Quantification of human adenovirus and norovirus in river water in the north-east of France

Global investigation of the presence of adenovirus in different types of water resources: a systematic review

Waterborne viruses such as adenoviruses cause major health problems in the world. Human adenoviruses are the second leading cause of childhood gastroenteritis worldwide. In recent years, the presence of the virus in aquatic resources has been shown in several studies. In this paper, the global presence of adenovirus in different types of water resources are reviewed through studying several surveys conducted in different countries worldwide. We designed one search study to collect the maximum number of related articles to this subject in international databases search engine via relevant keywords. After reviewing the articles, the most relevant ones were selected, and after classification and extracting the required information, they were reported in the tables presented in this study. In general, it was found that the highest rate of the presence of adenoviruses has been reported in sewage water, inlet, and outlet of the treatment plant while the lowest rate of the presence of adenovirus in the dam water. These findings demonstrate that treatment plant system has weakness in removing the adenovirus and are strongly recommended for treatment plants to use new and better protocols to remove this virus. In addition, appropriate diagnostic methods that combines molecular biological technique with infectivity assay should be implemented for detection of adenoviruses in water resources.

Development of a Nanoplate-Based Digital PCR Test Method for Quantitative Detection of Human Adenovirus DNA

Objective

Digital polymerase chain reaction (dPCR) assay is an advanced PCR technique that allows for the simultaneous detection and absolute quantification of diverse pathogens.Commercially validated kits available for detecting all subtypes of human adenovirus (HAdV) are limited. This study aimed to demonstrate the development of an in-house nanoplate-based dPCR assay with high sensitivity, even at low copy numbers.

Materials and Methods

In this methodological study, the standardized HAdV DNA was prepared by amplifying the specific hexon gene region with real-time PCR and purifying the HAdV DNA using magnetic beads from HAdV-positive extractions. Dilutions were tested in triplicate during three independent runs to determine the dynamic range, the limit of detection (LoD), the limit of quantification (LoQ), precision, and reproducibility. The primer and probe sequences used in the study were selected based on a literature review to ensure the detection of all HAdV serotypes in a single run. The selected primers were verified using the US National Center for Biotechnology Information (NBCI) nBLAST tools, and the target sequence was determined using the BioEdit software. The DNA concentration of the stock solution was measured using a Qubit fluorometer. The estimated copy number of the stock solution per milliliter was calculated based on the length of the amplified base sequence and fluorometer measurement.

Results

The dynamic range of the test was determined to be from 770.4 to 0.9476 cp/μl, with the LoD and LoQ values both being 0.9476 cp/μl. The coefficient of determination (r 2) value of the test was 0.9986.

Conclusion

The results demonstrated that the dPCR method could be an ideal tool for the diagnosis and absolute quantification of human adenoviruses, especially in low copy numbers. In order to determine the reproducibility of the test and validate the method for field use, it needs to be developed and adapted in various laboratories and supported by clinical studies.

Assessment of different factors on the influence of glass wool concentration for detection of main swine viruses in water samples

Viruses existed in wastewaters might pose a biosecurity risk to human and animal health. However, it is generally difficult to detect viruses in wastewater directly as they usually occur in low numbers in water. Therefore, processing large volumes of water to concentrate viruses in a much smaller final volume for detection is necessary. Glass wool has been recognized as an effective material to concentrate multiple in water, and in this study, we assessed the use of glass wools on concentrating pseudorabies virus (PRV), African swine fever virus (ASFV), and porcine epidemic diarrhea virus (PEDV) in water samples. The influence of pH values, water matrix, water volume, filtration rate, temperature on the effect of the method concentrating these viruses for detection was evaluated in laboratory. Our results revealed that glass wool was suitable for the concentration of above-mentioned viruses from different water samples, and demonstrated a good application effect for water with pH between 6.0-9.0. Furthermore, glass wool also showed a good recovery effect on concentrating viral nucleic acids and viral particles, as well as living viruses. In addition, combining use of glass wool with skim milk, polyethylene glycol (PEG)-NaCl, or ultracentrifuge had good effects on concentrating ASFV, PRV, and PEDV. Detection of wastewater samples (n = 70) collected from 70 pig farms in 13 regions across Hubei Province in Central China after glass-wool-concentration determined one sample positive for ASFV, eighteen samples positive for PRV, but no sample positive for PEDV. However, these positive samples were detected to be negative before glass wool enrichment was implemented. Our results suggest that glass wool-based water concentration method developed in this study represents an effective tool for detecting viruses in wastewater.

Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance

Contaminated irrigation water is among many potential vehicles of human pathogens to food plants, constituting significant public health risks especially for the fresh produce category. This review discusses some available guidelines or regulations for microbiological safety of irrigation water, and provides a summary of some common methods used for characterizing microbial contamination. The goal of such exploration is to understand some of the considerations that influence formulation of water testing guidelines, describe priority microbial parameters particularly with respect to food safety risks, and attempt to determine what methods are most suitable for their screening. Furthermore, the review discusses factors that influence the potential for microbiologically polluted irrigation water to pose substantial risks of pathogenic contamination to produce items. Some of these factors include type of water source exploited, irrigation methods, other agro ecosystem features/practices, as well as pathogen traits such as die-off rates. Additionally, the review examines factors such as food safety knowledge, other farmer attitudes or inclinations, level of social exposure and financial circumstances that influence adherence to water testing guidelines and other safe water application practices. A thorough understanding of relevant risk metrics for the application and management of irrigation water is necessary for the development of water testing criteria. To determine sampling and analytical approach for water testing, factors such as agricultural practices (which differ among farms and regionally), as well as environmental factors that modulate how water quality may affect the microbiological safety of produce should be considered. Research and technological advancements that can improve testing approach and the determination of target levels for hazard characterization or description for the many different pollution contexts as well as farmer adherence to testing requirements, are desirable.

Virus inactivation by sequential ultraviolet-chlorine disinfection: Synergistic effect and mechanism

The COVID-19 outbreak has raised concerns about the efficacy of the disinfection process followed in water treatment plants in preventing the spread of viruses. Ultraviolet (UV) and chlorine multi-barrier disinfection processes are commonly used in water treatment plants; however, their effects on virus inactivation are still unclear. In this study, the effects of different disinfection processes (i.e., UV, free chlorine, and their combination) on waterborne viruses were analyzed using bacteriophage surrogates (i.e., MS2 and PR772) as alternative indicators. The results showed that the inactivation rates of PR772 by either UV or free chlorine disinfection were higher than those of MS2. PR772 was approximately 1.5 times more sensitive to UV disinfection and 8.4 times more sensitive to chlorine disinfection than MS2. Sequential UV-chlorine disinfection had a synergistic effect on virus inactivation, which was enhanced by an increase in the UV dose. As compared with single free chlorine disinfection, UV irradiation at 40 mJ cm^-2 enhanced MS2 and PR772 inactivation significantly with a 2.7-fold (MS2) and a 1.7-fold (PR772) increase in the inactivation rate constants on subsequent chlorination in phosphate buffered saline. The synergistic effect was also observed in real wastewater samples, in which the MS2 inactivation rate increased 1.4-fold on subsequent chlorination following UV irradiation at 40 mJ cm^-2. The mechanism of the synergistic effect of sequential UV-chlorine disinfection was determined via sodium dodecyl sulfate-polyacrylamide gel electrophoresis, using MS2 as an indicator. The results showed that the synergistic effect was due to damage to MS2 surface proteins caused by previous UV disinfection, which enhanced the sensitivity of MS2 to chlorination. This study provides a feasible approach for the efficient inactivation of viruses in water supply and drainage.

Mastadenovirus Molecular Diversity in Waste and Environmental Waters from the Lisbon Metropolitan Area

In face of the absence of epidemiological data regarding the circulation of human adenoviruses (HAdV) in Portugal, this study aimed at the evaluation of their molecular diversity in waste and environmental waters in the Lisbon Metropolitan Area (LMA). Using samples collected between 2018 and 2021, the HAdV hexon protein-coding sequence was partially amplified using three nested touch-down PCR protocols. The amplification products obtained were analyzed in parallel by two approaches: molecular cloning followed by Sanger sequencing and Next-Generation Sequencing (NGS) using Illumina^® sequencing. The analysis of NGS-generated data allowed the identification of a higher diversity of HAdV-A (19%), -B (1%), -C (3%), -D (24%), and -F (25%) viral types, along with murine adenovirus (MAdV-2; 30%) in the wastewater treatment plant samples. On the other hand, HAdV-A (19%), -D (32%), and -F (36%) were identified in environmental samples, and possibly MAdV-2 (14%). These results demonstrate the presence of fecal contamination in environmental waters and the assessment of the diversity of this virus provides important information regarding the distribution of HAdV in LMA, including the detection of HAdV-F41, the most frequently reported in water worldwide.

