Concentration of norovirus during wastewater treatment and its impact on oyster contamination

A comparative study of human norovirus and human sapovirus contamination in oysters (Crassostrea gigas) tissues from physical markets and e-commerce platforms in Guangzhou, China

Human norovirus (HuNoV) and human sapovirus (HuSaV) are the common foodborne viruses that can be transmitted through the consumption of contaminated shellfish. With the rise of e-commerce, these platforms have become an important channel for Chinese consumers to purchase seafood products. However, the potential impact of this new commercial model on viral contamination necessitates further investigation. This study aimed to compare the levels of HuNoV and HuSaV contamination in oysters (Crassostrea gigas) sourced from physical markets and e-commerce platforms. From July 2021 to June 2022, we collected oysters from both online e-commerce platform (n = 108) and offline markets (n = 108) in Guangzhou to assess HuNoV and HuSaV contamination. The HuNoV contamination rate in oysters from offline markets (61.1%) was found to be higher than that from online e-commerce platforms (54.6%) (p > 0.05). The contamination rate of HuSaV was 16.7% in online e-commerce platforms and 18.5% in offline markets, with a significance level of p > 0.05. Except for the HuNoV GI contamination levels in oysters from offline platforms, which were predominantly in the range of 105 to 106 genome copies per gram (GC/g), the highest proportions of contamination for HuNoV GI (online platforms), HuNoV GII, and HuSaV in oysters were found to be in the range of 103-104 GC/g. Additionally, the prevalence of HuSaV was significantly higher in winter (p < 0.05), while the prevalence of HuNoV did not show seasonal differences. This study demonstrates the presence of HuNoV and HuSaV in oysters marketed online and offline, highlighting the high contamination rate of foodborne viruses in oysters.

Seasonality of enteric viruses and correlation of hepatitis a virus in wastewater with clinical cases

Human adenovirus F41 (HAdV-41), norovirus genogroup II (HNV-GII), rotavirus group A (RVA), and hepatitis A virus (HAV) are responsible for millions of illnesses every year in Canada. Wastewater-based epidemiology is one way to monitor the prevalence of these underreported (HAV) and non-reportable (HAdV-41, HNV-GII, RVA) food and waterborne enteric viruses. In this study, we monitored the presence of these four viruses in wastewater over 16 months from September 2022 until December 2023 using samples from two locations in southern Ontario. Viruses in 286 wastewater samples were concentrated using PEG precipitation and quantified using a multiplex RT-qPCR assay for HAdV-41, HNV-GII, and RVA, and a singleplex RT-qPCR assay for HAV. In agreement with historical clinical data, HNV-GII and RVA had seasonal peaks in wastewater in the winter (HNV-GII, up to 1.09 × 103 gene copies (GC)/mL) and spring (RVA, up to 1.20 × 102 GC/mL). The concentration of HAdV-41 in wastewater had a significant seasonal peak in the fall of 2022 (up to 4.65 × 104 GC/mL) that was not repeated in the fall of 2023. The detection of HAV in 24 of 127 samples was correlated with four clinical cases in one sewershed with a one-week wastewater lead time.

Protocol for detection of pathogenic enteric RNA viruses by regular monitoring of environmental samples from wastewater treatment plants using droplet digital PCR

BACKGROUND

The present comprehensive protocol is focused on the detection of pathogenic enteric RNA viruses, explicitly focusing on norovirus genogroup Ⅱ (GⅡ), astrovirus, rotavirus, Aichi virus, sapovirus, hepatitis A and E viruses in wastewater treatment plants through droplet digital PCR (ddPCR). Enteric viruses are of significant public health concern, as they are the leading cause of diseases like gastroenteritis. Regular monitoring of environmental samples, particularly from wastewater treatment plants, is crucial for early detection and control of these viruses. This research aims to improve the understanding of the prevalence and dynamics of enteric viruses in urban India and will serve as a model for similar studies in other regions. Our protocol's objective is to establish a novel ddPCR-based methodology for the detection and molecular characterization of enteric viruses present in wastewater samples sourced from Bhopal, India. Our assay is capable of accurately quantifying virus concentrations without standard curves, minimizing extensive optimization, and enhancing sensitivity and precision, especially for low-abundance targets.

METHODS

The study involves fortnightly collecting and analyzing samples from nine wastewater treatment plants over two years, ensuring comprehensive coverage and consistent data. Our study innovatively applies ddPCR to simultaneously detect and quantify enteric viruses in wastewater, a more advanced technique. Additionally, we will employ next-generation sequencing for detailed viral genome identification in samples tested positive for pathogenic viruses.

CONCLUSION

This study will aid in understanding these viruses' genetic diversity and mutation rates, which is crucial for developing tailored intervention strategies. The findings will be instrumental in shaping public health responses and improving epidemiological surveillance, especially in localities heaving sewage networks.

Monitoring viruses and beta-lactam resistance genes through wastewater surveillance during a COVID-19 surge in Suwon, South Korea

The present study reports data on a long-term campaign for monitoring SARS-CoV-2, norovirus, hepatitis A virus, and beta-lactam resistance genes in wastewater samples from a wastewater treatment plant during COVID-19 surge in Suwon, South Korea. Real-time digital PCR (RT-dPCR) assays indicated 100 % occurrence of all but hepatitis A virus and blaNDM gene in influent wastewater samples. CDC-N1 assay detected SARS-CoV-2 in all influent samples with an average log-transformed concentration of 5.1 ± 0.39 and the highest level at 6.02 gene copies/L. All samples were also positive for norovirus throughout the study with a mean concentration 5.67 ± 0.65 log10 gene copies/L. On the contrary, all treated wastewater (effluent) tested negative for both viruses' genetic materials. Furthermore, plasmid-mediated AmpC β-lactamases (PABLs) genes blaDHA, blaACC, and blaFOX, extended-spectrum β-lactamases (ESBLs) genes blaTEM and blaCTX, and Klebsiella pneumoniae carbapenemase (blaKPC) gene were measured at average concentrations of 7.05 ± 0.26, 5.60 ± 0.35, 7.82 ± 0.43, 8.38 ± 0.20, 7.64 ± 0.29, and 7.62 ± 0.41 log10 gene copies/L wastewater, respectively. Beta-lactam resistance genes showed strong correlations (r), the highest being 0.86 for blaKPC - blaFOX, followed by 0.82 for blaTEM - blaCTX and 0.79 for blaTEM - blaDHA. SARS-CoV-2 RNA occurrence in the wastewater was strongly associated (r = 0.796) with COVID-19 cases in the catchment during the initial study period of six months. A positive association of the SARS-CoV-2 RNA with the prevalence of COVID-19 cases showed a promising role of community-scale monitoring of pathogens to provide considerable early signals of infection dynamics. High concentrations of beta-lactam resistance genes in wastewater indicated a high concern for one of the biggest global health threats in South Korea and the need to find control measures. Moreover, antibiotic-resistance genes in treated wastewater flowing through water bodies and agricultural environments indicate further dissemination of antibiotic resistance traits and increasing microbial antibiotic resistance.

Evaluation of virus removal in membrane bioreactor (MBR) and conventional activated sludge (CAS) processes based on long-term monitoring at two wastewater treatment plants

The membrane bioreactor (MBR) process always offers better wastewater treatment than conventional activated sludge (CAS) treatment. However, the difference in their efficacy of virus reduction remains unknown. To investigate this, we monitored virus concentrations before and after MBR and CAS processes over 2 years. Concentrations of norovirus genotypes I and II (NoV GI and GII), aichivirus (AiV), F-specific RNA phage genotypes I, II, and III (GI-, GII-, and GIII-FRNAPHs), and pepper mild mottle virus (PMMoV) were measured by a quantitative polymerase chain reaction (qPCR) method at two municipal wastewater treatment plants (WWTPs A and B) in Japan. Virus concentration datasets containing left-censored data were estimated by using both maximum likelihood estimation (MLE) and robust regression on order statistics (rROS) approaches. PMMoV was the most prevalent at both WWTPs, with median concentrations of 7.5 to 8.8 log10 copies/L before treatment. Log10 removal values (LRVs) of all viruses based on means and standard deviations of concentrations before and after treatment were consistently higher following MBR than following CAS. We used NoV GII as a model pathogen in a quantitative microbial risk assessment of the treated water, and we estimated the additional reductions required following MBR and CAS processes to meet the guideline of 10-6 DALYs pppy for safe wastewater reuse.

Current decontamination challenges and potentially complementary solutions to safeguard the vulnerable seafood industry from recalcitrant human norovirus in live shellfish: Quo Vadis?

