The genetic diversity of human noroviruses detected in river water in Korea

Occurrence of microbial indicators, pathogenic bacteria and viruses in tropical surface waters subject to contrasting land use

Fecal indicator bacteria, such as Escherichia coli (E.coli) and Enterococcus, have been widely used to indicate the presence of pathogens. However, the suitability of fecal indicator bacteria to represent health risks is still being challenged, particularly in tropical aquatic environments. The objective of this study is to understand the occurrence and prevalence of indicators and pathogens in areas with contrasting land use, as well as to identify the major correlations between indicators, pathogens and environmental parameters. The spatial and temporal variation of indicators and pathogens was studied to examine the distribution patterns for areas with different land use, and the impact of seasonal changes on microbial populations. A total of 234 water samples were sampled for two years from reservoirs and their tributaries, and tested for fecal indicator bacteria, coliphages, human specific markers, pathogenic bacteria and viruses. The prevalence of indicators and pathogens in reservoirs were generally low, while relatively high concentrations were observed in tributaries to varying degrees. Of the enteric viruses, norovirus GII was among the most prevalent and had the highest concentration. Although strong correlations were found between indicators, only relatively weak correlations were found between indicators and pathogens. The results in this study showed that none of the bacteria/phage indicators were universal predictors for pathogens. Inclusion of the alternative indicators, Methanobrevibacter smithii, Bacteroides and human polyomaviruses (HPyVs) to monitoring programs could help to determine whether the fecal source was human. The microbial distribution patterns allow the classification of sampling sites to different clusters and thus, help to identify sites which have poor water quality. This approach will be useful for water quality management to pinpoint factors that influence water quality and help to prioritize sites for restoration of water quality.

A review on recent progress in the detection methods and prevalence of human enteric viruses in water

Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at low concentrations in aquatic environments, they should be concentrated into smaller volumes prior to downstream molecular biological applications, such as quantitative polymerase chain reaction (qPCR). This review describes recent progress made in the development of concentration and detection methods of human enteric viruses in water, and discusses their applications for providing a better understanding of the prevalence of the viruses in various types of water worldwide. Maximum concentrations of human enteric viruses in water that have been reported in previous studies are summarized to assess viral abundances in aquatic environments. Some descriptions are also available on recent applications of sequencing analyses used to determine the genetic diversity of viral genomes in water samples, including those of novel viruses. Furthermore, the importance and significance of utilizing appropriate process controls during viral analyses are discussed, and three types of process controls are considered: whole process controls, molecular process controls, and (reverse transcription (RT)-)qPCR controls. Although no standards have been established for acceptable values of virus recovery and/or extraction-(RT-)qPCR efficiency, use of at least one of these appropriate control types is highly recommended for more accurate interpretation of observed data.

Estimation of Human Norovirus Infectivity from Environmental Water Samples by In Situ Capture RT-qPCR Method

Human noroviruses (HuNoVs) are highly infectious viruses for which water is an important medium of transmission. In this study, we explored a new in situ capture RT-qPCR (ISC-RT-qPCR) methodology to estimate the infectivity of HuNoV in environmental water samples. This assay was based on capturing encapsidated HuNoV by viral receptors, followed by in situ amplification of the captured viral genomes by RT-qPCR. We demonstrated that the ISC-RT-qPCR did not capture and enable signal amplification of heat-denatured Tulane Virus (TV) and HuNoVs. We further demonstrated that the sensitivity of ISC-RT-qPCR was equal or better than that of conventional RT-qPCR procedures for the detection of HuNoV GI and GII. We then utilized the ISC-RT-qPCR to detect HuNoV in environmental water samples for comparison against that from a conventional RT-qPCR procedure. TV was used as a process control virus. While complete inhibition of TV genomic signal was observed in 27% of samples tested by RT-qPCR, no inhibition of TV genomic signal was observed by ISC-RT-qPCR. From 72 samples tested positive for HuNoV GI signal by RT-qPCR, only 20 (27.8%) of these samples tested positive by ISC-RT-qPCR, suggesting that 72.2% of RT-qPCR-positive samples were unlikely to be infectious. From 16 samples tested positive for HuNoV GII signal by RT-qPCR, only one of these samples tested positive by ISC-RT-qPCR. Five samples that had initially tested negative for HuNoV GII signal by RT-qPCR, was tested as positive by ISC-RT-qPCR. Overall, ISC-RT-qPCR method provided an alternative assay to estimate infectivity of HuNoV in environmental samples.