Global public health implications of human exposure to viral contaminated water

Enteric viruses are common waterborne pathogens found in environmental water bodies contaminated with either raw or partially treated sewage discharge. Examples of these viruses include adenovirus, rotavirus, noroviruses, and other caliciviruses and enteroviruses like coxsackievirus and polioviruses. They have been linked with gastroenteritis, while some enteric viruses have also been implicated in more severe infections such as encephalitis, meningitis, hepatitis (hepatitis A and E viruses), cancer (polyomavirus), and myocarditis (enteroviruses). Therefore, this review presents information on the occurrence of enteric viruses of public health importance, diseases associated with human exposure to enteric viruses, assessment of their presence in contaminated water, and their removal in water and wastewater sources. In order to prevent illnesses associated with human exposure to viral contaminated water, we suggest the regular viral monitoring of treated wastewater before discharging it into the environment. Furthermore, we highlight the need for more research to focus on the development of more holistic disinfection methods that will inactivate waterborne viruses in municipal wastewater discharges, as this is highly needed to curtail the public health effects of human exposure to contaminated water. Moreover, such a method must be devoid of disinfection by-products that have mutagenic and carcinogenic potential.

Optical Quantification by Nanopores of Viruses, Extracellular Vesicles, and Nanoparticles

Nanopores combined with optical approaches can be used to detect viral particles. In this work, we demonstrate the ability of hydrodynamical driving and optical sensing to identify and quantify viral particles in a biological sample. We have developed a simple and rapid method which requires only fluorescent labeling of the particles and can therefore be applied to a wide range of virus type. The system operates in real time and at the single particle level while providing a low error on concentration (4%) and a low limit of detection of 10⁵ particles/mL for an acquisition time of 60 s with the ability to increase the acquisition time to achieve a lower limit.

Inactivation efficacy and mechanism of pulsed corona discharge plasma on virus in water

The presence of viruses in water is a major risk for human and animal health due to their high resistance to disinfection. Pulsed corona discharge plasma (PCDP) efficiently inactivates bacteria by causing damage to biological macromolecules, but its effect on waterborne virus has not been reported. This study evaluated the inactivation efficacy of PCDP to viruses using spring viremia of carp virus (SVCV) as a model. The results showed that 4-log₁₀ reduction of SVCV infectivity in cells was reached after 120 s treatment, and there was no significant difference in survival of fish infected with SVCV inactivated by PCDP for 240 s or more longer compared to the control fish without virus challenge, thus confirming the feasibility of PCDP to waterborne virus inactivation. Moreover, the high input energy density caused by voltage significantly improved the inactivation efficiency. The further research indicated that reactive species (RS) generated by pulsed corona discharge firstly reacted with phosphoprotein (P) and polymerase complex proteins (L) through penetration into the SVCV virions, and then caused the loss of viral infectivity by damage to genome and other structural proteins. This study has significant implications for waterborne virus removal and development of novel disinfection technologies.

Metagenomic Analysis of Viral Community in the Yangtze River Expands Known Eukaryotic and Prokaryotic Virus Diversity in Freshwater

Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P ​> ​0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource.

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First insight into viral community composition in large river ecosystem.

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Virus hallmark genes present both diverse and conservative characteristics.

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The composition of viral communities is similar on the whole.

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Slight regional variation of virome is existed in individual areas.

Rapid Assessment of SARS-CoV-2 Transmission Risk for Fecally Contaminated River Water

Following the outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2), airborne water droplets have been identified as the main transmission route. Identifying and breaking all viable transmission routes are critical to stop future outbreaks, and the potential of transmission by water has been highlighted. By modifying established approaches, we provide a method for the rapid assessment of the risk of transmission posed by fecally contaminated river water and give example results for 39 countries. The country relative risk of transmission posed by fecally contaminated river water is related to the environment and the populations' infection rate and water usage. On the basis of in vitro data and using temperature as the primary controller of survival, we then demonstrate how viral loads likely decrease after a spill. These methods using readily available data suggest that sewage spills into rivers within countries with high infection rates could provide infectious doses of >40 copies per 100 mL of water. The approach, implemented in the supplementary spreadsheet, can provide a fast estimate of the upper and lower viral load ranges following a riverine spill. The results enable evidence-based research recommendations for wastewater epidemiology and could be used to evaluate the significance of fecal-oral transmission within freshwater systems.