Safeguarding the seafood industry is important given its contribution to supporting our growing global population. However, shellfish are filter feeders that bioaccumulate microbial contaminants in their tissue from wastewater discharged into the same coastal growing environments leading to significant human disease outbreaks unless appropriately mitigated. Removal or inactivation of enteric viruses is very challenging particularly as human norovirus (hNoV) binds to specific histo-blood ligands in live oyster tissue that are consumed raw or lightly cooked. The regulatory framework that sets out use of clean seawater and UV disinfection is appropriate for bacterial decontamination at the post-harvest land-based depuration (cleaning) stage. However, additional non-thermal technologies are required to eliminate hNoV in live shellfish (particularly oysters) where published genomic studies report that low-pressure UV has limited effectiveness in inactivating hNoV. The use of the standard genomic detection method (ISO 15, 216-1:2017) is not appropriate for assessing the loss of infectious hNoV in treated live shellfish. The use of surrogate viral infectivity methods appear to offer some insight into the loss of hNoV infectiousness in live shellfish during decontamination. This paper reviews the use of existing and potentially other combinational treatment approaches to enhance the removal or inactivation of enteric viruses in live shellfish. The use of alternative and complementary novel diagnostic approaches to discern viable hNoV are discussed. The effectiveness and virological safety of new affordable hNoV intervention(s) require testing and validating at commercial shellfish production in conjunction with laboratory-based research. Appropriate risk management planning should encompass key stakeholders including local government and the wastewater industry. Gaining a mechanistic understanding of the relationship between hNoV response at molecular and structural levels in individually treated oysters as a unit will inform predictive modeling and appropriate treatment technologies. Global warming of coastal growing environments may introduce additional contaminant challenges (such as invasive species); thus, underscoring need to develop real-time ecosystem monitoring of growing environments to alert shellfish producers to appropriately mitigate these threats.

Integrating life cycle assessment with quantitative microbial risk assessment for a holistic evaluation of sewage treatment plant

An integrated approach was employed in the present study to combine life cycle assessment (LCA) with quantitative microbial risk assessment (QMRA) to assess an existing sewage treatment plant (STP) at Roorkee, India. The midpoint LCA modeling revealed that high electricity consumption (≈ 576 kWh.day^-1) contributed to the maximum environmental burdens. The LCA endpoint result of 0.01 disability-adjusted life years per person per year (DALYs pppy) was obtained in terms of the impacts on human health. Further, a QMRA model was developed based on representative sewage pathogens, including E. coli O157:H7, Giardia sp., adenovirus, norovirus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The public health risk associated with intake of pathogen-laden aerosols during treated water reuse in sprinkler irrigation was determined. A cumulative health risk of 0.07 DALYs pppy was obtained, where QMRA risks contributed 86 % of the total health impacts. The annual probability of illness per person was highest for adenovirus and norovirus, followed by SARS-CoV-2, E. coli O157:H7 and Giardia sp. Overall, the study provides a methodological framework for an integrated LCA-QMRA assessment which can be applied across any treatment process to identify the hotspots contributing maximum environmental burdens and microbial health risks. Furthermore, the integrated LCA-QMRA approach could support stakeholders in the water industry to select the most suitable wastewater treatment system and establish regulations regarding the safe reuse of treated water.

Coliphages as viral indicators in municipal wastewater: A comparison between the ISO and the USEPA methods based on a systematic literature review

The use of traditional faecal indicator bacteria as surrogate organisms for pathogenic viruses in domestic wastewater has been noted as a problematic as concentrations and removal rates of bacteria and viruses do not seem to correlate. In this sense, bacteriophages (phages) emerge as potential viral indicators, as they are commonly found in wastewater in high levels, and can be quantified using simple, fast, low-cost methods. Somatic and F-specific coliphages comprise groups of phages commonly used as indicators of water quality. There are two internationally recognised methods to detect and enumerate coliphages in water samples, the International Standardization Organization (ISO) and the US Environmental Protection Agency (USEPA) methods. Both methods are based on the lysis of specific bacterial host strains infected by phages. Within this context, this systematic literature review aimed at gathering concentrations in raw and treated domestic wastewater (secondary, biological treatment systems and post-treatment systems), and removal efficiencies of somatic and F-specific coliphages obtained by ISO and USEPA methods, and then compare both methods. A total of 33 research papers were considered in this study. Results showed that the ISO method is more commonly applied than the USEPA method. Some discrepancies in terms of concentrations and removal efficiencies were observed between both methods. Higher removal rates were observed for both somatic and F-specific coliphages in activated sludge systems when using the USEPA method compared to the ISO method; in other secondary (biological) treatment systems, this was observed only for F-specific coliphages. The use of different standardised methods available might lead to difficulties in obtaining and comparing phage data in different conditions and locations. Future research comparing both ISO and USEPA methods as well as viral and bacterial pathogens and indicators in WWTP is recommended.

Study on the Effect of Relaying on Norovirus Reduction from Crassostrea gigas Oysters

Norovirus (NoV) is the most important cause of seafood-borne gastroenteritis worldwide, mainly associated with the consumption of raw oysters. NoV is often present in oysters that comply with existing control standards for shellfish. Therefore, the improvement of post-harvest treatments and practices can represent one of the main strategies to reduce the incidence of viral diseases related to shellfish. This study aimed to investigate long-term relays for the reduction of NoV levels in live oysters, during the high-risk cold months, by transferring the oysters from a more contaminated site to two sites with lower NoV levels. The efficacy of relaying was evaluated by analyzing oyster samples collected at days 0 (T0) and 30 (T30) for NoV levels using a real-time quantitative PCR (RT-qPCR). The NoV level at the relay sites was consistently lower than at the harvest site. The relay process for 30 days in seawater with a lower NoV level resulted in a decrease in the NoV load compared to day 0 with significant reductions depending on the site and genogroup of NoV considered. These results suggest that long-term relaying of oysters to reduce NoV levels is promising and could help growers to improve oyster safety; however, further investigations are needed.

Impact of COVID-19 Nonpharmaceutical Interventions on the Extent of Norovirus Contamination in Oyster Production Areas in Ireland during Winter 2020 to 2021

ABSTRACT

A significant decrease in norovirus prevalence and concentration was observed in oyster production areas in Ireland during winter 2020 to 2021. Oyster production areas impacted by human wastewater discharges that had been undergoing norovirus surveillance since 2018 were investigated. Samples collected in the winter seasons of 2018 to 2019 and 2019 to 2020, prior to when the COVID-19 pandemic interventions were applied, showed a prevalence of 94.3 and 96.6%, respectively, and geometric mean concentrations of 533 and 323 genome copies per g, respectively. These values decreased significantly during the winter of 2020 to 2021 (prevalence of 63.2% and geometric concentration of below the limit of quantification), coinciding with the control measures to mitigate the transmission of severe acute respiratory syndrome coronavirus 2 of the genus Betacoronavirus. Divergence between norovirus GI and GII prevalence and concentrations was observed over the 3-year monitoring period. Norovirus GII was the dominant genogroup detected in winter 2020 to 2021, with over half of samples positive, although concentrations detected were significantly lower than prepandemic winters, with a geometric mean concentration of below the limit of quantification.

HIGHLIGHTS

Wastewater reuse for irrigation of produce: A review of research, regulations, and risks

The burden of disease caused by the contamination of ready-to-eat produce with common waterborne microbial pathogens suggests that irrigation supplies should be closely monitored and regulated. Simultaneously freshwater resources have become increasingly scarce worldwide while global demand continues to grow. Since the turn of the 20th century with the advent of modern wastewater treatment plants, the reuse of treated wastewater is considered a safe and viable water source for irrigation of ready-to-eat vegetables. However strict, and often costly, treatment regimens mean that only a fraction of the world's wastewater supplies are being put to reuse. The purpose of this review is to explore the available literature on the risks associated with reuse water for ready-to-eat produce production including different approaches to reducing those risks as the demand for reuse water increases. It is not the intent of the authors to determine which methods of treatment should be applied, which pathogens should be considered of greatest concern, or which regulations should be applied. Rather, it is meant to be a discussion of the evolving guidelines governing irrigation with reuse water, potential risks from known pathogens common to produce production and recommendations for improving the adoption of water reuse moving forward. To date, there is little evidence to suggest that adequately treated reuse water poses more risk for produce-related illness or outbreaks than other sources of irrigation water. However, multiple epidemiological and quantitative risk assessment models suggest that guidelines for the use of reuse water should be regionally specific and based on local growing practices, available technologies for wastewater treatment, and overall population health. Though research suggests water reuse is generally safe, the assumptions of risk are both personal and of public interest, they should be considered carefully before water reuse is either allowed or disallowed in produce production environments.

