Norovirus and FRNA bacteriophage determined by RT-qPCR and infectious FRNA bacteriophage in wastewater and oysters

Evaluating approach uncertainties of quantitative detection of SARS-CoV-2 in wastewater: Concentration, extraction and amplification

Substantial uncertainties pose challenges to the accuracy of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) quantification in wastewater. We conducted a comprehensive evaluation of two concentration methods, three nucleic acid extraction methods, and the amplification performance of eight primer-probe sets. Our results showed that the two concentration methods exhibited similar recovery rates. Specifically, using a 30 kDa cut-off ultrafilter and a centrifugal force of 2500 g achieved the highest virus recovery rates (27.32 ± 8.06 % and 26.37 ± 7.77 %, respectively), with lower corresponding quantification uncertainties of 29.51 % and 29.47 % in ultrafiltration methods. Similarly, a 15 % PEG concentration with 1.5 M NaCl markedly improved virus recovery (26.76 ± 5.92 % and 28.47 ± 6.74 %, respectively), and reducing variation to 22.16 % and 23.66 % in the PEG precipitation method. Additionally, employing a vigorous bead-beating approach at 6 m/s during viral RNA extraction significantly increased RNA yield, with an efficiency reaching up to 82.18 %. Among the evaluated eight primer-probe sets, the E_Sarbeco primer-probe set provided the most stable and consistent quantitative results across various sample matrices. These findings are crucial for establishing robust viral quantification protocols and enhancing methodological precision for effective wastewater surveillance, enabling sensitive and precise detection of SARS-CoV-2.

Microcosm experiment investigating climate-induced thermal effects on human virus viability in seawater: qPCR vs capsid integrity for enhanced risk management

Climate change is intensifying extreme weather events in coastal areas, leading to more frequent discharge of untreated wastewater containing human viruses into coastal waters. This poses a health risk, especially during heatwaves when bathing activity increases. A study examined the survival and viability of seven common wastewater viruses in seawater at different temperatures. Viral genomes were quantified using direct qPCR, whilst viability was assessed using Capsid Integrity qPCR. Results showed that T90 values from direct qPCR were much higher than those from CI-qPCR, suggesting that risk mitigation should be based on viral integrity tests. All viruses remained potentially viable for at least 72 h in environmental seawater and longer in sterile artificial seawater, highlighting the importance of biotic processes in viral inactivation. Viral persistence decreased with increasing temperature. Whilst heatwaves may partially reduce risks from human viral pathogens in coastal waters, they do not eliminate them entirely.

Comprehensive analysis and assessment of exposure to enteric viruses and bacteria in shellfish

Shellfish species, including oysters, clams, and mussels, are extensively cultured in coastal waters. Its location is determined by factors such as nutrient availability, water temperature, tidal cycle, and the presence of contaminants such as Escherichia coli and enteric viruses. With the expansion and intensification of human activities at vicinities, the presence of anthropogenic contaminants has increased, threatening shellfish farms and consumer safety give the prevalent consumption of raw shellfish. This literature review aims to provide a comprehensive analysis of the dietary exposure and assess the risk associated with enteric viruses and bacteria detected in shellfish. The predominant bacteria and viruses detected in shellfish are reported, and the potential interrelation is discussed. The main characteristics of each contaminant and shellfish were reviewed for a more comprehensive understanding. To facilitate a direct estimation of exposure, the estimated daily intake (EDI) of bacteria was calculated based on the average levels of E. coli in shellfish, as reported in the literature. The mean daily ingestion of seafood in each of the five continents was considered. Asia exhibited the highest intake of contaminants, with an average of ±5.6 E. coli units/day.kg body weight in cockles. Simulations were conducted using recommended shellfish consumption levels established by state agencies, revealing significantly lower (p < 0.01) EDI for all continents compared to estimations based on recommended levels. This indicates a higher risk associated with healthy shellfish ingestion, potentially leading to increased intoxication incidents with a change in dietary habits. To promote a healthier lifestyle through increased shellfish consumptions, it is imperative to reduce the exposure of shellfish species to bacteria and enteric viruses. The conventional use of E. coli as the sole indicator for consumption safety and water quality in shellfish farms has been deemed insufficient. Instances where shellfish met E. coli limits established by state agencies were often found to be contaminated with human enteric viruses. Therefore, a holistic approach considering the entire production chain is necessary to support the shellfish industry and ensure food safety.

Study of Shellfish Growing Area During Normal Harvesting Periods and Following Wastewater Overflows in an Urban Estuary With Complex Hydrography

Viral testing combined with hydrographic studies is considered standard good practice in determining microbiological impacts on shellfish growing areas following wastewater overflows. In this study, norovirus genogroup I and II, indicators of viral contamination (F-RNA bacteriophage genogroup II (F-RNA GII), crAssphage, pepper mild mottle virus) and Escherichia coli were monitored during periods of normal harvesting and following overflows in two commercial shellfish growing areas in Otago Harbour (Aotearoa New Zealand). Dye tracing, drogue tracking and analysis of particle tracking modelling were also undertaken to assess the dispersion, dilution and time of travel of wastewater discharged from a pump station discharge that impacts the growing areas. Norovirus was not detected in any of the 218 shellfish samples tested. PMMoV and crAssphage were more prevalent than F-RNA GII as determined by RT-qPCR. The dye study indicated long residence time of the waters (≥5 days) in the embayment impacted by the discharge. No relationships were found between the concentrations of viral indicators or E. coli and wastewater dilution, distance between the discharge and the growing areas or time since the last overflow. For the three spills studied (≤327 m3), there was little evidence of microbiological impact on the growing areas. This was likely associated with a deep shipping channel that enhances water flushing in the harbour and reduces contaminant transport to the growing areas. We recommend flexibility in the approach for closure/reopening growing areas impacted by spills, particularly for small duration/volume spills and when norovirus is not present in the community.

