Human norovirus RNA persists in seawater under simulated winter conditions but does not bioaccumulate efficiently in Pacific Oysters (Crassostrea gigas)

The coagulation process for enveloped and non-enveloped virus removal in turbid water: Removal efficiencies, mechanisms and its application to SARS-CoV-2 Omicron BA.2

The coagulation process has a high potential as a treatment method that can handle pathogenic viruses including emerging enveloped viruses in drinking water treatment process which can lower infection risk through drinking water consumption. In this study, a surrogate enveloped virus, bacteriophage Փ6, and surrogate non-enveloped viruses, including bacteriophage MS-2, T4, ՓX174, were used to evaluate removal efficiencies and mechanisms by the conventional coagulation process with alum, poly‑aluminum chloride, and ferric chloride at pH 5, 7, and 9 in turbid water. Also, treatability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a recent virus of global concern by coagulation was evaluated as SARS-CoV-2 can presence in drinking water sources. It was observed that an increase in the coagulant dose enhanced the removal efficiency of turbidity and viruses, and the condition that provided the highest removal efficiency of enveloped and non-enveloped viruses was 50 mg/L of coagulants at pH 5. In addition, the coagulation process was more effective for enveloped virus removal than for the non-enveloped viruses, and it demonstrated reduction of SARS-CoV-2 Omicron BA.2 over 0.83-log with alum. According to culture- and molecular-based assays (qPCR and CDDP-qPCR), the virus removal mechanisms were floc adsorption and coagulant inactivation. Through inactivation with coagulants, coagulants caused capsid destruction, followed by genome damage in non-enveloped viruses; however, damage to a lipid envelope is suggested to contribute to a great extend for enveloped virus inactivation. We demonstrated that conventional coagulation is a promising method for controlling emerging and re-emerging viruses in drinking water.

Temperature and particles interact to affect human norovirus and MS2 persistence in surface water

Modeling the fate and transport of viruses and their genetic material in surface water is necessary to assess risks associated with contaminated surface waters and to inform environmental surveillance efforts. Temperature has been identified as a key variable affecting virus persistence in surface waters, but the effects of the presence of biological and inert particles and of their interaction with temperature have not been well characterized. We assessed these effects on the persistence of human norovirus (HuNoV) genotype II.4 purified from stool and MS2 in surface water. Raw or filter-sterilized creek water microcosms were inoculated and incubated in the dark at 10 °C, 15 °C, and 20 °C. HuNoV (i.e., genome segments and intact capsids) and MS2 (i.e., infectious MS2, genome segments, and intact capsids) concentrations were followed over 36 days. The range in positive, significant first-order decay rate constants for HuNoV in this study was 0.14 to 0.69 day-1 compared with 0.026 to 0.71 day-1 for that of MS2. Decay rate constants for HuNoV genome segments and infectious MS2 were largest in creek water that included biological and inert particles and incubated at higher temperatures. In addition, for HuNoV and MS2 incubated in raw or filter-sterilized creek water at 15 °C, capsid damage was not identified as a dominant inactivation mechanism. Environmental processes and events that affect surface water biological and inert particles, temperature, or both could lead to variable virus decay rate constants. Incorporating the effects of particles, temperature, and their interaction could enhance models of virus fate and transport in surface water.

Persistence of Human Norovirus (GII) in Surface Water: Decay Rate Constants and Inactivation Mechanisms

Human norovirus (HuNoV) is an important cause of acute gastroenteritis and can be transmitted by water exposures, but its persistence in water is not well understood. Loss of HuNoV infectivity in surface water was compared with persistence of intact HuNoV capsids and genome segments. Surface water from a freshwater creek was filter-sterilized, inoculated with HuNoV (GII.4) purified from stool, and incubated at 15 or 20 °C. We measured HuNoV infectivity via the human intestinal enteroid system and HuNoV persistence via reverse transcription-quantitative polymerase chain reaction assays without (genome segment persistence) or with (intact viral capsid persistence) enzymatic pretreatment to digest naked RNA. For infectious HuNoV, results ranged from no significant decay to a decay rate constant ("k") of 2.2 day^-1. In one creek water sample, genome damage was likely a dominant inactivation mechanism. In other samples from the same creek, loss of HuNoV infectivity could not be attributed to genome damage or capsid cleavage. The range in k and the difference in the inactivation mechanism observed in water from the same site could not be explained, but variable constituents in the environmental matrix could have contributed. Thus, a single k may be insufficient for modeling virus inactivation in surface waters.