Back-estimation of norovirus infections through wastewater-based epidemiology: A systematic review and parameter sensitivity

The amount of norovirus RNA (Ribonucleic Acid) in raw wastewater, collected from a wastewater treatment plant (WWTP), can provide an indication of disease prevalence within the sampled catchment. However, an accurate back-estimation might be impeded by the uncertainties from in-sewer/in-sample degradation of viral RNA, variable shedding magnitude, and difficulties in measurement within raw wastewater. The current study reviewed the published literature regarding the factors of norovirus shedding, viral RNA decay in wastewater, and the occurrence of norovirus RNA in raw wastewater based on molecular detection. Sensitivity analysis for WBE back-estimation was conducted using the reported data of the factors mentioned above considering different viral loads in wastewater samples. It was found that the back-estimation is more sensitive to analytical detection uncertainty than shedding variability for norovirus. Although seasonal temperature change can lead to variation of decay rates and may influence the sensitivity of this pathogen-specific parameter, decay rates of norovirus RNA contribute negligibly to the variance in estimating disease prevalence, based on the available data from decay experiments in bulk wastewater under different temperatures. However, the effects of in-sewer transportation on viral RNA decay and retardation by sewer biofilms on pipe surfaces are largely unknown. Given the highest uncertainty from analytical measurement by molecular methods and complexity of in-sewer processes that norovirus experienced during the transportation to WWTP, future investigations are encouraged to improve the accuracy of viral RNA detection in wastewater and delineate viral retardation/interactions with wastewater biofilms in real sewers.

Recent Developments in Isothermal Amplification Methods for the Detection of Foodborne Viruses

Foodborne and enteric viruses continue to impose a significant public health and economic burden globally. As many of these viruses are highly transmissible, the ability to detect them portably, sensitively, and rapidly is critical to reduce their spread. Although still considered a gold standard for detection of these viruses, real time polymerase chain reaction (PCR)-based technologies have limitations such as limited portability, need for extensive sample processing/extraction, and long time to result. In particular, the limitations related to the susceptibility of real time PCR methods to potential inhibitory substances present in food and environmental samples is a continuing challenge, as the need for extensive nucleic acid purification prior to their use compromises the portability and rapidity of such methods. Isothermal amplification methods have been the subject of much investigation for these viruses, as these techniques have been found to be comparable to or better than established PCR-based methods in portability, sensitivity, specificity, rapidity, and simplicity of sample processing. The purpose of this review is to survey and compare reports of these isothermal amplification methods developed for foodborne and enteric viruses, with a special focus on the performance of these methods in the presence of complex matrices.

Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes

We investigated the potential use and quantification of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA (Adenovirus and crAssphage) and RNA enteric viruses (Pepper mild mottle virus, Norovirus genogroups GI and GII, Rotavirus Astrovirus, and Sapovirus) as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantified in the extracted samples via quantitative PCR using TaqMan assays. Overall, the average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.1023 and 0.9921) than the average gene copies assessed in the effluents for DNA and RNA viruses and uidA in terms of both volume and biomass. A significant reduction (p-value ≤ 0.0438) of Adenovirus and Noroviruses genogroups GI and GII was observed in activated sludge samples compared with those for raw sewage per volume. Higher GCNs of enteric viruses were observed in dewatered sludge samples compared to liquid samples in terms of volume (g of sample) and biomass (ng of nucleic acids). Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA, indicating that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Viruses such as Noroviruses genogroups GI and GII, and Rotavirus were detected during colder months. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used confidently as complementary viral indicators of human fecal pollution.

Risk Assessment of Norovirus Illness from Consumption of Raw Oysters in the United States and in Canada

Human norovirus (NoV) is the leading cause of foodborne illness in the United States and Canada. Bivalve molluscan shellfish is one commodity commonly identified as being a vector of NoV. Bivalve molluscan shellfish are grown in waters that may be affected by contamination events, tend to bioaccumulate viruses, and are frequently eaten raw. In an effort to better assess the elements that contribute to potential risk of NoV infection and illness from consumption of bivalve molluscan shellfish, the U.S. Department of Health and Human Services/Food and Drug Administration (FDA), Health Canada (HC), the Canadian Food Inspection Agency (CFIA), and Environment and Climate Change Canada (ECCC) collaborated to conduct a quantitative risk assessment for NoV in bivalve molluscan shellfish, notably oysters. This study describes the model and scenarios developed and results obtained to assess the risk of NoV infection and illness from consumption of raw oysters harvested from a quasi-steady-state situation. Among the many factors that influence the risk of NoV illness for raw oyster consumers, the concentrations of NoV in the influent (raw, untreated) and effluent (treated) of wastewater treatment plants (WWTP) were identified to be the most important. Thus, mitigation and control strategies that limit the influence from human waste (WWTP outfalls) in oyster growing areas have a major influence on the risk of illness from consumption of those oysters.

Systematic review of the relative concentrations of noroviruses and fecal indicator bacteria in wastewater: considerations for use in quantitative microbial risk assessment

Human noroviruses are a leading cause of food- and water-borne disease, which has led to an interest in quantifying norovirus health risks using quantitative microbial risk assessment (QMRA). Given the limited availability of quantitative norovirus data to input to QMRA models, some studies have applied a conversion factor to estimate norovirus exposure based on measured fecal indicator bacteria (FIB) concentrations. We conducted a review of peer-reviewed publications to identify the concentrations of noroviruses and FIB in raw, secondary-treated, and disinfected wastewater. A meta-analysis was performed to determine the ratios of norovirus-FIB pairs in each wastewater matrix and the variables that significantly impact these ratios. Norovirus-to-FIB ratios were found to be significantly impacted by the norovirus genotype, month of sample collection, geographic location, and the extent of wastewater treatment. Additionally, we evaluated the impact of using a FIB-to-virus conversion factor in QMRA and found that the choice of conversion ratio has a great impact on estimated health risks. For example, the use of a conversion ratio previously used in the World Health Organization Guidelines for the Safe Use of Wastewater, Excreta and Greywater predicted health risks that were significantly lower than those estimated with measured norovirus concentrations used as inputs. This work emphasizes the gold standard of using measured pathogen concentrations directly as inputs to exposure assessment in QMRA. While not encouraged, if one must use a FIB-to-virus conversion ratio to estimate norovirus dose, the ratio should be chosen carefully based on the target microorganisms (i.e., strain, genotype, or class), prevalence of disease, and extent of wastewater treatment.

Can shellfish be used to monitor SARS-CoV-2 in the coastal environment?

The emergence and worldwide spread of SARS-CoV-2 raises new concerns and challenges regarding possible environmental contamination by this virus through spillover of human sewage, where it has been detected. The coastal environment, under increasing anthropogenic pressure, is subjected to contamination by a large number of human viruses from sewage, most of them being non-enveloped viruses like norovirus. When reaching coastal waters, they can be bio-accumulated by filter-feeding shellfish species such as oysters. Methods to detect this viral contamination were set up for the detection of non-enveloped enteric viruses, and may need optimization to accommodate enveloped viruses like coronaviruses (CoV). Here, we aimed at assessing methods for the detection of CoV, including SARS-CoV-2, in the coastal environment and testing the possibility that SARS-CoV-2 can contaminate oysters, to monitor the contamination of French shores by SARS-CoV-2 using both seawater and shellfish. Using the porcine epidemic diarrhea virus (PEDV), a CoV, as surrogate for SARS-CoV-2, and Tulane virus, as surrogate for non-enveloped viruses such as norovirus, we assessed and selected methods to detect CoV in seawater and shellfish. Seawater-based methods showed variable and low yields for PEDV. In shellfish, the current norm for norovirus detection was applicable to CoV detection. Both PEDV and heat-inactivated SARS-CoV-2 could contaminate oysters in laboratory settings, with a lower efficiency than a calicivirus used as control. Finally, we applied our methods to seawater and shellfish samples collected from April to August 2020 in France, where we could detect the presence of human norovirus, a marker of human fecal contamination, but not SARS-CoV-2. Together, our results validate methods for the detection of CoV in the coastal environment, including the use of shellfish as sentinels of the microbial quality of their environment, and suggest that SARS-CoV-2 did not contaminate the French shores during the summer season.

Evaluation of Norovirus Reduction in Environmentally Contaminated Pacific Oysters During Laboratory Controlled and Commercial Depuration

Norovirus contamination of oysters is the lead cause of non-bacterial gastroenteritis and a significant food safety concern for the oyster industry. Here, norovirus reduction from Pacific oysters (Crassostrea gigas), contaminated in the marine environment, was studied in laboratory depuration trials and in two commercial settings. Norovirus concentrations were measured in oyster digestive tissue before, during and post-depuration using the ISO 15216-1 quantitative real-time RT-PCR method. Results of the laboratory-based studies demonstrate that statistically significant reductions of up to 74% of the initial norovirus GII concentration was achieved after 3 days at 17-21 °C and after 4 days at 11-15 °C, compared to 44% reduction at 7-9 °C. In many trials norovirus GII concentrations were reduced to levels below 100 genome copies per gram (gcg^-1; limit of quantitation; LOQ). Virus reduction was also assessed in commercial depuration systems, routinely used by two Irish oyster producers. Up to 68% reduction was recorded for norovirus GI and up to 90% for norovirus GII reducing the geometric mean virus concentration close to or below the LOQ. In both commercial settings there was a significant difference between the levels of reduction of norovirus GI compared to GII (p < 0.05). Additionally, the ability to reduce the norovirus concentration in oysters to < LOQ differed when contaminated with concentrations below and above 1000 gcg^-1. These results indicate that depuration, carried out at elevated (> 11 °C) water temperatures for at least 3 days, can reduce the concentration of norovirus in oysters and therefore consumer exposure providing a practical risk management tool for the shellfish industry.