Emergence of Norovirus GII.17-associated Outbreak and Sporadic Cases in Korea from 2014 to 2015

Human norovirus are major causative agent of nonbacterial acute gastroenteritis. In general, genogroup (G) II.4 is the most prominent major genotype that circulate in human population and the environment. However, a shift in genotypic trends was observed in Korea in December 2014. In this study, we investigated the trend of norovirus genotype in detail using the database of Acute Diarrhea Laboratory Surveillance (K-EnterNet) in Korea. GII.17 has since become a major contributor to outbreaks of norovirus-related infections and sporadic cases in Korea, although the reason for this shift remain unknown.

Quantitative farm-to-fork human norovirus exposure assessment of individually quick frozen raspberries and raspberry puree

A quantitative human norovirus (NoV) exposure model describing transmission of NoV during pre-harvest, harvest and further processing of soft red fruits exemplified by raspberries is presented. The outcomes of the model demonstrate the presence of NoV in raspberry puree or individual quick frozen (IQF) raspberry fruits and were generated by Monte Carlo simulations by combining GoldSim® and @Risk® software. Input data were collected from scientific literature, observational studies and assumptions. NoV contamination of soft red fruits is assumed to take place at farms by application of contaminated water for pesticides dilution or by berries' pickers shedding NoV. The model was built simulating that a collection center received berries from ten farms with a total of 245 food handlers picking soft red fruits during a 10-hour day shift. Given 0, 5 and 20 out of 245 berries' pickers were shedding NoV, these conditions were calculated to result in a mean NoV contamination of respectively 0.47, 14.1 and 36.2 NoV particles per kg raspberries in case all raspberries are mixed to one day-batch of 11tons. The NoV contamination of the fruits was mainly driven by the route of NoV shedding food pickers (95.8%) rather than by spraying contaminated pesticide water (4.2%) (baseline scenario with 5 shedding pickers and contaminated pesticide water). Inclusion of appropriate hand washing procedures or hand washing followed by hand disinfection resulted in estimated reductions of the mean NoV levels from 14.1 to 0.16 and 0.17 NoV particles per kg raspberries, respectively, for the baseline scenario with 5 out of 245 food pickers shedding NoV. The use of a mild heat treatment (30s at 75°C) during further processing of berries to purees was noted to reduce mean NoV levels substantially from 14.1 to 0.2 NoV particles per kg raspberry puree. For IQF raspberries, the NoV contamination is heterogeneously distributed and resulted in a mean contamination of 3.1 NoV particles per 250g package containing approximately 115 berries. This farm-to-fork model is a useful tool for evaluating NoV mitigation strategies in the soft red fruit supply chain.

Molecular epidemiology of norovirus in asymptomatic food handlers in Busan, Korea, and emergence of genotype GII.17

The molecular epidemiology of norovirus infections was studied in food handlers without any symptoms from January to December 2015 in Busan city, Korea. A total of 2,174 fecal specimens from asymptomatic food handlers were analyzed, and 2.3% (49/2,174) were norovirus-positive. Fourteen of 335 samples (4.2%) were positive in January; fifteen of 299 samples (5.0%) in February, and seven of 189 samples (3.7%) in December. However, norovirus was rarely detected in other months. From sequencing analysis, 11 genotypes (five GI and six GII genotypes) were detected. Among the 42 capid gene sequences identified, 14 were from the GI genogroup, while 28 were from the GII genogroup. The most commonly detected genotype was GII.17, comprising 15 (35.7%) of positive samples. From January 2012 to December 2015, 5,138 samples were collected from gastroenteritis patients and outbreaks in Busan. The most detected genotype in 2012, 2013, and 2014 was GII.4 (121, 24, and 12 cases, respectively), but in 2015, GII.17 (25 cases) was the most common. The GII.4 genotype was the major cause of acute gastroenteritis from 2012 to 2014, but the GII.17 genotype became the most prevalent cause in 2015. Continued epidemiological surveillance of GII.17 is needed, together with assessment of the risk of norovirus infection.