Rapid Assessment of SARS-CoV-2 Transmission Risk for Fecally Contaminated River Water

Following the outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2), airborne water droplets have been identified as the main transmission route. Identifying and breaking all viable transmission routes are critical to stop future outbreaks, and the potential of transmission by water has been highlighted. By modifying established approaches, we provide a method for the rapid assessment of the risk of transmission posed by fecally contaminated river water and give example results for 39 countries. The country relative risk of transmission posed by fecally contaminated river water is related to the environment and the populations' infection rate and water usage. On the basis of in vitro data and using temperature as the primary controller of survival, we then demonstrate how viral loads likely decrease after a spill. These methods using readily available data suggest that sewage spills into rivers within countries with high infection rates could provide infectious doses of >40 copies per 100 mL of water. The approach, implemented in the supplementary spreadsheet, can provide a fast estimate of the upper and lower viral load ranges following a riverine spill. The results enable evidence-based research recommendations for wastewater epidemiology and could be used to evaluate the significance of fecal-oral transmission within freshwater systems.

Detection and disinfection of COVID-19 virus in wastewater

The coronavirus disease 2019, COVID-19, caused by the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, appears as a major pandemic having adverse impact on public health and economic activities. Since viral replication in human enterocytes results in its faecal shedding, wastewater surveillance is an ideal, non-invasive, cost-effective and an early warning epidemiological approach to detect the genetic material of SARS-CoV-2. Here, we review techniques for the detection of SARS-CoV-2 in municipal wastewater, and disinfectants used to control viral spread. For detection, concentration of ribonucleic acid involves ultrafiltration, ultracentrifugation and polyethylene glycol precipitation. Identification is done by reverse transcriptase amplification, nucleic acid sequence-based amplification, helicase dependent amplification, loop-mediated isothermal amplification, recombinase polymerase amplification, high throughput screening and biosensor assays. Disinfectants include ultraviolet radiations, ozone, chlorine dioxide, hypochlorites and hydrogen peroxide. Wastewater surveillance data indicates viral presence within longer detection window, and provides transmission dynamics earlier than classical methods. This is particularly relevant for pre-symptomatic and asymptomatic COVID-19 cases.

SARS-CoV-2 in environmental perspective: Occurrence, persistence, surveillance, inactivation and challenges

The unprecedented global spread of the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2 is depicting the distressing pandemic consequence on human health, economy as well as ecosystem services. So far novel coronavirus (CoV) outbreaks were associated with SARS-CoV-2 (2019), middle east respiratory syndrome coronavirus (MERS-CoV, 2012), and SARS-CoV-1 (2003) events. CoV relates to the enveloped family of Betacoronavirus (βCoV) with positive-sense single-stranded RNA (+ssRNA). Knowing well the persistence, transmission, and spread of SARS-CoV-2 through proximity, the faecal-oral route is now emerging as a major environmental concern to community transmission. The replication and persistence of CoV in the gastrointestinal (GI) tract and shedding through stools is indicating a potential transmission route to the environment settings. Despite of the evidence, based on fewer reports on SARS-CoV-2 occurrence and persistence in wastewater/sewage/water, the transmission of the infective virus to the community is yet to be established. In this realm, this communication attempted to review the possible influx route of the enteric enveloped viral transmission in the environmental settings with reference to its occurrence, persistence, detection, and inactivation based on the published literature so far. The possibilities of airborne transmission through enteric virus-laden aerosols, environmental factors that may influence the viral transmission, and disinfection methods (conventional and emerging) as well as the inactivation mechanism with reference to the enveloped virus were reviewed. The need for wastewater epidemiology (WBE) studies for surveillance as well as for early warning signal was elaborated. This communication will provide a basis to understand the SARS-CoV-2 as well as other viruses in the context of the environmental engineering perspective to design effective strategies to counter the enteric virus transmission and also serves as a working paper for researchers, policy makers and regulators.