Mega-scale desalination Efficacy (Reverse Osmosis, Electrodialysis, Membrane Distillation, MED, MSF) during COVID-19: Evidence from salinity, pretreatment methods, temperature of operation

The unprecedented situation of the COVID-19 pandemic heavily polluted water bodies whereas the presence of SARS-CoV-2, even in treated wastewater in every corner of the world is reported. The main aim of the present study is to show the effectiveness and feasibility of some well-known desalination technologies which are reverse osmosis (RO), Electrodialysis (ED), Membrane Distillation (MD), multi effect distillation (MED), and multi stage flashing (MSF) during the COVID-19 pandemic. Systems’ effectiveness against the novel coronavirus based on three parameters of nasopharynx/nasal saline-irrigation, temperature of operation and pretreatment methods are evaluated. First, based on previous clinical studies, it showed that using saline solution (hypertonic saline >0.9% concentration) for gargling/irrigating of nasal/nasopharynx/throat results in reducing and replication of the viral in patients, subsequently the feed water of desalination plants which has concentration higher than 3.5% (35000ppm) is preventive against the SARS-CoV-2 virus. Second, the temperature operation of thermally-driven desalination; MSF and MED (70-120°C) and MD (55-85°C) is high enough to inhibit the contamination of plant structure and viral survival in feed water. The third factor is utilizing various pretreatment process such as chlorination, filtration, thermal/precipitation softening, ultrafiltration (mostly for RO, but also for MD, MED and MSF), which are powerful treatment methods against biologically-contaminated feed water particularly the SARS-CoV-2. Eventually, it can be concluded that large-scale desalination plants during COVID-19 and similar situation are completely reliable for providing safe drinking water.

Use of F-Specific RNA Bacteriophage to Estimate Infectious Norovirus Levels in Oysters

Contamination of bivalve shellfish, particularly oysters, with norovirus is recognised as a significant food safety risk. Methods for quantification of norovirus in oysters using the quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) are well established, and various studies using RT-qPCR have detected norovirus in a considerable proportion of oyster samples, both in the UK and elsewhere. However, RT-qPCR detects viral genome, and by its nature is unable to discriminate between positive results caused by infectious viruses and those caused by non-infectious remnants including damaged virus particles and naked RNA. As a result, a number of alternative or complementary approaches to RT-qPCR testing have been proposed, including the use of infectious viral indicator organisms, most frequently F-specific RNA bacteriophage (F-RNA phage). In this study, we investigated the relationships between F-RNA phage and norovirus in digestive tissues from two sets of oyster samples, one randomly collected at retail (630 samples), and one linked to suspected norovirus illness outbreaks (nine samples). A positive association and correlation between PCR-detectable levels of genogroup II F-RNA bacteriophage (associated with human faecal contamination) and norovirus was found in both sets of samples, with more samples positive for genogroup II phage, at generally higher levels than norovirus. Levels of both viruses were higher in outbreak-related than retail samples. Infectious F-RNA phage was detected in 47.8% of all retail samples, and for a subset of 224 samples where characterisation of phage was carried out, infectious GII phage was detected in 30.4%. Infectious GII phage was detected in all outbreak-related samples. Determination of infectivity ratios by comparing levels of PCR-detectable (copies/g) and infectious GII phage (pfu/g) revealed that in the majority of cases less than 10% of virus detected by RT-qPCR was infectious. Application of these ratios to estimate infectious norovirus levels indicated that while 77.8% of outbreak-related samples contained > 5 estimated infectious norovirus/g, only 13.7% of retail samples did. Use of a combination of levels of PCR-detectable norovirus and infectious F-RNA phage showed that while only 7.0% of retail samples contained both > 100 copies/g norovirus and > 10 pfu/g F-RNA phage, these combined levels were present in 77.8% of outbreak-related samples, and 75.9% of retail samples with > 5 estimated infectious norovirus/g. We therefore suggest that combining RT-qPCR testing with a test for infectious F-RNA phage has the potential to better estimate health risks, and to better predict the presence of infectious norovirus than RT-qPCR testing alone.