Distribution of Human Norovirus in the Coastal Waters of South Korea

The presence of human norovirus in the aquatic environment can cause outbreaks related to recreational activities and the consumption of norovirus-contaminated clams. In this study, we investigated the prevalence of norovirus genogroups I (GI) and II (GII) in the coastal aquatic environment in South Korea (March 2014 to February 2015). A total of 504 water samples were collected periodically from four coastal areas (total sites = 63), of which 44 sites were in estuaries (clam fisheries) and 19 were in inflow streams. RT-PCR analysis targeting ORF2 region C revealed that 20.6% of the water samples were contaminated by GI (13.3%) or GII (16.6%). The prevalence of human norovirus was higher in winter/spring than in summer/fall, and higher in inflow streams (50.0%) than in estuaries (7.9%). A total of 229 human norovirus sequences were identified from the water samples, and phylogenetic analysis showed that the sequences clustered into eight GI genotypes (GI.1, 2, 3, 4, 5, 6, 7, and 9) and nine GII genotypes (GII.2, 3, 4, 5, 6, 11, 13, 17, and 21). This study highlighted three issues: 1) a strong correlation between norovirus contamination via inflow streams and coastal areas used in clam fisheries; 2) increased prevalence of certain non-GII.4 genotypes, exceeding that of the GII.4 pandemic variants; 3) seasonal shifts in the dominant genotypes of both GI and GII.

Environmental Surveillance of Genogroup I and II Noroviruses in Shandong Province, China in 2013

Noroviruses are the most common cause of epidemic gastroenteritis. However, the case-based surveillance is limited in China. In this study, we analyzed the results of environmental surveillance conducted in two cities of Shandong Province, China from January to December in 2013. Twenty-four sewage samples were collected and concentrated via membrane absorption/elution method. After reverse transcription-PCR, cloning and sequencing on ORF2 region, norovirus nucleic acid was detected in all 24 sewage samples. A total of 403 norovirus sequences of 16 genotypes were detected, among which GII.3 (22.6%), GI.2 (17.1%), GI.5 (13.4%), GI.3 (11.9%), GII.4 (7.7%), and GII.6 (6.7%) were the 6 most common genotypes. Phylogenetic analysis revealed multiple lineages within most common genotypes, especially in GI.3, whereas all GII.4 sequences belonged to Sydney 2012 strain. Recombination events were observed in 5 GI and 4 GII sequences within or near the ORF1/ORF2 overlap. This is the first report on systematic environmental surveillance on norovirus in China. The data presented here reveal co-circulation and high genetic diversity of multiple norovirus genotypes in the two cities, and suggest continued environmental surveillance can provide valuable information on norovirus circulation in the population.

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.

First norovirus outbreaks associated with consumption of green seaweed (Enteromorpha spp.) in South Korea

In February 2012, an outbreak of gastroenteritis was reported in school A; a successive outbreak was reported at school B. A retrospective cohort study conducted in school A showed that seasoned green seaweed with radishes (relative risk 7·9, 95% confidence interval 1·1-56·2) was significantly associated with illness. Similarly, a case-control study of students at school B showed that cases were 5·1 (95% confidence interval 1·1-24·8) times more likely to have eaten seasoned green seaweed with pears. Multiple norovirus genotypes were detected in samples from students in schools A and B. Norovirus GII.6 isolated from schools A and B were phylogenetically indistinguishable. Green seaweed was supplied by company X, and norovirus GII.4 was isolated from samples of green seaweed. Green seaweed was assumed to be linked to these outbreaks. To our knowledge, this is the first reported norovirus outbreak associated with green seaweed.

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.

A review of known and hypothetical transmission routes for noroviruses

Human noroviruses (NoVs) are considered a worldwide leading cause of acute non-bacterial gastroenteritis. Due to a combination of prolonged shedding of high virus levels in feces, virus particle shedding during asymptomatic infections, and a high environmental persistence, NoVs are easily transmitted pathogens. Norovirus (NoV) outbreaks have often been reported and tend to affect a lot of people. NoV is spread via feces and vomit, but this NoV spread can occur through several transmission routes. While person-to-person transmission is without a doubt the dominant transmission route, human infective NoV outbreaks are often initiated by contaminated food or water. Zoonotic transmission of NoV has been investigated, but has thus far not been demonstrated. The presented review aims to give an overview of these NoV transmission routes. Regarding NoV person-to-person transmission, the NoV GII.4 genotype is discussed in the current review as it has been very successful for several decades but reasons for its success have only recently been suggested. Both pre-harvest and post-harvest contamination of food products can lead to NoV food borne illness. Pre-harvest contamination of food products mainly occurs via contact with polluted irrigation water in case of fresh produce or with contaminated harvesting water in case of bivalve molluscan shellfish. On the other hand, an infected food handler is considered as a major cause of post-harvest contamination of food products. Both transmission routes are reviewed by a summary of described NoV food borne outbreaks between 2000 and 2010. A third NoV transmission route occurs via water and the spread of NoV via river water, ground water, and surface water is reviewed. Finally, although zoonotic transmission remains hypothetical, a summary on the bovine and porcine NoV presence observed in animals is given and the presence of human infective NoV in animals is discussed.