Assessment of wastewater derived pollution using viral monitoring in two estuaries

Human wastewater-derived pollution of the environment is an emerging health risk that increases the number of waterborne and foodborne illnesses globally. To better understand and mitigate such health risks, we investigated the prevalence of faecal indicator bacteria, Escherichia coli, and indicator virus (crAssphage) along with human and animal enteric viruses (adenoviruses, noroviruses, sapoviruses, hepatitis E virus) in shellfish and water samples collected from two shellfish harvesting areas in the UK. Human noroviruses were detected at higher detection rates in oyster and water samples compared to mussels with peaks during the autumn-winter seasons. Human enteric viruses were sporadically detected during the warmer months, suggesting potential introduction by tourists following the relaxation of COVID-19 lockdown measures. Our results suggest that viral indicators are more suitable for risk assessment and source tracking than E. coli. The detection of emerging hepatitis and sapoviruses, support the need for comprehensive viral monitoring in shellfish harvesting areas.

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.

CrAssphage as an indicator of human-fecal contamination in water environment and virus reduction in wastewater treatment

Viral indicators of human-fecal contamination in wastewaters and environmental waters have been getting much attention in the past decade. Cross-assembly phage (crAssphage) is the most abundant DNA virus in human feces. Recently, the usefulness of crAssphage as a microbial source tracking and water quality monitoring tool for human-fecal contamination has been highlighted. Here, we conducted a comprehensive review on crAssphage in water, focusing on detection methodology, concentration range in various waters and wastewaters, specificity to human-fecal contamination, and reduction in wastewater treatment systems. This review highlights that crAssphage is globally distributed in wastewaters and various fecal-contaminated water bodies at high concentrations without seasonal fluctuations. CrAssphage is highly specific to human-fecal contamination and is rarely found in animal feces. It also has a good potential as a performance indicator to ensure virus reduction in wastewater treatment systems. Accordingly, crAssphage could be an effective tool for monitoring of human-fecal contamination and potential presence of fecal pathogenic microbes in environmental waters. Bridging the research gaps highlighted in this review would make crAssphage a powerful tool to support the control of water-related health risks.

Sewage surveillance for SARS-CoV-2: Molecular detection, quantification, and normalization factors

The presence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in wastewater systems provides a primary indication of the coronavirus disease 2019 (COVID-19) spread throughout communities worldwide. Droplet digital polymerase chain reaction (dd-PCR) or reverse transcription-polymerase chain reaction (RT-PCR) administration of SARS-CoV-2 in wastewaters provides a reliable and efficient technology for gathering secondary local-level public health data. Often the accuracy of prevalence estimation is hampered by many methodological issues connected with wastewater surveillance. Still, more studies are needed to use and create efficient approaches for deciphering the actual SARS-CoV-2 indication from noise in the specimens/samples. Nearly 39-65% of positive patients and asymptomatic carriers expel the virus through their faeces however, only ∼6% of the infected hosts eject it through their urine. COVID-19 positive patients can shed the remnants of the SARS-CoV-2 RNA virus within the concentrations ∼10³-10⁸ copies/L. However, it can decrease up to 10² copies/L in wastewaters due to dilution. Environmental virology and microbiology laboratories play a significant role in the identification and analysis of SARS-CoV-2 ribonucleic acid (RNA) in waste and ambient waters worldwide. Virus extraction or recovery from the wastewater (However, due to lack of knowledge, established procedures, and integrated quality assurance/quality control (QA/QC) approaches, the novel coronavirus RNA investigation for estimating current illnesses and predicting future outbreaks is insufficient and/or conducted inadequately. The present manuscript is a technical review of the various methods and factors considered during the identification of SARS-CoV-2 genetic material in wastewaters and/or sludge, including tips and tricks to be taken care of during sampling, virus concentration, normalization, PCR inhibition, and trend line smoothening when compared with clinically active/positive cases.

Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function

Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.