Analysis of the European baseline survey of norovirus in oysters

The European Commission requested scientific technical assistance for the analysis of a European Union coordinated monitoring programme on the prevalence of norovirus in raw oysters. A total of 2,180 valid samples were taken from production areas and 2,129 from dispatch centres, taken over two consecutive years, ensuring the precision and the confidence desired in the estimation. The prevalence at production areas was estimated to be 34.5% (CI: 30.1-39.1%), while for batches from dispatch centres it was 10.8% (CI: 8.2-14.4%). The analyses show a strong seasonal effect, with higher contamination in the period November to April, as well as lower contamination for Class A areas than other classes. These associations were observed in both production areas and batches from dispatch centres. The results for both genogroups were above the respective limit of quantification (LOQ) in less than 10% of the samples taken. The simple substitution of not-detected and positive samples below the LOQ, by half of the limit of detection and half of the LOQ, respectively, produced estimates of the proportion of samples above or equal to 300 copies per gram (cpg) comparable to the statistical model. The current bacteriological microbiological criteria applicable to live bivalve molluscs might be complemented by a norovirus criterion. The analyses of the substitution approach show that selection of a potential limit within a microbiological criterion close to or lower than the LOQ (for example, less than 300 cpg, given the current test used in this survey) would be difficult to apply. This survey only assessed thresholds from the perspective of the analytical capability and not that of human health risk.

Aquatic fate of a double-stranded RNA in a sediment---water system following an over-water application

Determining the rate of biodegradation of double-stranded RNA (dsRNA) in the environment is an essential element of a comprehensive risk assessment of an RNA-based agricultural product. This information is used during problem formulation to define relevant routes and durations of environmental exposure for in planta-expressed dsRNA. Although exposure to biotechnology-derived crops expressing dsRNA traits in the aquatic environment is predicted to be minimal, little is known regarding the fate of dsRNA in these environments. To assess exposure to aquatic environments, a study was conducted to measure the rate of biodegradation of DvSnf7 dsRNA in aerobic water-sediment systems. Aquatic systems containing natural water and sediments that varied in physical and chemical characteristics were treated with dsRNA by applying DvSnf7 dsRNA directly to the water column. In the present study, DvSnf7 dsRNA dissipated rapidly from the water phase and was undetectable within 7 d as measured by QuantiGene (Affymetrix) and a sensitive insect bioassay in these diverse systems. Degradation kinetics estimated a half-life (time to 50% dissipation [DT50]) of less than 3 d and a time to 90% dissipation of approximately 4 d. Further analysis indicated that DvSnf7 dsRNA had DT50 values of less than 6 d in both sediment-free systems containing natural water and systems with only sediment. Taken together, the results of the present study indicate that dsRNA-based agricultural products rapidly degrade and consequently are unlikely to persist in aquatic environments. Environ Toxicol Chem 2017;36:727-734. © 2016 SETAC.

An Outbreak of Norovirus Infection from Shellfish Soup Due to Unforeseen Insufficient Heating During Preparation

Norovirus causes large outbreaks involving all age groups and are considered the most common cause of infectious foodborne diseases worldwide. The aim of this study was to describe a norovirus outbreak connected to insufficient heat treatment during preparation of a shellfish soup in serving portions, during a company Christmas celebration in Norway, December 2013. A questionnaire sent to the employees, showed that 67 % (n = 43) of the celebration participants, reported gastrointestinal symptoms including stomach pain, vomiting, diarrhoea and light fever in the period between 24 and 48 h post celebration. Several dishes were served, including shellfish soup made with carpet shell clams (Tapes rhomboides) in porcelain cups. Consuming this soup, was the only significant risk factor for infection. Norovirus GI and GII were detected in the remaining raw shellfish. To mimic the time and temperature obtained during bivalve soup preparation, raw chopped shellfish tissue and raw cepa onion were added in porcelain cups tempered to 20 °C. To each of these cups, boiling soup base was added. The temperature in the shellfish tissue was continuously recorded, and showed a maximum of 49 °C in the period between 3 and 7 min after adding the boiling soup base. After 1 h the temperature was 30 °C. This time and temperature combination was obviously not sufficient for inactivation of norovirus present in the shellfish tissue. In conclusion, the heat-absorbing capacity of cold ingredients, utensils and table wear porcelain should not be underestimated during food production. Consumers who want to avoid eating raw shellfish, should not assume that the shellfish tissue in preparation as described in our study is adequately heat treated.