Epidemiological and molecular analysis of a waterborne outbreak of norovirus GII.4

Contaminated water is one of the main sources of norovirus (NoV) gastroenteritis outbreaks globally. Waterborne NoV outbreaks are infrequently attributed to GII.4 NoV. In September 2009, a NoV outbreak affected a small school in Guangdong Province, China. Epidemiological investigations indicated that household use water, supplied by a well, was the probable source (relative risk 1·9). NoV nucleic acid material in concentrated well-water samples was detected using real-time RT-PCR. Nucleotide sequences of NoV extracted from diarrhoea and well-water specimens were identical and had the greatest sequence identity to corresponding sequences from the epidemic strain GII.4-2006b. Our report documents the first laboratory-confirmed waterborne outbreak caused by GII.4 NoV genotype in China. Our investigations indicate that well water, intended exclusively for household use but not for consumption, caused this outbreak. The results of this report serve as a reminder that private well water intended for household use should be tested for NoV.

Molecular epidemiology of rotavirus and norovirus in Ile-Ife, Nigeria: high prevalence of G12P[8] rotavirus strains and detection of a rare norovirus genotype

Rotavirus (RV) and norovirus (NoV) are considered the most common causes of viral gastroenteritis in children. In this study, the prevalence of RV and NoV infection in 55 children with diarrhea from the rural community Akinlalu in Southwestern Nigeria was investigated using real-time PCR assays. The RV and NoV strains were genotyped by PCR and/or sequencing. RV and NoV infections occurred with a prevalence of 34.5% and 25.5% respectively, with predominance in children <1 year. Most infections occurred during the dry season with increasing prevalence of RV as the dry season progressed (October-January). Infections with RV VP6 subgroup (SG) II were more prevalent (27.3%) than SGI (7.3%). Similarly, NoV genogroup II infections were more common (23.6%) than genogroup I (1.8%). Five children out of 55 (9.1%) were co-infected with both RV and NoV. Notably, G12P[8] was the predominant RV strain (36.8%, n = 7), observed for the first time in Nigeria. The VP7 gene of the G12 strains clustered within lineage III, sharing high nucleotide identity with each other (>99%) indicating introduction in Nigeria from a single donor. Furthermore, a putative novel genotype within genogroup I NoV was detected, which till date has only been reported once in humans. To conclude, a high prevalence of the emerging G12P[8] RV strain was observed for the first time in Nigeria, as well as a putative novel NoV genotype in humans. These results provide new information which can be important for future vaccine evaluations and possible introduction in Nigeria.

Reliability of non-culturable virus monitoring by PCR-based detection methods in environmental waters containing various concentrations of target RNA

Owing to the lack of practical cell culture system for human noroviruses (HuNoV), various detection methods based on conventional reverse transcription-PCR (RT-PCR) and the quantitative real-time PCR have been major tools for monitoring environmental water safety. In this study, we showed that the proportion of water sample concentrates used for one-step RT-PCR significantly influences false-negative findings of the non-culturable viruses. In total, 59 archived samples of previously analyzed water concentrates were reexamined for HuNoV RNA by the one-step RT-PCR and semi-nested PCR. Using new aliquots for RNA extraction for every trial, up to 20 PCR trials were performed for each archive to determine whether the crosscheck results supported the previous determinations. We reconfirmed that 27.6% (8/29) of the samples were HuNoV-positive samples: 6.7% (1/15) from groundwater, 33.3% (3/9) from river water, and 80% (4/5) from treated sewage effluent (TSE). These results corresponded to the ratio of previously negative HuNoV samples now identified as positive (8/30): 6.7% (1/15) from groundwater, 20% (1/5) from river water, and 60% (6/10) from TSE. To elucidate the cause of these results, 16 different concentrations of murine norovirus (MNV) RNA (from 2×10(2) to 8×10(3) copies, divided into 10 tubes for each concentration) were subjected to one-step RT-PCR. The detection frequency and reproducibility decreased sharply when the number of MNV RNA copies fell below threshold levels. These observations suggest that the proportion of water concentrate used for PCR-based detection should be considered carefully when deciding viral presence in certain types of environmental water, particularly in regard with legal controls.