Application of crAssphage, F-RNA phage and pepper mild mottle virus as indicators of human faecal and norovirus contamination in shellfish

Shellfish growing waters contaminated with inadequately treated human wastewater is a major source of norovirus in shellfish and poses a significant human health risk to consumers. Microbial source tracking (MST) markers have been widely used to identify the source (s) of faecal contamination in water but data are limited on their use for shellfish safety. This study evaluated the source specificity, sensitivity, occurrence and concentration of three viral MST markers i.e. cross-assembly phage (crAssphage), F-specific RNA bacteriophage genogroup II (F-RNA phage GII) and pepper mild mottle virus (PMMoV) using animal faeces (n = 119; 16 animal groups), influent wastewater (n = 12), effluent wastewater (n = 16) and shellfish (n = 33). CrAssphage, F-RNA phage GII and PMMoV had source specific values of 0.97, 0.99 and 0.91, respectively. The sensitivity of MST markers was confirmed by their 100% detection frequency in influent wastewaters. The frequency of detection in effluent wastewater ranged from 81.3% (F-RNA phage GII) to 100% (PMMoV). Concentration of F-RNA phage GII was one log₁₀ (influent wastewater) and 2-3 log₁₀ (effluent wastewater) lower than crAssphage and PMMoV, respectively. Despite lower prevalence of F-RNA phage GII in oysters and mussels compared to crAssphage and PMMoV, concentrations of the three MST markers were similar in mussels. As an indicator of norovirus contamination in shellfish, crAssphage and PMMoV had greater predictive sensitivity (100%; [95% CI; 81.5%-100%)]) and F-RNA phage GII had greater predictive specificity (93.3%; [95% CI; 68.1%-99.8%]). In contrast, crAssphage and F-RNA phage GII have similar accuracy for predicting norovirus in shellfish, however, PMMoV significantly overestimated its presence. Therefore, a combination of crAssphage and F-RNA phage GII analysis of shellfish could provide a robust estimation of the presence of human faecal and norovirus contamination.

Viral indicators for tracking domestic wastewater contamination in the aquatic environment

Waterborne enteric viruses are an emerging cause of disease outbreaks and represent a major threat to global public health. Enteric viruses may originate from human wastewater and can undergo rapid transport through aquatic environments with minimal decay. Surveillance and source apportionment of enteric viruses in environmental waters is therefore essential for accurate risk management. However, individual monitoring of the >100 enteric viral strains that have been identified as aquatic contaminants is unfeasible. Instead, viral indicators are often used for quantitative assessments of wastewater contamination, viral decay and transport in water. An ideal indicator for tracking wastewater contamination should be (i) easy to detect and quantify, (ii) source-specific, (iii) resistant to wastewater treatment processes, and (iv) persistent in the aquatic environment, with similar behaviour to viral pathogens. Here, we conducted a comprehensive review of 127 peer-reviewed publications, to critically evaluate the effectiveness of several viral indicators of wastewater pollution, including common enteric viruses (mastadenoviruses, polyomaviruses, and Aichi viruses), the pepper mild mottle virus (PMMoV), and gut-associated bacteriophages (Type II/III FRNA phages and phages infecting human Bacteroides species, including crAssphage). Our analysis suggests that overall, human mastadenoviruses have the greatest potential to indicate contamination by domestic wastewater due to their easy detection, culturability, and high prevalence in wastewater and in the polluted environment. Aichi virus, crAssphage and PMMoV are also widely detected in wastewater and in the environment, and may be used as molecular markers for human-derived contamination. We conclude that viral indicators are suitable for the long-term monitoring of viral contamination in freshwater and marine environments and that these should be implemented within monitoring programmes to provide a holistic assessment of microbiological water quality and wastewater-based epidemiology, improve current risk management strategies and protect global human health.

Spatial and temporal profiles of enteric viruses in the coastal waters of Tokyo Bay during and after a series of rainfall events

Recreational activities in coastal waters that are polluted by enteric viruses can result in gastroenteritis etc. In this study, the pollution profiles of enteric viruses were examined in the coastal area of Tokyo Bay, Japan, by collecting 57 water samples from three different depths (0.5 m, 3.0 m, and 5.0 m) during and after a series of heavy rainfall events. Vertically spatial and temporal changes in the concentrations of NoV genogroup I (GI) and genogroup II (GII), pepper mild mottle virus (PMMoV), and Aichi virus (AiV) were determined using quantitative reverse transcription-polymerase chain reaction, while those of the bacterial indicator, Escherichia coli, and F-specific RNA bacteriophages (FRNA phages) were monitored using culture methods. PMMoV was highly abundant (1.4 × 10⁴-6.8 × 10⁶ genome copies/L), whereas the concentrations of the other enteric viruses were relatively low (AiV, 1.3 × 10²-2.9 × 10⁴; GI, 2.9 × 10-5.6 × 10³; GII, 2.5 × 10-1.2 × 10⁴ genome copies/L). All of the viruses showed lower fluctuations in concentration than E. coli, which increased up to 460-fold after the rainfall event and then decreased over the subsequent two weeks. The maximum vertical difference in E. coli concentration was observed immediately after the rainfall. The E. coli reached the surface and then gradually spread down, whereas the virus concentrations exhibited few fluctuations due to the remaining effects of the previous combined sewer overflows. These findings indicate that viruses have a relatively long retention period over fecal indicator bacteria in this coastal area.

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.

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.