SARS-CoV-2 from Urban to Rural Water Environment: Occurrence, Persistence, Fate, and Influence on Agriculture Irrigation. A Review

The novel coronavirus disease (COVID-19), originating from China, has rapidly crossed borders, infecting people worldwide. While its transmission may occur predominantly via aerosolization of virus-laden droplets, the possibility of other routes of contagion via the environment necessitates considerable scientific consideration. SARS-CoV-2 viral RNA has been detected in the feces of infected persons, and studies also have reported its occurrence in wastewater and surface water bodies. Therefore, water may be a possible route of virus outbreaks. Agricultural irrigation is the largest use of water globally, accounting for 70% of water use worldwide. Ensuring adequate water quality within irrigation practices is fundamental to prevent harm to plants and soils, maintain food safety, and protect public health. This review aims to gather information on possible SARS-CoV-2 transmission routes within urban and rural water environments, looking into the detection, persistence, and fate of SARS-CoV-2. Based on published literature, the effect of current treatment technologies in wastewater treatment plants (WWTPs) on SARS-CoV-2 inactivation has also been investigated. Preliminary research efforts that concentrated on SARS-CoV-2 indicate that the risk of virus transmission from the aquatic environment may currently be non-existent, although a few studies have reported the presence of SARS-CoV RNA in soils, whereas there are still no studies on the detection of SARS-CoV-2 in crops.

Metagenomics of Wastewater Influent from Southern California Wastewater Treatment Facilities in the Era of COVID-19

Sequencing wastewater may be useful for detecting pathogens and assaying microbial water quality. We concentrated, extracted, and sequenced nucleic acids from 17 composite influent wastewater samples spanning seven southern California wastewater treatment facilities in May 2020. Bacteria were the most proportionally abundant taxonomic group present, followed by viruses and archaea.

Performic Acid Disinfection of Municipal Secondary Effluent Wastewater: Inactivation of Murine Norovirus, Fecal Coliforms, and Enterococci

Performic acid (PFA) is an emerging disinfectant to inactivate bacterial and viral microorganisms in wastewater. In this study, the inactivation kinetics of murine norovirus (MNV) by PFA, in phosphate buffer and municipal secondary effluent wastewater, are reported for the first time. PFA decay followed first-order kinetics and the inactivation of MNV was governed by the exposure of microorganisms to PFA, i.e., the integral of the PFA concentration over time (integral CT or ICT). The extension of the Chick-Watson model, in the ICT domain, described well the reduction of MNV by PFA, with determined ICT-based inactivation rate constants, k_d, of 1.024 ± 0.038 L/(mg·min) and 0.482 ± 0.022 L/(mg·min) in phosphate buffer and wastewater, respectively, at pH 7.2. Furthermore, the simultaneous PFA inactivation of MNV and fecal indicators indigenously present in wastewater such as fecal coliforms and enterococci showed that 1-log reduction could be achieved with ICT of 2, 1.5, and 3.5 mg·min/L, respectively. When compared with the most commonly used peracid disinfectant of municipal wastewater, peracetic acid (PAA), the ICT requirements determined using the fitted ICT-based kinetic models were ∼20 times higher for PAA than PFA, indicating a much stronger inactivation power of the PFA molecule.

Environmental and Adaptive Changes Necessitate a Paradigm Shift for Indicators of Fecal Contamination

Changes in the occurrence, distribution, and seasonal variation of waterborne pathogens due to global climate change may increase the risk of human exposure to these microorganisms, thus heightening the need for more reliable surveillance systems. Routine monitoring of drinking water supplies and recreational waters is performed using fecal indicator microorganisms, such as Escherichia coli , Enterococcus spp., and coliphages. However, the presence and numbers of these indicators, especially E. coli and Enterococcus spp., do not correlate well with those of other pathogens, especially enteric viruses, which are a major cause of waterborne outbreaks associated with contaminated water and food, and recreational use of lakes, ponds, rivers, and estuarine waters. For that reason, there is a growing need for a surveillance system that can detect and quantify viral pathogens directly in water sources to reduce transmission of pathogens associated with fecal transmission. In this review, we present an updated overview of relevant waterborne enteric viruses that we believe should be more commonly screened to better evaluate water quality and to determine the safety of water use and reuse and of epidemiological data on viral outbreaks. We also discuss current methodologies that are available to detect and quantify these viruses in water resources. Finally, we highlight challenges associated with virus monitoring. The information presented in this review is intended to aid in the assessment of human health risks due to contact with water sources, especially since current environmental and adaptive changes may be creating the need for a paradigm shift for indicators of fecal contamination.

Molecular evolution of GII.P17-GII.17 norovirus associated with sporadic acute gastroenteritis cases during 2013-2018 in Zhoushan Islands, China

In this study, we investigated the molecular characteristics and spatio-temporal dynamics of GII.P17-GII.17 norovirus in Zhoushan Islands during 2013-2018. We collected 1849 samples from sporadic acute gastroenteritis patients between January 2013 and August 2018 in Zhoushan Islands, China. Among the 1849 samples, 134 (7.24%) samples were positive for human norovirus (HuNoV). The complete sequence of GII.17 VP1 gene was amplified from 31 HuNoV-positive samples and sequenced. A phylogenetic tree was constructed based on the full-length sequence of the VP1 gene. Phylogenetic analysis revealed that the GII.17 genotype detected during 2014-2018 belongs to the new GII.17 Kawasaki variant. Divergence analysis revealed that the time of the most recent common ancestor (TMRCA) of GII.17 in Zhoushan Islands was estimated to be between 1997 and 1998. The evolutionary rate of the VP1 gene of the GII.17 genotype norovirus was 1.14 × 10^-3 (95% HPD: 0.62-1.73 × 10^-3) nucleotide substitutions/site/year. The spatio-temporal diffusion analysis of the GII.17 genotype identified Hong Kong as the epicenter for GII.17 dissemination. The VP1 gene sequence of Zhoushan Island isolates correlated with that of Hong Kong and Japan isolates.

Evaluating the fate of bacterial indicators, viral indicators, and viruses in water resource recovery facilities

A year-long sampling campaign at nine water resource recovery facilities (WRRFs) was conducted to assess the treatability and fate of bacterial indicators, viral indicators, and viruses. Influent concentrations of viral indicators (male-specific and somatic coliphages) and bacterial indicators (Escherichia coli and enterococci) remained relatively constant, typically varying by one order of magnitude over the course of the year. Annual average bacterial indicator reduction ranged from 4.0 to 6.7 logs, and annual average viral indicator reduction ranged from 1.6 to 5.4 logs. Bacterial and viral indicator reduction depended on the WRRF's treatment processes, and bacterial indicator reduction was greater than viral indicator reduction for many processes. Viral reduction (adenovirus 41, norovirus GI, and norovirus GII) was more similar to viral indicator reduction than bacterial indicator reduction. Overall, this work suggests that viral indicator reduction in WRRFs is variable and depends on specific unit processes. Moreover, for the same unit treatment process, viral indicator reduction and bacterial indicator reduction can vary. PRACTITIONER POINTS: A year-long sampling campaign was conducted at nine water resource recovery facilities (WRRFs). The treatability and fate of bacterial indicators, viral indicators, and viruses were assessed. Viral indicator reduction in WRRFs is variable and depends on specific unit processes. For the same unit treatment process, viral indicator reduction and bacterial indicator reduction can vary.

Enhanced insights from human and animal host-associated molecular marker genes in a freshwater lake receiving wet weather overflows

This study investigated the magnitude of wet weather overflow (WWO)-driven sewage pollution in an urban lake (Lake Parramatta) located in Sydney, New South Wales, Australia. Water samples were collected during a dry weather period and after two storm events, and tested for a range of novel and established sewage- [Bacteroides HF183, crAssphage CPQ_056 and pepper mild mottle virus (PMMoV)] and animal feces-associated (Bacteroides BacCan-UCD, cowM2 and Helicobacter spp. associated GFD) microbial source tracking marker genes along with the enumeration of culturable fecal indicator bacteria (FIB), namely Escherichia coli (E. coli) and Enterococcus spp. The magnitude of general and source-specific fecal pollution was low in water samples collected during dry weather compared to storm events. The levels of HF183, crAssphage and PMMoV in water samples collected during storm events were as high as 6.39, 6.33 and 5.27 log10 GC/L of water, respectively. Moderate to strong positive correlations were observed among the quantitative occurrence of sewage-associated marker genes. The concentrations of HF183 and PMMoV in most storm water samples exceeded the risk benchmark threshold values established in the literature for primary contact recreators. None of the samples tested was positive for the cowM2 (cow) marker gene, while BacCan-UCD (dog) and GFD (avian) animal-associated markers were sporadically detected in water samples collected from both dry weather and storm events. Based on the results, the ongoing advice that swimming should be avoided for several days after storm events appears appropriate. Further research to determine the decay rates of sewage-associated marker genes in relation to each other and enteric viruses would help refine current advice. Microbial source tracking approaches employed in this study provided insights into sources of contamination over currently used FIB.

Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing

Noroviruses are a leading cause of epidemic and pandemic acute gastroenteritis (AGE) worldwide, and contaminated food and water are important routes for its transmission. Raw sewage has been used for viral surveillance to monitor the emergence of new norovirus strains with the potential to cause epidemics. In this study, we investigated norovirus occurrence and norovirus RNA levels in 156 samples collected from May 2013 to May 2014, across three different stages (52 samples each) of a wastewater treatment plant (WWTP) in Rio de Janeiro, Brazil. We also explored norovirus GII diversity in raw sewage samples by next-sequencing generation (NGS). In addition, we examined norovirus prevalence and molecular epidemiology from acute gastroenteritis cases. Using RT-qPCR, norovirus GI and GII was detected in 38.5% and 96.1% of raw sewage samples, 40.4% and 96.1% of primary effluent samples and 1.9% and 5.8% of final effluent samples, respectively. Norovirus RNA levels varied from 4 to 6.2 log₁₀ genome copies per litre (gc L^-1) for GI and from 4.4 to 7.3 log₁₀ gc L^-1 for GII. Using MiSeq NGS, we identified 13 norovirus genotypes over the one-year period, with six dominant capsid genotypes, including GII.4, GII.17, GII.5, GII.2, GII.3 and GII.1. GII.4 noroviruses were the most prevalent in wastewater samples (68.5%), and a similar trend was observed in AGE cases (71%). The emergent GII.17 was the second most prevalent genotype (14.3%) identified in the raw sewage samples, however, it was not detected in clinical cases. Due to the high burden of norovirus outbreaks and the lack of vaccine and antiviral drugs, it is essential to understand the genotypic diversity of norovirus at the population level. Complementary data obtained from both clinical and environmental (sewage) samples proved to be an effective strategy to monitor the circulation and emergence of norovirus epidemic genotypes.

A dynamic transport model for quantification of norovirus internalization in lettuce from irrigation water and associated health risk

Food production using recycled wastewater offers a sustainable way forward in light of limited freshwater resources. However, concerns of food safety should be addressed to protect public health. To this end, we developed a dynamic transport model to track norovirus from the irrigation water to the root and shoot of lettuce during the growth period. These processes were embodied in a system of ordinary differential equations that also incorporated plant growth, transpiration rate, viral attachment and detachment to culture media, viral decay, and plant barrier effects. Model parameters were either obtained from the literature or through fitting the model to experimental data from a study reporting human norovirus transport in hydroponically grown lettuce. The results showed that lettuce grown hydroponically resulted in a higher risk than lettuce grown in soil. In both cases, the risk predicted failed to meet the risk benchmarks established by the U.S. EPA and WHO. Viral attachment to growth media, such as the soil particles, was an important mechanism for risk reduction. A sensitivity analysis revealed that harvesting time and irrigation time are important factors influencing the viral loads in lettuce. Hence, this pathogen transport model provides a framework for investigating the effects of time and other factors on disease burdens from water reuse in agriculture, underscoring the utility of a dynamic model. In the absence of a routine monitoring of contaminants in the recycled irrigation water and food crops, a quantitative risk assessment based on objective scientific knowledge is the best approach to guide the policy decisions on water reuse practices.

Pandemic GII.4 Sydney and Epidemic GII.17 Kawasaki308 Noroviruses Display Distinct Specificities for Histo-Blood Group Antigens Leading to Different Transmission Vector Dynamics in Pacific Oysters

Noroviruses are the major cause of foodborne outbreaks of acute gastroenteritis, which are often linked to raw oyster consumption. Previous studies have suggested histo-blood group antigens (HBGA)-like structures in the oyster tissues as ligands for norovirus binding and persistence. To better understand how oysters function as vectors for the most common human noroviruses, we first tested the ability of the norovirus strains GI.1 West Chester, the pandemic GII.4 Sydney, and the epidemic GII.17 Kawasaki308 strains to interact with oyster tissues. Secondly, we explored how the HBGA preferences of these strains can affect their persistence in oyster tissues. We found limited HBGA expression in oyster tissues. HBGAs of A and H type 1 were present in the digestive tissues and palps of the Pacific oyster Crassostrea gigas, while the gills and mantle lacked any HBGA structures. By using Virus-like particles (VLPs), which are antigenically and morphologically similar to native virions, we were able to demonstrate that VLPs of GI.1 West Chester norovirus reacted with the digestive tissues and palps. Despite of the lack of HBGA expression in mantle, dominant GII.4 Sydney strain readily bound to all the oyster tissues, including the digestive tissues, gills, palps, and mantle. In contrast, no binding of the epidemic GII.17 Kawasaki308 VLPs to any of the investigated oyster tissues was observed. In synthetic HBGA and saliva-binding assays, GI.1 reacted with A type, H type, and Le^b (Lewis b) HBGAs. GII.4 Sydney VLPs showed a broad binding pattern and interacted with various HBGA types. Compared to GI.1 and GII.4 VLPs, the GII.17 Kawasaki308 VLPs only weakly associated with long-chain saccharides containing A type, B type, H type, and Le^b blood group epitopes. Our findings indicate that GI.1 and GII.4 noroviruses are likely to be concentrated in oysters, by binding to HBGA-like glycans, and therefore potentially leading to increased long term transmission. In regards to the GII.17 Kawasaki308 strain, we suggest that oysters can only function as short term transmission vector in periods of high environmental virus concentrations.

The Impact of Winter Relocation and Depuration on Norovirus Concentrations in Pacific Oysters Harvested from a Commercial Production Site

Oysters contaminated with norovirus present a significant public health risk when consumed raw. In this study, norovirus genome copy concentrations were determined in Pacific oysters (Magallana gigas) harvested from a sewage-impacted production site and then subjected to site-specific management procedures. These procedures consisted of relocation of oysters to an alternative production area during the norovirus high-risk winter periods (November to March) followed by an extended depuration (self-purification) under controlled temperature conditions. Significant differences in norovirus RNA concentrations were demonstrated at each point in the management process. Thirty-one percent of oyster samples from the main harvest area (Site 1) contained norovirus concentrations > 500 genome copies/g and 29% contained norovirus concentrations < 100 genome copies/g. By contrast, no oyster sample from the alternative harvest area (Site 2) or following depuration contained norovirus concentrations > 500 genome copies/g. In addition, 60 and 88% of oysters samples contained norovirus concentrations < 100 genome copies/g in oysters sampled from Site 2 and following depuration, respectively. These data demonstrate that site-specific management processes, supported by norovirus monitoring, can be an effective strategy to reduce, but not eliminate, consumer exposure to norovirus genome copies.

Weekly variations in norovirus genogroup II genotypes in Japanese oysters

Increased levels of norovirus contamination in oysters were reportedly associated with a gastroenteritis epidemic occurring upstream of an oyster farming area. In this study, we monitored the norovirus concentration in oysters weekly between November 2014 and March 2015 and investigated the statistical relationship between norovirus genogroup II (GII) concentrations in oyster and sewage samples and the number of gastroenteritis cases in the area using cross-correlation analysis. A peak correlation coefficient (R = 0.76) at a time lag of +1 week was observed between the number of gastroenteritis cases and norovirus GII concentrations in oysters, indicating that oyster contamination is correlated with the number of gastroenteritis cases with a 1-week delay. Moreover, weekly variations in norovirus GII genotypes in oysters were evaluated using pyrosequencing. Only GII.3 was detected in November and December 2014, whereas GII.17 and GII.4 were present from January to March 2015. GII.17 Kawasaki 2014 strains were detected more frequently than GII.4 Sydney 2012 strains in oyster samples, as previously observed in stool and sewage samples collected during the same study period in Miyagi, Japan. Our observations indicate that there is a time lag between the circulation of norovirus genotypes in the human population and the detection of those genotypes in oysters.