Detection and molecular characterization of human noroviruses in Korean groundwater between 2008 and 2010

RT-PCR, nucleotide sequencing, and phylogenetic analysis were performed for genotyping and molecular characterization of noroviruses isolated from Korean groundwater. Among 160 samples collected from 80 sites between 2008 and 2010, 14 samples (8.7 %) from 12 sites were positive for noroviruses (NoVs). The percentages of NoV-positive samples in 2008, 2009, and 2010 were 22.2, 3.2, and 0 %, respectively, representing a yearly decrease. GII-positive samples (n = 9, 5.6 %) outnumbered GI-positive samples (n = 5, 3.1 %). The genotypes of the GI NoVs were GI.2, GI.5, and GI.6, and the genotypes of the GII NoVs were all GII.4. One sample, HM623465, was very similar to CUK-3 and CBNU2 and two GII.4 sequences isolated from the stool of Korean gastroenteritis patients. A BLASTN search revealed several nucleotide sequences highly similar to those of NoVs isolated in this study. The original isolation sources for these similar NoVs were mostly stool (n = 731, 80.0 %) and groundwater (n = 135, 14.8 %), and all the countries from which they were isolated were almost in Asia (96.0 %); specifically, China (n = 192, 21.0 %), Japan (n = 383, 41.9 %), Korea (n = 296, 32.4 %), and other Asian countries (n = 6, 0.7 %). These results suggest that Korean groundwater might be contaminated with NoVs from the stool of infected patients and that these NoVs in turn cause new cases of gastroenteritis through a typical fecal-oral route with region-specific circulation. Therefore, it is important to properly treat sewage, which may include waterborne viruses and manage point sources in groundwater for national health and sanitation. In addition, continuous molecular surveillance remains important for understanding circulating NoVs.

One-year weekly survey of noroviruses and enteric adenoviruses in the Tone River water in Tokyo metropolitan area, Japan

To investigate the actual fluctuations in the concentrations of noroviruses (NoVs) GI and GII, and enteric adenoviruses (EAdVs) in river water and its relationship with the number of acute infectious gastroenteritis patients, one-year weekly quantitative monitoring of NoVs GI and GII and EAdVs was performed in the Tone River in Japan where the surface water is utilized for the main production of drinking water for the Tokyo Metropolitan Area from October 2009 to September 2010. Noroviruses GI and GII and EAdVs were detected in 28 (54%), 33 (63%), and 23 (44%) of the 52 samples (1 L each), respectively. The concentrations of NoVs GI and GII and EAdVs fluctuated strongly and were more abundant in winter and early spring. The concentration of NoVs GI was transiently greater than 10,000 copies/L. The number of acute infectious gastroenteritis patients in the upper river basin was highly correlated with all the viral concentrations, while general microbial indicator data such as turbidity and heterotrophic plate count were independent of viral concentration as suggested in previous studies. To the best of our knowledge, this is the first study that clearly shows the strong correlation of the number of gastroenteritis with virus contamination in lower river basin.

Diverse norovirus genotypes identified in sewage-polluted river water in South Africa

This study aimed to assess norovirus (NoV) contamination and genotype diversity in surface water in Gauteng, South Africa. Between January 2008 and December 2010, three rivers, namely Klip, Suikerbosrant, and Rietspruit were monitored for NoV genogroup (G)I and GII. Viruses were recovered using the glass wool adsorption-elution technique and detected by real-time reverse transcription–polymerase chain reaction. From 2008 to 2010, NoVs were detected in 66% (70/106) of Klip river samples. The Rietspruit and Suikerbosrant rivers were contaminated with NoV in 95% (20/21) and 21% (5/24) of samples, respectively. NoV-positive samples comprised of 33% GI, 29% GII and 38% of both GI and GII strains. Based on partial capsid gene analysis (region C), 16 NoV genotypes (6 GI, 10 GII) were identified. The major genotypes detected were GI.4, GI.5 and GII.4. These rivers could be a potential source of NoV infection for communities using the water for domestic or recreational purposes.