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.

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.

Persistence and Elimination of Human Norovirus in Food and on Food Contact Surfaces: A Critical Review

This critical review addresses the persistence of human norovirus (NoV) in water, shellfish, and processed meats; on berries, herbs, vegetables, fruits, and salads; and on food contact surfaces. The review focuses on studies using NoV; information from studies involving only surrogates is not included. It also addresses NoV elimination or inactivation by various chemical, physical, or processing treatments. In most studies, persistence or elimination was determined by detection and quantification of the viral genome, although improved methods for determining infectivity have been proposed. NoV persisted for 60 to 728 days in water, depending on water source. It also persisted on berries, vegetables, and fruit, often showing <1-log reduction within 1 to 2 weeks. NoV was resilient on carpets, Formica, stainless steel, polyvinyl chloride, and ceramic surfaces; during shellfish depuration; and to repeated freeze-thaw cycles. Copper alloy surfaces may inactivate NoV by damaging viral capsids. Disinfection was achieved for some foods or food contact surfaces using chlorine, calcium or sodium hypochlorite, chlorine dioxide, high hydrostatic pressure, high temperatures, pH values >8.0, freeze-drying, and UV radiation. Ineffective disinfectants included hydrogen peroxide, quaternary ammonium compounds, most ethanol-based disinfectants, and antiseptics at normally used concentrations. Thorough washing of herbs and produce was effective in reducing, but not eliminating, NoV in most products. Washing hands with soap generally reduced NoV by <2 log. Recommendations for future research needs are provided.

Environmental fate of double-stranded RNA in agricultural soils

A laboratory soil degradation study was conducted to determine the biodegradation potential of a DvSnf7 dsRNA transcript derived from a Monsanto genetically modified (GM) maize product that confers resistance to corn rootworm (CRW; Diabrotica spp.). This study provides new information to improve the environmental assessment of dsRNAs that become pesticidal through an RNAi process. Three agricultural soils differing in their physicochemical characteristics were obtained from the U.S., Illinois (IL; silt loam), Missouri (MO; loamy sand) and North Dakota (ND; clay loam), and exposed to the target dsRNA by incorporating insect-protected maize biomass and purified (in vitro-transcribed) DvSnf7 RNA into soil. The GM and control (non-GM maize) materials were added to each soil and incubated at ca. 22°C for 48 hours (h). Samples were collected at 12 time intervals during the incubation period, extracted, and analyzed using QuantiGene molecular analysis and insect bioassay methods. The DT₅₀ (half-life) values for DvSnf7 RNA in IL, MO, and ND soils were 19, 28, and 15 h based on QuantiGene, and 18, 29, and 14 h based on insect bioassay, respectively. Furthermore, the DT₉₀ (time to 90% degradation) values for DvSnf7 RNA in all three soils were <35 h. These results indicate that DvSnf7 RNA was degraded and biological activity was undetectable within approximately 2 days after application to soil, regardless of texture, pH, clay content and other soil differences. Furthermore, soil-incorporated DvSnf7 RNA was non-detectable in soil after 48 h, as measured by QuantiGene, at levels ranging more than two orders of magnitude (0.3, 1.5, 7.5 and 37.5 µg RNA/g soil). Results from this study indicate that the DvSnf7 dsRNA is unlikely to persist or accumulate in the environment. Furthermore, the rapid degradation of DvSnf7 dsRNA provides a basis to define relevant exposure scenarios for future RNA-based agricultural products.

Sample preparation prior to molecular amplification: complexities and opportunities

Molecular amplification using Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) is currently considered as the gold standard to detect enteric human pathogenic viruses such as norovirus and hepatitis A virus in food and water. However, the molecular-based detection requires an adequate sampling strategy and a sample preparation specific for viruses. Sampling for enteric human viruses in water and food should not necessarily follow bacterial sampling plans. The development of a reference detection method including sample preparation as proposed in ISO/TS 15216 represents a milestone to facilitate the evaluation of the performance and eventually validation of future virus detection methods. The potential viral infectivity linked to a positive PCR result is a remaining issue and pretreatments allowing the differentiation of infectious viruses would be useful for future risk assessments.