Impacts of virus processing on human norovirus GI and GII persistence during disinfection of municipal secondary wastewater effluent

Noroviruses cause significant global health burdens and waterborne transmission is a known exposure pathway. Chlorination is the most common method of disinfection for water and wastewater worldwide. The purpose of this study was to investigate the underlying causes for discrepancies in human norovirus (hNoV) resistance to free chlorine that have been previously published, and to assess hNoV GI and GII persistence during disinfection of municipal secondary wastewater (WW) effluent. Our results reveal that choice of hNoV purification methodology prior to seeding the viruses in an experimental water matrix influences disinfection outcomes in treatment studies. Common hNoV purification processes such as solvent extraction and 0.45-μm filtration were ineffective in removing high levels of organics introduced into water or wastewater samples when seeding norovirus positive stool. These methods resulted in experimental water matrices receiving an additional 190 mg/L as Cl₂ of 15-s chlorine demand and approximately 440 mg/L as Cl₂ of 30-min chlorine demand due to seeding norovirus positive stool at 1% w/v. These high organic loads impact experimental water chemistry and bias estimations of hNoV persistence. Advanced purification of norovirus positive stool using sucrose cushion ultracentrifugation and ultrafiltration reduced 15-s chlorine demands by 99% and TOC by 93% for loose (i.e. unformed diarrhea) stools. Using these methods, hNoV GI and GII persistence was investigated during free chlorination of municipal WW. A suite five of kinetic inactivation models was fit to viral reverse transcription-qPCR reduction data, and model predicted CT values for 1, 2, and 3 log₁₀ reduction of hNoV GI in municipal WW by free chlorine were 0.3, 2.1, and 7.8 mg-min/L, respectively. Model predicted CT values for reduction of hNoV GII in WW were 0.4, 2.0, and 7.0 mg-min/L, respectively. These results indicate that current WW treatment plant disinfection practices employing free chlorine are likely protective for public health with regards to noroviruses, and will achieve at least 3-log reduction of hNoV GI and GII RNA despite previous reports of high hNoV resistance.

Asymptomatic norovirus infection associated with swimming at a tropical beach: A prospective cohort study

Background

Swimming in fecally-contaminated waterbodies can result in gastrointestinal infections. However, the pathogenic microorganisms responsible are not well understood because sporadic cases of illness are not reported completely, exposure information is often not collected, and epidemiology studies rely on self-reported symptoms. Noroviruses are considered a likely cause because they are found in high densities in sewage, resistant to wastewater treatment and survive in the environment. In this study, saliva samples were collected from subjects at a beach in Puerto Rico and tested for evidence of norovirus-specific IgG responses as an indicator of incident norovirus infection.

Methods

Saliva samples were collected from 1298 participants using an oral swab. Samples were collected on the day of the beach visit (S1); after 10–12 days (S2); and after three weeks (S3). Saliva was tested for IgG responses to GI.1 and GII.4 noroviruses using a microsphere based multiplex salivary immunoassay. Immunoconversion was defined as a four-fold increase in median fluorescence intensity (MFI) from S1 to S2 with the S3 sample at least three times above the S1 MFI.

Results

Thirty-four subjects (2.6%) immunoconverted to GI.1 or GII.4 norovirus. Swimmers who immersed their head in water had a higher rate of immunoconversion (3.4%), compared to either non-swimmers (0.0%, p = 0.003) or waders and non-swimmers combined (0.4%, Odds Ratio: 5.07, 95% Confidence Interval:1.48–17.00). Immunoconversion was not associated with gastrointestinal symptoms.

Conclusions

This is the first study to demonstrate an association between swimming at a beach impacted by fecal contamination and asymptomatic norovirus infection. The findings implicate recreational water as potentially important transmission pathway for norovirus infection.

Oyster Contamination with Human Noroviruses Impacted by Urban Drainage and Seasonal Flooding in Vietnam

This study investigated the level of norovirus contamination in oysters collected at a lagoon receiving urban drainage from Hue City for 17 months (August 2015-December 2016). We also investigated the genetic diversity of norovirus GI and GII in oyster and wastewater samples by using pyrosequencing to evaluate the effect of urban drainage on norovirus contamination of oysters. A total of 34 oyster samples were collected at two sampling sites (stations A and B) in a lagoon. Norovirus GI was more frequently detected than GII (positive rate 79 vs. 41%). Maximum concentrations of GI and GII were 2.4 × 10⁵ and 2.3 × 10⁴ copies/g, respectively. Co-contamination with GI and GII was observed in 35% of samples. Norovirus GII concentration was higher at station A in the flood season than in the dry season (P = 0.04, Wilcoxon signed-rank test). Six genotypes (GI.2, GI.3, GI.5, GII.2, GII.3, and GII.4) were identified in both wastewater and oyster samples, and genetically similar or identical sequences were obtained from the two types of samples. These observations suggest that urban drainage and seasonal flooding contribute to norovirus contamination of oysters in the study area.

The application of bacteriophages as novel indicators of viral pathogens in wastewater treatment systems

Many wastewater treatment technologies have been shown to remove bacterial pathogens more effectively than viral pathogens and, in aquatic environments, levels of traditional faecal indicator bacteria (FIB) do not appear to correlate consistently with levels of human viral pathogens. There is, therefore, a need for novel viral indicators of faecal pollution and surrogates of viral pathogens, especially given the increasing importance of indirect and direct wastewater reuse. Potential candidates include bacteriophages (phages) and the study described here sought to elucidate the relationship between three groups of phages (somatic coliphages (SOMPH), F-RNA coliphages (F-RNAPH) and human-specific phages infecting B. fragilis (Bf124PH) - enumeration using double layer agar technique) and viral pathogens (human adenovirus (HuAdV) and norovirus (NoV) - enumeration using molecular methods) through full-scale municipal wastewater treatment processes. FIB (faecal coliforms (FC) and intestinal enterococci (ENT) - enumeration using membrane filtration) were also monitored. Samples were collected every fortnight, during a twelve-month period, at each stage of four full-scale wastewater treatment plants (WWTP) in southern England (two activated sludge (AS) and two trickling filter (TF) plants) (n = 360 samples). FIB and SOMPH were consistently found in all samples tested, whereas F-RNAPH, Bf124PH and HuAdV were less frequently detected, especially following AS treatment. The detection rate of NoV was low and consequently discussion of this group of viruses is limited. Concentrations of SOMPH and FIB were statistically higher (p value < 0.05) than concentrations of F-RNAPH, Bf124PH and HuAdV in raw wastewater. FIB were more effectively removed than phages in both systems. Removal rates of HuAdV were similar to those of phages at the secondary treatment stage of both systems. In TF systems, HuAdV were removed at the same rate as F-RNAPH, but at lower rates than SOMPH and Bf124PH. The findings suggest that phages (in particular SOMPH) are better indicators of the fate of viral pathogens in WWTP than existing FIB and that these organisms may have a useful role to play in future sanitation safety planning.

F-Specific RNA Bacteriophages, Especially Members of Subgroup II, Should Be Reconsidered as Good Indicators of Viral Pollution of Oysters

Norovirus (NoV) is the leading cause of gastroenteritis outbreaks linked to oyster consumption. In this study, we investigated the potential of F-specific RNA bacteriophages (FRNAPH) as indicators of viral contamination in oysters by focusing especially on FRNAPH subgroup II (FRNAPH-II). These viral indicators have been neglected because their behavior is sometimes different from that of NoV in shellfish, especially during the depuration processes usually performed before marketing. However, a significant bias needs to be taken into account. This bias is that, in the absence of routine culture methods, NoV is targeted by genome detection, while the presence of FRNAPH is usually investigated by isolation of infectious particles. In this study, by targeting both viruses using genome detection, a significant correlation between the presence of FRNAPH-II and that of NoV in shellfish collected from various European harvesting areas impacted by fecal pollution was observed. Moreover, during their depuration, while the long period of persistence of NoV was confirmed, a similar or even longer period of persistence of the FRNAPH-II genome, which was over 30 days, was observed. Such a striking genome persistence calls into question the relevance of molecular methods for assessing viral hazards. Targeting the same virus (i.e., FRNAPH-II) by culture and genome detection in specimens from harvesting areas as well as during depuration, we concluded that the presence of genomes in shellfish does not provide any information on the presence of the corresponding infectious particles. In view of these results, infectious FRNAPH detection should be reconsidered as a valuable indicator in oysters, and its potential for use in assessing viral hazard needs to be investigated.IMPORTANCE This work brings new data about the behavior of viruses in shellfish, as well as about the relevance of molecular methods for their detection and evaluation of the viral hazard. First, a strong correlation between the presence of F-specific RNA bacteriophages of subgroup II (FRNAPH-II) and that of norovirus (NoV) in shellfish impacted by fecal contamination has been observed when both viruses are detected using molecular approaches. Second, when reverse transcription-PCR and culture are used to detect FRNAPH-II in shellfish, it appears that the genomes of the viruses present a longer period of persistence than infectious virus, and thus, virus genome detection fails to give information about the concomitant presence of infectious viruses. Finally, this study shows that FRNAPH persist at least as long as NoV does. These data are major arguments to reconsider the potential of FRNAPH as indicators of shellfish viral quality.