A model for estimating pathogen variability in shellfish and predicting minimum depuration times

Norovirus is a major cause of viral gastroenteritis, with shellfish consumption being identified as one potential norovirus entry point into the human population. Minimising shellfish norovirus levels is therefore important for both the consumer’s protection and the shellfish industry’s reputation. One method used to reduce microbiological risks in shellfish is depuration; however, this process also presents additional costs to industry. Providing a mechanism to estimate norovirus levels during depuration would therefore be useful to stakeholders. This paper presents a mathematical model of the depuration process and its impact on norovirus levels found in shellfish. Two fundamental stages of norovirus depuration are considered: (i) the initial distribution of norovirus loads within a shellfish population and (ii) the way in which the initial norovirus loads evolve during depuration. Realistic assumptions are made about the dynamics of norovirus during depuration, and mathematical descriptions of both stages are derived and combined into a single model. Parameters to describe the depuration effect and norovirus load values are derived from existing norovirus data obtained from U.K. harvest sites. However, obtaining population estimates of norovirus variability is time-consuming and expensive; this model addresses the issue by assuming a ‘worst case scenario’ for variability of pathogens, which is independent of mean pathogen levels. The model is then used to predict minimum depuration times required to achieve norovirus levels which fall within possible risk management levels, as well as predictions of minimum depuration times for other water-borne pathogens found in shellfish. Times for Escherichia coli predicted by the model all fall within the minimum 42 hours required for class B harvest sites, whereas minimum depuration times for norovirus and FRNA+ bacteriophage are substantially longer. Thus this study provides relevant information and tools to assist norovirus risk managers with future control strategies.

Development of artificial intelligence approach to forecasting oyster norovirus outbreaks along Gulf of Mexico coast

This paper presents an artificial intelligence-based model, called ANN-2Day model, for forecasting, managing and ultimately eliminating the growing risk of oyster norovirus outbreaks. The ANN-2Day model was developed using Artificial Neural Network (ANN) Toolbox in MATLAB Program and 15-years of epidemiological and environmental data for six independent environmental predictors including water temperature, solar radiation, gage height, salinity, wind, and rainfall. It was found that oyster norovirus outbreaks can be forecasted with two-day lead time using the ANN-2Day model and daily data of the six environmental predictors. Forecasting results of the ANN-2Day model indicated that the model was capable of reproducing 19years of historical oyster norovirus outbreaks along the Northern Gulf of Mexico coast with the positive predictive value of 76.82%, the negative predictive value of 100.00%, the sensitivity of 100.00%, the specificity of 99.84%, and the overall accuracy of 99.83%, respectively, demonstrating the efficacy of the ANN-2Day model in predicting the risk of norovirus outbreaks to human health. The 2-day lead time enables public health agencies and oyster harvesters to plan for management interventions and thus makes it possible to achieve a paradigm shift of their daily management and operation from primarily reacting to epidemic incidents of norovirus infection after they have occurred to eliminating (or at least reducing) the risk of costly incidents.

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.

Development of genetic programming-based model for predicting oyster norovirus outbreak risks

Oyster norovirus outbreaks pose increasing risks to human health and seafood industry worldwide but exact causes of the outbreaks are rarely identified, making it highly unlikely to reduce the risks. This paper presents a genetic programming (GP) based approach to identifying the primary cause of oyster norovirus outbreaks and predicting oyster norovirus outbreaks in order to reduce the risks. In terms of the primary cause, it was found that oyster norovirus outbreaks were controlled by cumulative effects of antecedent environmental conditions characterized by low solar radiation, low water temperature, low gage height (the height of water above a gage datum), low salinity, heavy rainfall, and strong offshore wind. The six environmental variables were determined by using Random Forest (RF) and Binary Logistic Regression (BLR) methods within the framework of the GP approach. In terms of predicting norovirus outbreaks, a risk-based GP model was developed using the six environmental variables and various combinations of the variables with different time lags. The results of local and global sensitivity analyses showed that gage height, temperature, and solar radiation were by far the three most important environmental predictors for oyster norovirus outbreaks, though other variables were also important. Specifically, very low temperature and gage height significantly increased the risk of norovirus outbreaks while high solar radiation markedly reduced the risk, suggesting that low temperature and gage height were associated with the norovirus source while solar radiation was the primary sink of norovirus. The GP model was utilized to hindcast daily risks of oyster norovirus outbreaks along the Northern Gulf of Mexico coast. The daily hindcasting results indicated that the GP model was capable of hindcasting all historical oyster norovirus outbreaks from January 2002 to June 2014 in the Gulf of Mexico with only two false positive outbreaks for the 12.5-year period. The performance of the GP model was characterized with the area under the Receiver Operating Characteristic curve of 0.86, the true positive rate (sensitivity) of 78.53% and the true negative rate (specificity) of 88.82%, respectively, demonstrating the efficacy of the GP model. The findings and results offered new insights into the oyster norovirus outbreaks in terms of source, sink, cause, and predictors. The GP model provided an efficient and effective tool for predicting potential oyster norovirus outbreaks and implementing management interventions to prevent or at least reduce norovirus risks to both the human health and the seafood industry.