Molecular detection and genotyping of human noroviruses in influent and effluent water at a wastewater treatment plant in Japan

AIMS

To investigate the prevalence, seasonality and genotype distribution of human noroviruses (NoVs) in wastewater in Japan.

METHODS AND RESULTS

Influent and effluent water samples were collected monthly for a year from a wastewater treatment plant and examined for the presence of genogroups I and II (GI and GII) NoVs. Using real-time reverse transcription (RT)-PCR assays, 12 (100%) influent and six (50%) effluent samples were positive for both GI and GII NoV genomes, with a higher prevalence in winter. A total of 152 different NoV strains, comprising 84 GI and 68 GII strains, were identified using seminested RT-PCR assays followed by cloning and sequence analysis. These strains were classified into nine GI genotypes (GI/1, 2, 4, 5, 8, 9, 11, 12 and 14) and 13 GII genotypes (GII/1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15 and 16), showing considerable genetic diversity.

CONCLUSIONS

Based on the partial capsid gene sequences, we identified a great number of NoV strains belonging to many genotypes, demonstrating that genetically diverse NoV strains are co-circulating in aquatic environments and human populations.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results clearly demonstrate the seasonal trend and genetic diversity of NoVs in wastewater.

Prevalence and diversity of norovirus genogroups I and II in Hong Kong marine waters and detection by real-time PCR

Marine waters from six sites around Hong Kong with varying levels of sewage pollution were examined for noroviruses (NoVs) by PCR cloning and sequencing of a highly-variable N-terminal region of the VP1 capsid gene, at the ORF1-ORF2 junction of NoV. Phylogenetic analysis of genogroups GI- and GII-specific PCR clones obtained from different marine sites indicated that human NoV GI.1 and GII.4 strains are the most prevalent genotypes circulating in Hong Kong waters. GI- and GII-specific TaqMan-based real-time PCR assays targeting the ORF1-ORF2 junction of NoVs were used to quantify NoV particles in marine water samples in parallel with total Escherichia coli counts which were enumerated on TBX medium. No correlation of any significance between NoV and E. coli counts was observed which highlighted the inadequacy in using E. coli as a fecal indicator to predict the level of NoVs in marine waters to protect public health.

A duplex real-time RT-PCR assay for the simultaneous genogroup-specific detection of noroviruses in both clinical and environmental specimens

Norovirus (NoV) is the major etiological agent causing foodborne and waterborne outbreaks worldwide. We developed a novel duplex real-time quantitative RT-PCR assay designed for the simultaneous detection of and discrimination between NoV genogroups GI and GII, by targeting the short junction region between ORF1 and ORF2, with sensitivity and efficiency comparable to those of each simplex RT-PCR assay. This new duplex assay was evaluated against clinical stool (n = 82) and environmental (groundwater or surface water, n = 60) specimens from South Korea, and the results were compared with those of conventional RT-PCR (cRT-PCR) assays. The duplex assay detected more positive samples than did the cRT-PCR for both clinical (74 vs. 71) and, more strikingly, environmental (24 vs. 10) specimens. No cross-reactivity against specimens containing other enteric viruses such as rotavirus, adenovirus, and poliovirus were observed. These results suggest that this newly developed duplex real-time RT-PCR assay can be used for the sensitive and simultaneous genogroup-specific detection of NoV in both clinical and environmental specimens.

Investigation of norovirus occurrence in groundwater in metropolitan Seoul, Korea

Groundwater is an important source of drinking and household water worldwide. Hence, the quality of groundwater is very important for preventing waterborne disease outbreaks and should be properly monitored. This study investigated the prevalence of waterborne viruses and fecal indicators in groundwater in metropolitan Seoul and Gyeonggi province, South Korea. A total of 116 samples of groundwater were taken using NanoCeram filters during both summer (June to August) and fall-winter seasons (October to December) in 2008. Among 71 sampling sites, 28 (48.3%) and 18 (35.3%) were positive for norovirus (NoV) from the summer and fall-winter season, respectively. The identified genotypes of NoV include GI-1, 4, 8, 9 and GII-4, 10, 11 (or 17), 13, 15 (or 16). None of fecal indicators was significantly correlated with NoV in groundwater. Among the tested fecal indicators, somatic coliphage (95.3%) showed an excellent true-negative rate of NoV occurrence. The combination of chemical, microbial and viral indicators increased the positive predictive value (50-100%). This study demonstrated a high prevalence of NoV in groundwater in metropolitan Seoul areas and characterized the positive and negative predictive values of a fecal indicator for predicting NoV prevalence.