Two-year systematic study to assess norovirus contamination in oysters from commercial harvesting areas in the United Kingdom

The contamination of bivalve shellfish with norovirus from human fecal sources is recognized as an important human health risk. Standardized quantitative methods for the detection of norovirus in molluscan shellfish are now available, and viral standards are being considered in the European Union and internationally. This 2-year systematic study aimed to investigate the impact of the application of these methods to the monitoring of norovirus contamination in oyster production areas in the United Kingdom. Twenty-four monthly samples of oysters from 39 United Kingdom production areas, chosen to represent a range of potential contamination risk, were tested for norovirus genogroups I and II by using a quantitative real-time reverse transcription (RT)-PCR method. Norovirus was detected in 76.2% (643/844) of samples, with all sites returning at least one positive result. Both prevalences (presence or absence) and norovirus levels varied markedly between sites. However, overall, a marked winter seasonality of contamination by both prevalence and quantity was observed. Correlations were found between norovirus contamination and potential risk indicators, including harvesting area classifications, Escherichia coli scores, and environmental temperatures. A predictive risk score for norovirus contamination was developed by using a combination of these factors. In summary, this study, the largest of its type undertaken to date, provides a systematic analysis of norovirus contamination in commercial oyster production areas in the United Kingdom. The data should assist risk managers to develop control strategies to reduce the risk of human illness resulting from norovirus contamination of bivalve molluscs.

Comparison of norovirus RNA levels in outbreak-related oysters with background environmental levels

Norovirus is the principal agent of bivalve shellfish-associated gastroenteric illness worldwide. Numerous studies using PCR have demonstrated norovirus contamination in a significant proportion of both oyster and other bivalve shellfish production areas and ready-to-eat products. By comparison, the number of epidemiologically confirmed shellfish-associated outbreaks is relatively low. This suggests that factors other than the simple presence or absence of virus RNA are important contributors to the amount of illness reported. This study compares norovirus RNA levels in oyster samples strongly linked to norovirus or norovirus-type illness with the levels typically found in commercial production areas (non-outbreak-related samples). A statistically significant difference between norovirus levels in the two sets of samples was observed. The geometric mean of the levels in outbreak samples (1,048 copies per g) was almost one order of magnitude higher than for positive non-outbreak-related samples (121 copies per g). Further, while none of the outbreak-related samples contained fewer than 152 copies per g, the majority of positive results for non-outbreak-related samples was below this level. These observations support the concept of a dose-response for norovirus RNA levels in shellfish and could help inform the establishment of threshold criteria for risk management.

Randomized, double-blinded clinical trial for human norovirus inactivation in oysters by high hydrostatic pressure processing

Contamination of oysters with human noroviruses (HuNoV) constitutes a human health risk and may lead to severe economic losses in the shellfish industry. There is a need to identify a technology that can inactivate HuNoV in oysters. In this study, we conducted a randomized, double-blinded clinical trial to assess the effect of high hydrostatic pressure processing (HPP) on Norwalk virus (HuNoV genogroup I.1) inactivation in virus-seeded oysters ingested by subjects. Forty-four healthy, positive-secretor adults were divided into three study phases. Subjects in each phase were randomized into control and intervention groups. Subjects received Norwalk virus (8FIIb, 1.0 × 10(4) genomic equivalent copies) in artificially seeded oysters with or without HPP treatment (400 MPa at 25°C, 600 MPa at 6°C, or 400 MPa at 6°C for 5 min). HPP at 600 MPa, but not 400 MPa (at 6° or 25°C), completely inactivated HuNoV in seeded oysters and resulted in no HuNoV infection among these subjects, as determined by reverse transcription-PCR detection of HuNoV RNA in subjects' stool or vomitus samples. Interestingly, a white blood cell (granulocyte) shift was identified in 92% of the infected subjects and was significantly associated with infection (P = 0.0014). In summary, these data suggest that HPP is effective at inactivating HuNoV in contaminated whole oysters and suggest a potential intervention to inactivate infectious HuNoV in oysters for the commercial shellfish industry.