher infectivity and attack rates.