A risk-based approach for developing standards for irrigation with reclaimed water

A generalised quantitative risk assessment (QRA) is developed to assess the potential harm to human health resulting from irrigation with reclaimed water. The QRA is conducted as a backward calculation starting from a pre-defined acceptable risk level at the receptor point (defined as an annual infection risk of 10^-4 for pathogens and by reference doses (RfD) for chemical hazards) and results in an estimate of the corresponding acceptable concentration levels of the given hazards in the effluent. In this way the QRA is designed to inform the level of water treatment required to achieve an acceptable risk level and help establish reclaimed water quality standards. The QRA considers the exposure of human receptors to microbial and chemical hazards in the effluent through various exposure pathways and routes depending on the specific irrigation scenario. By considering multiple pathways and routes, a number of key aspects relevant to estimating human exposure to recycled water can be accounted for, including irrigation and crop handling practices (e.g., non-edible vs edible, spray vs. drip, withholding time) and volumes consumed (directly vs indirectly). The QRA relies on a large number of inputs, many of which were found to be highly uncertain. A possibilistic approach, based on fuzzy set theory, was used to propagate the uncertain input values through the QRA model to estimate the possible range of hazard concentrations that are deemed acceptable/safe for reclaimed water irrigation. Two scenarios were considered: amenity irrigation and irrigation of ready-to-eat food crops, and calculations were carried out for six example hazards (norovirus, Cryptosporidium, cadmium, lead, PCB118 and naphthalene) and using UK-specific input values. The human health risks associated with using reclaimed water for amenity irrigation were overall deemed low, i.e. the calculated acceptable concentration levels for most of the selected hazards were generally far greater than levels typically measured in effluent from wastewater treatment plants; however the predicted acceptable concentration levels for norovirus and Cryptosporidium suggested that disinfection by UV may be required before use. It was found that stricter concentration standards were required for hazards that are more strongly bound to soil and/or are more toxic/infectious. It was also found that measures that reduce the amount of effluent directly ingested by the receptor would significantly reduce the risks (by up to 2 orders of magnitude for the two pathogens). The results for the food crop irrigation scenario showed that stricter concentration standards are required to ensure the effluent is safe to use. For pathogens, the dominant exposure route was found to be ingestion of effluent captured on the surface of the crops indicating that risks could be significantly reduced by restricting irrigation to the non-edible parts of the crop. The results also showed that the exposure to some organic compounds and heavy metals through plant uptake and attached soil particles could be high and possibly pose unacceptable risk to human health. For both scenarios, we show that the predicted acceptable concentration levels are associated with large uncertainty and discuss the implications this has for defining quality standards and how the uncertainty can be reduced.

Evaluation of Chlorine Treatment Levels for Inactivation of Human Norovirus and MS2 Bacteriophage during Sewage Treatment

This study examined the inactivation of human norovirus (HuNoV) GI.1 and GII.4 by chlorine under conditions mimicking sewage treatment. Using a porcine gastric mucin-magnetic bead (PGM-MB) assay, no statistically significant loss in HuNoV binding (inactivation) was observed for secondary effluent treatments of ≤25 ppm total chlorine; for both strains, 50 and 100 ppm treatments resulted in ≤0.8-log₁₀ unit and ≥3.9-log₁₀ unit reductions, respectively. Treatments of 10, 25, 50, and 100 ppm chlorine inactivated 0.31, 1.35, >5, and >5 log₁₀ units, respectively, of the norovirus indicator MS2 bacteriophage. Evaluation of treatment time indicated that the vast majority of MS2 and HuNoV inactivation occurred in the first 5 min for 0.2-μm-filtered, prechlorinated secondary effluent. Free chlorine measurements of secondary effluent seeded with MS2 and HuNoV demonstrated substantial oxidative burdens. With 25, 50, and 100 ppm treatments, free chlorine levels after 5 min of exposure ranged from 0.21 to 0.58 ppm, from 0.28 to 16.7 ppm, and from 11.6 to 53 ppm, respectively. At chlorine treatment levels of >50 ppm, statistically significant differences were observed between reductions for PGM-MB-bound HuNoV (potentially infectious) particles and those for unbound (noninfectious) HuNoV particles or total norovirus particles. While results suggested that MS2 and HuNoV (measured as PGM-MB binding) behave similarly, although not identically, both have limited susceptibility to chlorine treatments of ≤25 ppm total chlorine. Since sewage treatment is performed at ≤25 ppm total chlorine, targeting free chlorine levels of 0.5 to 1.0 ppm, these results suggest that traditional chlorine-based sewage treatment does not inactivate HuNoV efficiently.IMPORTANCE HuNoV is ubiquitous in sewage. A receptor binding assay was used to assess inactivation of HuNoV by chlorine-based sewage treatment, given that the virus cannot be routinely propagated in vitro Results reported here indicate that chlorine treatment of sewage is not effective for inactivating HuNoV unless chlorine levels are above those routinely used for sewage treatment.

Bacteriophage removal efficiency as a validation and operational monitoring tool for virus reduction in wastewater reclamation: Review

The multiple-barrier concept is widely employed in international and domestic guidelines for wastewater reclamation and reuse for microbiological risk management, in which a wastewater reclamation system is designed to achieve guideline values of the performance target of microbe reduction. Enteric viruses are one of the pathogens for which the target reduction values are stipulated in guidelines, but frequent monitoring to validate human virus removal efficacy is challenging in a daily operation due to the cumbersome procedures for virus quantification in wastewater. Bacteriophages have been the first choice surrogate for this task, because of the well-characterized nature of strains and the presence of established protocols for quantification. Here, we performed a meta-analysis to calculate the average log₁₀ reduction values (LRVs) of somatic coliphages, F-specific phages, MS2 coliphage and T4 phage by membrane bioreactor, activated sludge, constructed wetlands, pond systems, microfiltration and ultrafiltration. The calculated LRVs of bacteriophages were then compared with reported human enteric virus LRVs. MS2 coliphage LRVs in MBR processes were shown to be lower than those of norovirus GII and enterovirus, suggesting it as a possible validation and operational monitoring tool. The other bacteriophages provided higher LRVs compared to human viruses. The data sets on LRVs of human viruses and bacteriophages are scarce except for MBR and conventional activated sludge processes, which highlights the necessity of investigating LRVs of human viruses and bacteriophages in multiple treatment unit processes.

Environmental indicators of oyster norovirus outbreaks in coastal waters

This paper presents an artificial intelligence-based approach to identifying environmental indicators of oyster norovirus outbreaks in coastal waters. It was found that oyster norovirus outbreaks are generally linked to the extreme combination of antecedent environmental conditions characterized by low water temperature, low solar radiation, low gage height, low salinity, strong wind, and heavy precipitation. Among the six environmental indicators, the most important three indicators, including water temperature, solar radiation and gage height, are capable of explaining 77.7% of model-predicted oyster norovirus outbreaks while the extremely low temperature alone may explain 37.2% of oyster norovirus outbreaks. It is, therefore, recommended that water temperature in oyster harvesting areas be monitored in the cold season and particularly the extremely low temperature during a low gage height be used as the primary indicator of oyster norovirus outbreaks. The findings are of profound significance to reducing the public health risk of norovirus outbreaks associated with consumption of oysters.

Assessment and risk modeling of airborne enteric viruses emitted from wastewater reused for irrigation

Reclamation of wastewater (WW) for irrigation, after treatment represents a challenge that could alleviate pressure on water resources and address the increasing demand for agriculture. However, the risks to human health must be assessed, particularly those related to human enteric viruses that resist standard treatments in most wastewater treatment plants (WWTP). The risks associated with exposure to viral bioaerosols near WWTP and near agricultural plots irrigated with WW are poorly documented. The objectives of this study were to 1) better characterize human enteric viruses found in bioaerosols near a "standard WWTP" and over fields irrigated with treated WW and 2) propose a numeric model to assess the health risk to populations located close to the irrigated areas, with particular attention to norovirus, which is responsible for most viral gastroenteritis in France. Water and air samples were collected at various locations in the largest French WW-irrigated site near Clermont-Ferrand, at the WWTP entrance and after treatment, in the air above activated sludge basins, and above fields irrigated with WW. Various enteric viruses were found in the water samples collected both before and after treatment. Norovirus was the most abundant with >10e4 genome copies/l (GC/L) before treatment and ~10e3 GC/L after treatment. Low quantities (<10e3GC/m³) were detected in the air above active sludge pools and irrigated plots. Hepatitis E virus was detected in all sampled compartments. A quantitative microbial risk assessment (QMRA) approach, including a simplified atmospheric dispersion model, allowed assessment of norovirus infection risk. The Bayesian QMRA approach considered wind speed measurements over 21years, and the variability and uncertainty of all measurements throughout the chain up to the risk. The probability of infection within one year for the most exposed WWTP employees was >10e-4 for strong wind speed (≥3m/s) and a constant emission rate of 8e3 GC/m³/s. This probability decreases by 3 log when the distance to the emission source is doubled. This information can aid development of safe water reuse policies in terms of local setback distance and wind conditions for wastewater reuse.