Characterization of Natural Organic Substances Potentially Hindering RT-PCR-Based Virus Detection in Large Volumes of Environmental Water

Quantitative detection of pathogenic viruses in the environmental water is essential for the assessment of water safety. It is known that some of natural organic substances interfere with virus detection processes, i.e., nucleic acid extraction and reverse transcription-PCR. Such substances are carried over into a sample after virus concentration. In this study, inhibitory substances in coastal water samples were characterized in view of their effects on efficiency of virus detection and property as organic matters. Among 81 samples tested, 77 (95%) showed low recoveries (<10%) of spiked murine norovirus. These recovery rates were correlated with the levels of organic matter present in virus concentrates as measured by ultraviolet absorbance at 254 nm (r = -0.70 - -0.71, p < 0.01). High-performance gel chromatography and fluorescence excitation-emission matrix spectroscopy revealed that organic fractions in the 10-100 kDa size range, which were not dominant in the original samples, and those possessing humic acid-like fluorescence properties were dominant in virus concentrates. The inhibitory effect was more pronounced during summer. Substances originating from seawater seemed to cause a more pronounced effect than those originating from wastewater. Our data highlight the previously unknown characteristics of natural inhibitory substances and are helpful in establishing an effective sample purification technique.

Determining the zone of impact of norovirus contamination in shellfish production areas through microbiological monitoring and hydrographic analysis

Norovirus (NoV) contamination of filter feeding bivalve shellfish is a well-recognised human health threat when shellfish are grown in sewage polluted waters. To date, the identification of high risk zones around sewage discharges in shellfish production areas (SPAs) has not been based on NoV data. This study utilised molecular methods for NoV analysis, combined with hydrographic studies, to determine the relationship between NoV concentrations in shellfish and sewage effluent dilution. Cages with mussels and oysters were placed at different distances downstream of sewage discharges in two coastal sites in England. The shellfish were tested for concentrations of NoV (genogroups I and II) and E. coli. Drogue tracking and dye tracing studies were conducted to quantify the dispersion and dilution of sewage effluent in the SPAs. Significant negative associations were found between both total concentrations of NoV (GI + GII) and E. coli and sewage effluent dilution in the SPAs. The total NoV concentrations predicted by the model at 300:1, 1000:1 and 5000:1 ratios of estuarine water to sewage effluent were 1200; 600; and 200 copies/g, respectively. The estimated area of NoV contamination varied according with local pollution source impacts and hydrographic characteristics. The results help to inform the derivation of sewage discharge buffer zones as a control measure for mitigating risk from human NoV contamination in SPAs.

Critical Review on the Public Health Impact of Norovirus Contamination in Shellfish and the Environment: A UK Perspective

We review the risk of norovirus (NoV) infection to the human population from consumption of contaminated shellfish. From a UK perspective, risk is apportioned for different vectors of NoV infection within the population. NoV spreads mainly by person-to-person contact or via unsanitary food handling. NoV also enters the coastal zone via wastewater discharges resulting in contamination of shellfish waters. Typically, NoV persists in the marine environment for several days, with its presence strongly linked to human population density, wastewater discharge rate, and efficacy of wastewater treatment. Shellfish bioaccumulate NoV and current post-harvest depuration is inefficient in its removal. While NoV can be inactivated by cooking (e.g. mussels), consumption of contaminated raw shellfish (e.g. oysters) represents a risk to human health. Consumption of contaminated food accounts for 3-11% of NoV cases in the UK (~74,000 cases/year), of which 16% are attributable to oyster consumption (11,800 cases/year). However, environmental and human factors influencing NoV infectivity remain poorly understood. Lack of standard methods for accurate quantification of infective and non-infective (damaged) NoV particles represent a major barrier, hampering identification of an appropriate lower NoV contamination limit for shellfish. Future management strategies may include shellfish quality assessment (at point of harvest or at point of supply) or harvesting controls. However, poor understanding of NoV inactivation in shellfish and the environment currently limits accurate apportionment and risk assessment for NoV and hence the identification of appropriate shellfish or environmental quality standards.

FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems

A particular challenge to water safety in populous intertropical regions is the lack of reliable faecal indicators to detect microbiological contamination of water, while the numerical relationships of specific viral indicators remain largely unexplored. The aim of this study was to investigate the numerical relationships of FRNA-bacteriophage genotypes, adenovirus 41, and human adenoviruses (HADV) in Mexican surface water systems to assess sewage contamination. We studied the presence of HADV, HADV41 and FRNA bacteriophage genotypes in water samples and quantified by qPCR and RT-qPCR. Virus and water quality indicator variances, as analyzed by principal component analysis and partial least squared regression, followed along the major percentiles of water faecal enterococci. FRNA bacteriophages adequately deciphered viral and point source water contamination. The strongest correlation for HADV was with FRNA bacteriophage type II, in water samples higher than the 50^th percentiles of faecal enterococci, thus indicating urban pollution. FRNA bacteriophage genotypes I and III virus indicator performances were assisted by their associations with electrical conductivity and faecal enterococci. In combination, our methods are useful for inferring water quality degradation caused by sewage contamination. The methods used have potential for determining source contamination in water and, specifically, the presence of enteric viruses where clean and contaminated water have mixed.