Nationwide groundwater surveillance of noroviruses in South Korea, 2008

To inspect the norovirus contamination of groundwater in South Korea, a nationwide study was performed in the summer (June to August) and winter (October to December) of 2008. Three-hundred sites designated by the government ministry were inspected. Water samples were collected for analysis of water quality, microorganism content, and viral content. Water quality was assessed by temperature, pH, turbidity, residual chlorine, and nitrite nitrogen content. Microorganism contents were analyzed bacteria, total coliforms, Escherichia coli, and bacteriophage. Virus analyses included panenterovirus and norovirus. Two primer sets were used for the detection of norovirus genotypes GI and GII, respectively. Of 300 samples, 65 (21.7%) were norovirus positive in the summer and in 52 (17.3%) were norovirus positive in the winter. The genogroup GI noroviruses that were identified were GI-1, GI-2, GI-3, GI-4, GI-5, GI-6, and GI-8 genotypes; those in the GII genogroup were GII-4 and GII-Yuri genotypes. The analytic data showed correlative relationships between the norovirus detection rate and the following parameters: water temperature and turbidity in physical-chemical parameters and somatic phage in microbial parameters. It is necessary to periodically monitor waterborne viruses that frequently cause epidemic food poisoning in South Korea for better public health and sanitary conditions.

Seasonal distribution and genetic diversity of genogroups I, II, and IV noroviruses in the Tamagawa River, Japan

We investigated the prevalence, seasonal dependence, and genetic diversity of noroviruses (NoVs) in the Tamagawa River, which runs through a densely populated region in Tokyo, Japan, from April 2003 to March 2004. A total of 60 water samples were collected from five sites from upstream to downstream along the river, and 500 mL of which was concentrated using the "cation-coated filter method". Of the 60 samples tested, genogroup I (GI) and GII NoVs were detected from 28 (47%) and 18 (30%) samples, respectively. GIV NoV was successfully detected from 2 (3%) samples with a newly developed seminested RT-PCR assay specific for GIV. The occurrence of NoVs in the river was significantly higher in winter/spring than in summer/autumn and also in mid- to downstream rather than upstream. A total of 176 different NoV strains were identified from river water samples based on the phylogenetic analysis of partial capsid gene sequences. GI, GII, and GIV strains were clustered into 7 (GI/1, 2, 4, 5, 8, 9, and 11), 8 (GII/2, 3, 4, 5, 6, 11, 12, and 16), and 1 (GIV/1) genotypes, respectively. The results suggest that genetically diverse NoV strains are circulating between human populations and aquatic environments.

Environmental surveillance and molecular characterization of human enteric viruses in tropical urban wastewaters

AIMS

To study the prevalence and genotypes of waterborne pathogenic viruses in urban wastewaters in the tropical region.

METHODS AND RESULTS

Viruses in wastewaters collected at three water reclamation plants in Singapore were studied by molecular methods. Over a 6-month sampling period, adenoviruses, astroviruses and both norovirus genogroups I (GI) and II (GII) were detected in 100% of the sewage and secondary effluent. Enteroviruses and hepatitis A viruses (HAV) were found in 94 and 78% of sewage, and 89 and 28% of secondary effluent, respectively. By using quantitative real-time PCR, estimated concentrations of astrovirus in the sewage were 1-2 orders of magnitude higher than those for adenovirus, noroviruses GI and GII. Genotyping of environmental isolates revealed multiple genotypes of GI and GII noroviruses. Coxsackieviruses A, astrovirus type 1 and adenovirus type 41 were prevalent. Norovirus GII/4 and coxsackievirus A24 isolates in wastewaters were closely related to respective outbreak strains isolated previously in Singapore.

CONCLUSIONS

This study showed the widespread occurrence of all tested enteric virus groups in urban wastewaters. Genetic diversity of astroviruses, enteroviruses and noroviruses in the tropical region was observed.