Levels of human Rotaviruses and Noroviruses GII in urban rivers running through the city mirror their infection prevalence in populations

Enteric viruses exposed to water pose a huge threat to global public health and can lead to waterborne disease outbreaks. A sudden increase in enteric viruses in some water matrices also underpins the prevalence of corresponding waterborne diseases in communities over the same time period. However, few efforts have been focused on water matrices whose viral pollution may best reflect the clinical prevalence in communities. Here, a one-year surveillance of human enteric viruses including Enteroviruses (EnVs), Rotaviruses (HRVs), Astroviruses (AstVs), Noroviruses GII (HuNoVsGII) and Mastadenoviruses (HAdVs) in four representative water matrices: an urban river (UR) running through city, effluent from Wastewater Treatment Plant (EW), raw water for Urban Water Treatment Plant (RW), and tap water (TW) were performed by qPCR. The relationship between the virus detection frequency at each site and their prevalence in clinical PCR assay was further analyzed. We found that the detection frequencies of HRVs, HuNoVsGII, and AstVs in stools peaked in winter, while EnVs peaked in autumn. No EnVs occurred in EW, RW, or TW, but HuNoVsGII and AstVs occurred intensively in winter. For UR, all types of enteric viruses could be detected and the levels of acute gastroenteritis viruses (HRVs, HuNoVsGII, AstVs, and HAdVs) were highest in autumn or winter, whereas EnVs peaked in summer. In terms of correlation analyses, only HRVs and HuNoVsGII levels in UR showed a strong positive correlation with their prevalence in clinical stool samples. This study indicated that HRVs and HuNoVsGII levels in URs may mirror the local virus prevalence, thereby implying the possibility of revealing their local epidemiology by monitoring them in the URs.

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.

Rapid detection of norovirus genogroup II in clinical and environmental samples using recombinase polymerase amplification

Norovirus is the leading cause of acute gastroenteritis all over the world, and the most genotype that causes its epidemic is norovirus genogroup II (NoVs GII). Rapid detection of NoVs is important because it can facilitate timely diagnosis. In this study, we designed universal specific primers and an Exo probe to hybridize to all genetic clusters of NoVs GII based on the conserved region at the ORF1-ORF2 junction of the genome. For the first time, we established a rapid and reliable reverse transcription recombinase polymerase amplification (RT-RPA) method for the detection of NoVs GII within 20 min. This method can specifically amplify NoVs GII, and the detection limit was as low as 1.66 × 10² copies/μL. The method was validated in terms of LOD, accuracy, and specificity. We tested 55 real samples including foods, water, and feces. The results showed a sensitivity of 96% and specificity of 100% to NoVs GII. The whole procedure can be operated by a mobile suitcase laboratory, which is useful for resource-limited diagnostic laboratories. This novel real-time RT-RPA assay is an accurate tool for point-of-care testing of NoVs, providing practical support for norovirus-caused disease diagnosis and prevention.

Droplet Digital PCR for Estimating Absolute Abundances of Widespread Pelagibacter Viruses

Absolute abundances of prokaryotes are typically determined by FISH. Due to the lack of a universal conserved gene among all viruses, metagenomic fragment recruitment is commonly used to estimate the relative viral abundance. However, the paucity of absolute virus abundance data hinders our ability to fully understand how viruses drive global microbial populations. The cosmopolitan marine Pelagibacter ubique is host for the highly widespread HTVC010P pelagiphage isolate and the extremely abundant uncultured virus vSAG 37-F6 recently discovered by single-virus genomics. Here we applied droplet digital PCR (ddPCR) to calculate the absolute abundance of these pelagiphage genotypes in the Mediterranean Sea and the Gulf of Maine. Abundances were between 360 and 8,510 virus mL-1 and 1,270–14,400 virus mL-1 for vSAG 37-F6 and HTVC010P, respectively. Illumina PCR-amplicon sequencing corroborated the absence of ddPCR non-specific amplifications for vSAG 37-F6, but showed an overestimation of 6% for HTVC010P from off-targets, genetically unrelated viruses. Absolute abundances of both pelagiphages, two of the most abundance marine viruses, suggest a large viral pelagiphage diversity in marine environments, and show the efficiency and power of ddPCR to disentangle the structure of marine viral communities. Results also highlight the need for a standardized workflow to obtain accurate quantification that allows cross data comparison.

'Don't put your head under water': enteric viruses in Brazilian recreational waters

Like in many other countries, virologic analyses are not routinely performed in Brazil in monitoring water quality for recreational purposes. We surveyed current research regarding viral contamination of recreational water environments in Brazil. Among the enteric viruses studied in Brazilian recreational waters, we highlight adenoviruses, rotaviruses, enteroviruses and noroviruses. Although there has been relatively little research on outbreaks related to bathing in recreational water environments in Brazil, noroviruses and adenoviruses are the viruses that are most often related to outbreaks. Better surveillance of the occurrence of enteric viruses in water could improve the assessment of risk to human health as well as indicate the sources of contamination and thus demonstrate the importance of adequate environmental sanitation.