Rapid and sensitive method to assess human viral pollution in shellfish using infectious F-specific RNA bacteriophages: Application to marketed products

F-specific RNA bacteriophages (FRNAPH) have been used as indicators of environmental fecal pollution for many years. While FRNAPH subgroup I (FRNAPH-I) are not host specific, some FRNAPH-II and -III strains appear specific to human pollution. Because a close relationship has been observed between FRNAPH-II genome and human norovirus (NoV) in shellfish, and because FRNAPH infectivity can easily be investigated unlike that of NoV, the detection of human infectious FRNAPH could therefore provide a valuable tool for assessing viral risk. In this study, an integrated cell culture real-time RT-PCR method has been developed to investigate infectious FRNAPH subgroup prevalence in oysters. This rapid screening method appears more sensitive than E. coli or NoV genome detection, and allows an FRNAPH subgroup present in low concentrations (0.05 PFU/g of oyster) to be detected in the presence of another 1000 times more concentrated, without any dissection step. Its application to marketed oysters (n = 135) over a 1-year period has allowed to identify the winter peak classically described for NoV or FRNAPH accumulation. Infectious FRNAPH were detected in 34% of batches, and 7% were suspected of having a human origin. This approach may be helpful to evaluate oyster's depuration processes, based on an infectious viral parameter.

Risk factors for norovirus contamination of shellfish water catchments in England and Wales

This study examines the relationships between concentrations of human noroviruses (NoV) genogroups I (GI) and II (GII) and Escherichia coli monitored in oysters from 31 commercial harvesting areas on the coast of England and Wales from May 2009 to April 2011 and demographic, hydrometric, climatic and pollution source characteristics of upstream river catchments using multiple regression techniques. The predictive environmental factors for E. coli contamination in the oysters were rainfall (cumulative 7days before sampling) while the predictive factors for NoV (GI+GII) were water temperature, catchment area and the combined volume of continuous sewage discharges in the catchment. Oysters from cold waters (<5°C) had significantly higher NoV content than those from warmer waters (>10°C). The association with water temperature may be consequential on the seasonal prevalence of the virus in the community or linked with oyster metabolic function. In a group of 10 study sites, mean concentrations of NoV increased as the number of stormwater spills at those sites also increased. The results of this study could be used to evaluate the likely impact of sewerage infrastructure improvements in catchments at risk of NoV contamination and to help identify sites suitable for shellfish farming.

Human norovirus in untreated sewage and effluents from primary, secondary and tertiary treatment processes

Wastewater treatments are considered important means to control the environmental transmission of human norovirus (NoV). Information about NoV concentrations in untreated and treated effluents, their seasonality and typical removal rates achieved by different treatment processes is required to assess the effectiveness of sewage treatment processes in reducing human exposure to NoV. This paper reports on a characterisation of concentrations of NoV (genogroups I and II) in untreated sewage (screened influent) and treated effluents from five full scale wastewater treatment works (WwTW) in England. Results are shown for effluent samples characteristic of primary- (primary settlement, storm tank overflows), secondary- (activated sludge, trickling filters, humus tanks) and tertiary (UV disinfection) treatments. NoV occurrence in untreated sewage varied between years. This variation was consistent with the annual variation of the virus in the community as indicated by outbreak laboratory reports. Significant differences were found between mean NoV concentrations in effluents subject to different levels of treatment. Primary settlement achieved approximately 1 log10 removal for both genogroups. Concentrations of NoV and Escherichia coli in untreated sewage were of the same order of magnitude of those in storm tank overflows. Of the secondary treatments studied, activated sludge was the most effective in removing NoV with mean log10 removals of 3.11 and 2.34 for GI and GII, respectively. The results of this study provide evidence that monitoring of NoV in raw sewage or treated effluents could provide early warning of an elevated risk for NoV and potentially help prevent outbreaks through environmental exposure. They also provide evidence that elimination of stormwater discharges and improvement of the efficiency of activated sludge for NoV removal would be effective for reducing the risk of environmental transmission.

Relevance of F-Specific RNA Bacteriophages in Assessing Human Norovirus Risk in Shellfish and Environmental Waters

Human noroviruses (HuNoVs) are the main cause of shellfish-borne gastroenteritis outbreaks. In the absence of routine technical approaches allowing infectious particles to be detected, this viral pathogen is currently targeted by genome research, leading to difficult interpretations. In this study, we investigated the potential of F-specific RNA bacteriophages (FRNAPH) as fecal and viral contamination indicators in shellfish and water from a local harvesting area. FRNAPH were also used as microbial source tracking tools. Constraints imposed by detection limits are illustrated here by the detection of infectious FRNAPH in several samples in the absence of FRNAPH genomes. The opposite situation was also observed, likely explained by the persistence of the genomes being greater than infectivity. Similar considerations may be applied to HuNoVs, suggesting that HuNoV genome targeting is of limited relevance in assessing infectious risks. While FRNAPH did not provide any benefits compared to Escherichia coli as fecal pollution indicators in water, novel observations were made in shellfish: contrary to E. coli, a seasonal trend of infectious FRNAPH concentrations was observed. These concentrations were higher than those found in water, confirming bioaccumulation in shellfish. This study also underlines a relationship between the presence of HuNoV genomes and those of human-specific FRNAPH subgroup II (FRNAPH-II) in shellfish collected throughout Europe. Further research should be undertaken to evaluate FRNAPH potential as an indicator of the presence of infectious HuNoVs. To this end, shellfish involved in HuNoV-caused gastroenteritis outbreaks should be analyzed for the presence of infectious FRNAPH-II.