SIGNIFICANCE AND IMPACT OF THE STUDY

The high prevalence and great genetic diversity of human enteric viruses in urban wastewaters strongly supports the need of further comprehensive studies for evaluating the public health risk associated with viral pathogens in water environments.

Assessment of norovirus contamination in environmental samples from Florianópolis City, Southern Brazil

AIMS

To assess norovirus (NoV) contamination in aquatic ecosystems in the city of Florianópolis, in Southern Brazil, to provide epidemiological data that can support actions for environmental contamination control.

METHODS AND RESULTS

An adsorption-elution method, followed by ultrafiltration, was performed to concentrate the viruses. NoV were detected using semi-nested PCR and quantified by real-time PCR. From June 2007 to May 2008, NoV were detected in 23% (22/94) of the samples analysed, including seawater, drinking water, superficial water (creek and brackish lagoon) and treated sewage. The mean viral loads for genogroups (G)I and GII in treated sewage samples were 297 and 440 genomic copies (gc) l(-1) , respectively, whereas creek water samples contained 2603 and 1361 gc l(-1) , respectively. Six samples were sequenced: two samples were GII.4, two were GII.2 and two were GI.3.

CONCLUSIONS

NoV were detected in all water types analysed, demonstrating the widespread contamination of this geographical area with several cocirculating strains belonging to GI and GII.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates the environmental spread of NoV in environmental waters and highlights the potential hazard for human health following the consumption of or contact with these waters, which could result in waterborne or foodborne acute gastroenteritis.

Evidence of the co-circulation of enteric viruses in sewage and in the population of Greater Cairo

AIMS

To characterize major enteric viruses (enterovirus, rotavirus, norovirus, astrovirus and adenovirus) in the sewage of Greater Cairo and to compare the results with clinical data collected during the same period.

METHODS AND RESULTS

Seventy-two sewage samples from two waste water treatment plants were collected from April 2006 through February 2007. Enteroviruses, noroviruses (NoVs) and rotaviruses (RVs) were detected by RT-PCR in 22%, 18% and 8.3% of the samples, respectively. No adenovirus and astrovirus was detected. G2P[8], G9P[8], G1P[8], G2P[4] and rare G12 RV isolates were detected in the environment as well as a bovine RV. The environmental NoV strains mostly belonged to genogroup I (84%). Rotaviruses and some of the NoVs were similar to those found in the clinical samples at the same time.

CONCLUSIONS

The comparison of environmental and clinical data suggests that similar RV and NoV isolates were circulating in the environment and in the population during the same period.

SIGNIFICANCE AND IMPACT OF THE STUDY

Few studies have investigated the prevalence and the epidemiology of RVs and NoVs in Cairo. This work is the first to establish a correlation between viral gastroenteritis and the concomitant presence of enteric viruses in the environment for Greater Cairo where combined environmental and clinical surveys should help to prevent infections caused by these major pathogens.

Prevalence and genotypes of human noroviruses in tropical urban surface waters and clinical samples in Singapore

The prevalence and genotypes of norovirus genogroup I (GI) and GII in tropical urban catchment waters and an estuarine bay were studied. A comparative analysis was performed with environmental isolates of noroviruses and concurrently identified clinical isolates in Singapore during gastroenteritis outbreaks between August 2006 to January 2007. Noroviruses in environmental water samples were concentrated by using ultrafiltration techniques and then analyzed by reverse transcription-seminested PCR assay targeting the partial capsid region of noroviruses and DNA sequencing. Among the 60 water samples collected, noroviruses were detected in 43 (71.7%) of these samples. Of these 43 norovirus-positive samples, the coexistence of both GI and GII strains was identified in 23 (53.5%) water samples. The phylogenetic analysis revealed multiple genotypes of noroviruses GI and GII in environmental water samples. GI and GII strains were clustered into seven and nine (including two unclassified) genotypes, respectively. The major norovirus genotypes in environmental water samples were GI/2 and GI/4 and GII/4. Genotyping of the 21 norovirus-positive clinical samples showed that all of the strains belonged to the GII/4 cluster. The environmental and clinical norovirus GII/4 isolates showed high levels of nucleotide sequence identity to each other and to the novel GII/4 variant associated with global epidemics of gastroenteritis during 2006. This study suggests the emergence and circulation of multiple novel norovirus GI and GII genotypes in water environments. Further comprehensive surveillance of water environments for noroviruses and routine clinical reporting is warranted.