Nanofluidic digital PCR for the quantification of Norovirus for water quality assessment

Sensitive detection of water- and foodborne enteric viruses is extremely relevant, especially due to the low concentrations in which they are found. Accurate and sensitive detection of Norovirus, the primary responsible for water- and foodborne outbreaks, is of particular importance. Quantification of Norovirus is commonly performed by quantitative RT-PCR (RT-qPCR). In recent years a new platform was developed, digital PCR, that quantifies without the need for a standard curve thus decreasing the errors associated with its utilization. The platform developed by LifeTechnologies, QuantStudio 3D Digital PCR is amongst the least studied digital platform and although it allows the direct detection of DNA targets it requires a two-step RT-PCR for the detection of RNA targets. In this work we developed a new protocol able to detect Norovirus using a one-step digital PCR reaction (RT-dPCR). The performance of the newly developed one-step digital PCR was compared to RT-qPCR for the detection of Norovirus genogroup I and genogroup II. The sensitivity of RT-dPCR was identical to that of RT-qPCR, and the quantitative data determined by both methods were not significantly different for most samples. This one-step absolute quantification approach is a useful tool to minimize the time spent currently using this particular platform to amplify viral RNA and to standardize quantification of enteric viruses in food and environmental samples. This study proved the usefulness of the newly developed RT-dPCR protocol for a sensitive and accurate detection of low-copy targets.

Bacteriophages as indicators of faecal pollution and enteric virus removal

Bacteriophages are an attractive alternative to faecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport, due to their closer morphological and biological properties. Based on a review of published data, we summarize densities of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in individual human waste, raw wastewater, ambient fresh and marine waters and removal through wastewater treatment processes utilizing traditional treatments. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the aquatic environment and provide an overview of the environmental factors affecting their survival. In summary, concentrations of bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Overall, our investigation indicates that bacteriophages may be adequate viral surrogates, especially in built systems, such as wastewater treatment plants.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacteriophage are alternative fecal indicators that may be better surrogates for viral pathogens than fecal indicator bacteria (FIB). This report offers a summary of the existing literature concerning the utility of bacteriophage as indicators of viral presence (fecal sources and surface waters) and persistence (in built infrastructure and aquatic environments). Our findings indicate that bacteriophage levels in all matrices examined are consistently lower than FIB, but similar to viral pathogens. Furthermore, in built infrastructure (e.g. wastewater treatment systems) bacteriophage closely mimic viral pathogen persistence suggesting they may be adequate sentinels of enteric virus removal.

Occurrence of norovirus in raw sewage - A systematic literature review and meta-analysis

Human noroviruses (NoV) are a leading cause of recreational waterborne illnesses and responsible for the majority of viral-associated gastrointestinal illnesses nationwide. We conducted a systematic literature review of published peer-reviewed publications to identify NoV density data in wastewater influent, and provided an approach for developing pathogen density distributions, using the NoV data. Literature review inclusion criteria included scope, study quality, and data availability. A non-parametric bootstrap statistical model was used to estimate the NoV distribution in wastewater influent. The approach used accounts for heterogeneity in study-specific distribution curves, sampling locations, and sampling season and provides a comprehensive representation of the data. Study results illustrate that pooling all of the available NoV data together in a meta-analysis provides a more comprehensive understanding of the technical literature than what could be appreciated from individual studies. The studies included in this analysis indicate a high density of NoV in wastewater influent (overall mean = 4.6 log₁₀ genome copies (GC)/liter (L)), with a higher density of NoV genogroup (G) II (overall mean = 4.9 log₁₀ GC/L) than for GI (overall mean = 4.4 log₁₀ GC/L for GI). The bootstrapping approach was also used to account for differences in seasonal and geographical occurrences of NoV GI and GII. The methods presented are reproducible and can be used to develop QMRA-ready density distributions for other viral pathogens in wastewater influent, effluent, and ambient waters. To our knowledge, our results are the first to quantitatively characterize seasonal and geographic differences, which could be particularly useful for future risk assessments.

Removal of human pathogenic viruses in a down-flow hanging sponge (DHS) reactor treating municipal wastewater and health risks associated with utilization of the effluent for agricultural irrigation

A down-flow hanging sponge (DHS) reactor has been developed as a cost-effective wastewater treatment system that is adaptable to local conditions in low-income countries. A pilot-scale DHS reactor previously demonstrated stable reduction efficiencies for chemical oxygen demand (COD) and ammonium nitrogen over a year at ambient temperature, but the pathogen reduction efficiency of the DHS reactor has yet to be investigated. In the present study, the reduction efficiency of a pilot-scale DHS reactor fed with municipal wastewater was investigated for 10 types of human pathogenic viruses (norovirus GI, GII and GIV, aichivirus, astrovirus, enterovirus, hepatitis A and E viruses, rotavirus, and sapovirus). DHS influent and effluent were collected weekly or biweekly for 337 days, and concentrations of viral genomes were determined by microfluidic quantitative PCR. Aichivirus, norovirus GI and GII, enterovirus, and sapovirus were frequently detected in DHS influent, and the log₁₀ reduction (LR) of these viruses ranged from 1.5 to 3.7. The LR values for aichivirus and norovirus GII were also calculated using a Bayesian estimation model, and the average LR (±standard deviation) values for aichivirus and norovirus GII were estimated to be 1.4 (±1.5) and 1.8 (±2.5), respectively. Quantitative microbial risk assessment was conducted to calculate a threshold reduction level for norovirus GII that would be required for the use of DHS effluent for agricultural irrigation, and it was found that LRs of 2.6 and 3.7 for norovirus GII in the DHS effluent were required in order to not exceed the tolerable burden of disease at 10^-4 and 10^-6 disability-adjusted life years loss per person per year, respectively, for 95% of the exposed population during wastewater reuse for irrigation.

Pyrosequencing Analysis of Norovirus Genogroup II Distribution in Sewage and Oysters: First Detection of GII.17 Kawasaki 2014 in Oysters

Norovirus GII.3, GII.4, and GII.17 were detected using pyrosequencing in sewage and oysters in January and February 2015, in Japan. The strains in sewage and oyster samples were genetically identical or similar, predominant strains belonging to GII.17 Kawasaki 2014 lineage. This is the first report of GII.17 Kawasaki 2014 in oysters.

Use of Mytilus edulis biosentinels to investigate spatial patterns of norovirus and faecal indicator organism contamination around coastal sewage discharges

Bivalve shellfish have the capacity to accumulate norovirus (NoV) from waters contaminated with human sewage. Consequently, shellfish represent a major vector for NoV entry into the human food chain, leading to gastrointestinal illness. Identification of areas suitable for the safe cultivation of shellfish requires an understanding of NoV behaviour upon discharge of municipal-derived sewage into coastal waters. This study exploited the potential of edible mussels (Mytilus edulis) to accumulate NoV and employed the ISO method for quantification of NoV within mussel digestive tissues. To evaluate the spatial spread of NoV from an offshore sewage discharge pipe, mesh cages of mussels were suspended from moorings deployed in a 9 km² grid array around the outfall. Caged mussels were retrieved after 30 days and NoV (GI and GII), total coliforms and E. coli enumerated. The experimentally-derived levels of NoV GI and GII in mussels were similar with total NoV levels ranging from 7 × 10¹ to 1.6 × 10⁴ genome copies g^-1 shellfish digestive gland (ΣGI + GII). NoV spread from the outfall showed a distinct plume which matched very closely to predictions from the tidally-driven effluent dispersal model MIKE21. A contrasting spatial pattern was observed for coliforms (range 1.7 × 10² to 2.1 × 10⁴ CFU 100 g^-1 shellfish tissue) and E. coli (range 0-1.2 × 10³ CFU 100 g^-1 shellfish tissue). These data demonstrate that hydrodynamic models may help inform effective exclusion zones for bivalve harvesting, whilst coliform/E. coli concentrations do not accurately reflect viral dispersal in marine waters and contamination of shellfish by sewage-derived viral pathogens.

Norovirus Dynamics in Wastewater Discharges and in the Recipient Drinking Water Source: Long-Term Monitoring and Hydrodynamic Modeling

Norovirus (NoV) that enters drinking water sources with wastewater discharges is a common cause of waterborne outbreaks. The impact of wastewater treatment plants (WWTPs) on the river Göta älv (Sweden) was studied using monitoring and hydrodynamic modeling. The concentrations of NoV genogroups (GG) I and II in samples collected at WWTPs and drinking water intakes (source water) during one year were quantified using duplex real-time reverse-transcription polymerase chain reaction. The mean (standard deviation) NoV GGI and GGII genome concentrations were 6.2 (1.4) and 6.8 (1.8) in incoming wastewater and 5.3 (1.4) and 5.9 (1.4) log₁₀ genome equivalents (g.e.) L^-1 in treated wastewater, respectively. The reduction at the WWTPs varied between 0.4 and 1.1 log₁₀ units. In source water, the concentration ranged from below the detection limit to 3.8 log₁₀ g.e. L^-1. NoV GGII was detected in both wastewater and source water more frequently during the cold than the warm period of the year. The spread of NoV in the river was simulated using a three-dimensional hydrodynamic model. The modeling results indicated that the NoV GGI and GGII genome concentrations in source water may occasionally be up to 2.8 and 1.9 log₁₀ units higher, respectively, than the concentrations measured during the monitoring project.