IMPORTANCE

This work provides new data about the use of F-specific RNA phages (FRNAPH) as a tool for evaluating fecal or viral contamination, especially in shellfish. In our case study, FRNAPH did not provide any benefits compared to E. coli as fecal pollution indicators in water but were found to be very useful in shellfish. Their concentrations in shellfish were higher than those found in the surrounding water, confirming bioaccumulation. This study also underlines a relationship between the presence of human norovirus genomes (HuNoVs) and those of FRNAPH subgroup II (FRNAPH-II). Considering that the two virus types have similar behaviors and since FRNAPH infectivity can be investigated, the specific detection of infectious FRNAPH-II could be regarded as an indication of the presence of infectious HuNoVs. The contribution of infectious human FRNAPH targeting for assessing the viral risk associated with HuNoVs in shellfish should thus be investigated.

Modeling and Prediction of Oyster Norovirus Outbreaks along Gulf of Mexico Coast

BACKGROUND

Oyster norovirus outbreaks often pose high risks to human health. However, little is known about environmental factors controlling the outbreaks, and little can be done to prevent the outbreaks because they are generally considered to be unpredictable.

OBJECTIVE

We sought to develop a mathematical model for predicting risks of oyster norovirus outbreaks using environmental predictors.

METHODS

We developed a novel probability-based Artificial Neural Network model, called NORF model, using 21 years of environmental and norovirus outbreak data collected from Louisiana oyster harvesting areas along the Gulf of Mexico coast, USA. The NORF model involves six input variables that were selected through stepwise regression analysis and sensitivity analysis.

RESULTS

We found that the model-based probability of norovirus outbreaks was most sensitive to gage height (the depth of water in an oyster bed) and water temperature, followed by wind, rainfall, and salinity, respectively. The NORF model predicted all historical oyster norovirus outbreaks from 1994 through 2014. Specifically, norovirus outbreaks occurred when the NORF model probability estimate was > 0.6, whereas no outbreaks occurred when the estimated probability was < 0.5. Outbreaks may also occur when the estimated probability is 0.5-0.6.

CONCLUSIONS

Our findings require further confirmation, but they suggest that oyster norovirus outbreaks may be predictable using the NORF model. The ability to predict oyster norovirus outbreaks at their onset may make it possible to prevent or at least reduce the risk of norovirus outbreaks by closing potentially affected oyster beds.

CITATION

Wang J, Deng Z. 2016. Modeling and prediction of oyster norovirus outbreaks along Gulf of Mexico coast. Environ Health Perspect 124:627-633; http://dx.doi.org/10.1289/ehp.1509764.

Removal of enteric viruses and Escherichia coli from municipal treated effluent by zebra mussels

Dreissena polymorpha is a widespread filter-feeder species, resistant to a broad range of environmental conditions and different types of pollutants,which has recently colonized Italian freshwaters. Although widely used to monitor pollution in freshwater environments, this species is also an important food source for some fish and water birds. It can also be used to concentrate or remove particulate organic matter to interrupt avian-to-human transmission of pollutants and control health risks for animals and humans. In this study, the accumulation/inactivation in D. polymorpha of human health-related spiked enteric viruses was described. The removal of endogenous Escherichia coli, the classical indicator of fecal contamination,was tested as well.Our preliminary lab-scale results demonstrate that zebra mussels can reduce significantly poliovirus titer after 24 h and rotavirus titer after 8 h. E. coli counts were also reduced in the presence of zebra mussels by about 1.5 log after 4 h and nearly completely after 24 h. The fate of the two enteric viruses after concentration by zebra mussels was also investigated after mechanical disruption of the tissues. To our knowledge, the accumulation from water and inactivation of human health-related enteric viruses by zebra mussels has never been reported.

Fate of Human Noroviruses in Shellfish and Water Impacted by Frequent Sewage Pollution Events

Knowledge of the fate of human noroviruses (NoV) in the marine environment is key to better controlling shellfish-related NoV gastroenteritis. We quantified NoV and Escherichia coli in sewage from storm tank discharges and treated effluent processed by a UV-disinfection plant following activated sludge treatment and studied the fate of these microorganisms in an oyster harvesting area impacted by frequent stormwater discharges and infrequent freshwater discharges. Oyster monitoring sites were positioned at intervals downstream from the wastewater treatment works (WwTW) outfall impacting the harvesting area. The decay rates of NoV in oysters as a function of the distance from the outfall were less rapid than those for E. coli that had concentrations of NoV of the same order of magnitude and were over 7 km away from the outfall. Levels of E. coli in oysters from more tidally influenced areas of the estuary were higher around high water than around low water, whereas tidal flows had no influence on NoV contamination in the oysters. The study provides comparative data on the contamination profiles and loadings of NoV and E. coli in a commercial oyster fishery impacted by a WwTW.

Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins

F-specific RNA bacteriophages (FRNAPH) have been widely studied as tools for evaluating fecal or viral pollution in water. It has also been proposed that they can be used to differentiate human from animal fecal contamination. While FRNAPH subgroup I (FRNAPH-I) and FRNAPH-IV are often associated with animal pollution, FRNAPH-II and -III prevail in human wastewater. However, this distribution is not absolute, and variable survival rates in these subgroups lead to misinterpretation of the original distribution. In this context, we studied FRNAPH distribution in urban wastewater and animal feces/wastewater. To increase the specificity, we partially sequenced the genomes of phages of urban and animal origins. The persistence of the genomes and infectivity were also studied, over time in wastewater and during treatment, for each subgroup. FRNAPH-I genome sequences did not show any specific urban or animal clusters to allow development of molecular tools for differentiation. They were the most resistant and as such may be used as fecal or viral indicators. FRNAPH-II's low prevalence and low sequence variability in animal stools, combined with specific clusters formed by urban strains, allowed differentiation between urban and animal pollution by using a specific reverse transcription-PCR (RT-PCR) method. The subgroup's resistance over time was comparable to that of FRNAPH-I, but its surface properties allowed higher elimination rates during activated-sludge treatment. FRNAPH-III's low sequence variability in animal wastewater and specific cluster formation by urban strains also allowed differentiation by using a specific RT-PCR method. Nevertheless, its low resistance restricted it to being used only for recent urban pollution detection. FRNAPH-IV was too rare to be used.

Distinct behaviors of infectious F-specific RNA coliphage genogroups at a wastewater treatment plant

The present study aimed to determine the differences in the behaviors of four F-specific RNA (F-RNA) coliphage genogroups (GI-GIV) during wastewater treatment. Raw sewage, aeration tank effluent, secondary-treated sewage, and return activated sludge were collected from a wastewater treatment plant in Japan at monthly intervals between March and December 2011 (n=10 each). F-specific coliphages were detected by plaque assay in all tested samples, with a concentration ranging from -0.10 to 3.66 log10 plaque-forming units/ml. Subsequently, eight plaques were isolated from each sample, followed by genogroup-specific reverse-transcription quantitative PCR (qPCR) for F-RNA coliphages and qPCR for F-specific DNA (F-DNA) coliphages. GI F-RNA coliphages were the most abundant in the secondary-treated sewage samples (73% of the plaque isolates), while GII F-RNA coliphages were the most abundant in the other three sample types (41-81%, depending on sample type). Based on the results of the quantification and genotyping, the annual mean concentrations of each F-specific coliphage type were calculated, and their reduction ratios during wastewater treatment were compared with those of indicator bacteria (total coliforms and Escherichia coli) and enteric viruses (human adenoviruses and GI and GII noroviruses). The mean reduction ratio of GI F-RNA coliphages was the lowest (0.93 log10), followed by those of the indicator bacteria and enteric viruses (1.59-2.43 log10), GII-GIV F-RNA coliphages (>2.60-3.21 log10), and F-DNA coliphages (>3.41 log10). These results suggest that GI F-RNA coliphages may be used as an appropriate indicator of virus reduction during wastewater treatment.

Environmental transmission of human noroviruses in shellfish waters

Human noroviruses (NoV) are the most common cause of epidemic gastroenteritis following consumption of bivalve shellfish contaminated with fecal matter. NoV levels can be effectively reduced by some sewage treatment processes such as activated sludge and membrane bioreactors. However, tertiary sewage treatment and substantial sewage dilution are usually required to achieve low concentrations of virus in shellfish. Most outbreaks have been associated with shellfish harvested from waters affected by untreated sewage from, for example, storm overflows or overboard disposal of feces from boats. In coastal waters, NoV can remain in suspension or associate with organic and inorganic matter and be accumulated by shellfish. Shellfish take considerably longer to purge NoV than fecal indicator bacteria when transferred from sewage-polluted estuarine waters to uncontaminated waters. The abundance and distribution of NoV in shellfish waters are influenced by the levels of sewage treatment, proximity of shellfish beds to sewage sources, rainfall, river flows, salinity, and water temperature. Detailed site-specific information on these factors is required to design measures to control the viral risk.

The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters

Anthropogenic activities have increased the load of faecal bacteria, pathogenic viruses and nutrients in rivers, estuaries and coastal areas through point and diffuse sources such as sewage discharges and agricultural runoff. These areas are used by humans for both commercial and recreational activities and are therefore protected by a range of European Directives. If water quality declines in these zones, significant economic losses can occur. Identifying the sources of pollution, however, is notoriously difficult due to the ephemeral nature of discharges, their diffuse source, and uncertainties associated with transport and transformation of the pollutants through the freshwater-marine interface. Further, significant interaction between nutrients, microorganisms and particulates can occur in the water column making prediction of the fate and potential infectivity of human pathogenic organisms difficult to ascertain. This interaction is most prevalent in estuarine environments due to the formation of flocs (suspended sediment) at the marine-freshwater interface. A range of physical, chemical and biological processes can induce the co-flocculation of microorganisms, organic matter and mineral particles resulting in pathogenic organisms becoming potentially protected from a range of biotic (e.g. predation) and abiotic stresses (e.g. UV, salinity). These flocs contain and retain macro- and micro- nutrients allowing the potential survival, growth and transfer of pathogenic organisms to commercially sensitive areas (e.g. beaches, shellfish harvesting waters). The flocs can either be transported directly to the coastal environment or can become deposited in the estuary forming cohesive sediments where pathogens can survive for long periods. Especially in response to storms, these sediments can be subsequently remobilised releasing pulses of potential pathogenic organisms back into the water column leading to contamination of marine waters long after the initial contamination event occurred. Further work, however, is still required to understand and predict the potential human infectivity of pathogenic organisms alongside the better design of early warning systems and surveillance measures for risk assessment purposes.