Development and application of a broadly reactive real-time reverse transcription-PCR assay for detection of murine noroviruses

Pepper mild mottle virus intended for use as a process indicator for drinking water treatment: Present forms and quantitative relations to norovirus and rotavirus in surface water

Pepper mild mottle virus (PMMoV) has been proposed as a potential indicator of human enteric viruses in environmental water and for viral removal during drinking water treatment. To investigate the occurrence and present forms of PMMoV and quantitative relations to norovirus GII and rotavirus A (RVA) in surface waters, 147 source water samples were collected from 21 drinking water treatment plants (DWTPs) in Japan between January 2018 and January 2021, and the concentrations of viruses in suspended and dissolved fractions were measured using real-time RT-PCR. PMMoV was detected in 81-100 % of samples in each sample month and observed concentrations ranged from 3.0 to 7.0 log10 copies/L. The concentrations of PMMoV were higher in dissolved fraction compared to suspended fractions, while different partitioning was observed for NoV GII depending on seasons. The concentrations of PMMoV were basically higher than those of norovirus GII (1.9-5.3 log10 copies/L) and RVA (1.9-6.6 log10 copies/L), while in 18 samples, RVA presented higher concentrations than PMMoV. Partial regions of VP7, VP4, and VP6 of the RVA in the 18 samples were amplified using nested PCR, and the genotypes were determined using an amplicon-based next-generation sequencing approach. We found that these source water samples included not only human RVA but also various animal RVA and high genetic diversity due to the existence of animal RVA was associated with a higher RVA concentration than PMMoV. Our findings suggest that PMMoV can be used as an indicator of norovirus GII and human RVA in drinking water sources and that the indicator performance should be evaluated by comparing to zoonotic viruses as well as human viruses.

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.

Sensitive electrochemical gold nanoparticle-based immunosensor for norovirus detection in food samples

Norovirus (NoV) infection is one of the most common non-bacterial causes of gastroenteritis among the population worldwide. From the point of view of medical diagnostics, it is important to develop a system that would sensitively and selectively detect norovirus from a patient's sample in order to control and limit its spread. In this paper, we present a stable and sensitive NoV (mouse model) detection matrix in infected food samples. The bio-platform was made of a modified gold electrode with a self-assembled l-cysteine monolayer, covered with gold nanoparticles, a linker and an antibody specific to the VP1 surface protein of the virus. Binding of the VP1 protein to the antibody caused a decrease in the current strength confirmed by electrochemical techniques - cyclic voltammetry (CV) and differential pulse voltammetry. The reduction of the current was proportional to the concentration of NoV sample. The biosensors showed high sensitivity and linearity in a range from 1 × 10-9 to 1 × 10-18 TCID50, with the detection limit of 1 × 10-18 TCID50. CV showed a diffusion-controlled process. In addition, each modification step was confirmed by scanning electron microscopy, electrochemical impedance spectroscopy, and CV. The described immunosensor showed excellent recovery values, good linearity and long-term stability, crucial parameters for biosensor construction.

Development of a simple and low-cost method using Moringa seeds for efficient virus concentration in wastewater

Effective virus concentration methods are essential for detecting pathogenic viruses in environmental waters and play a crucial role in wastewater-based epidemiology. However, the current methods are often expensive, complicated, and time-consuming, which limits their practical application. In this study, a simple and low-cost method was developed using the extract of Moringa oleifera (MO) seeds (MO method) to recover both enveloped and non-enveloped viruses, including pepper mild mottle virus (PMMoV), murine norovirus (MNV), Aichivirus (AiV), murine hepatitis virus (MHV), and influenza A virus subtype H1N1[H1N1] in wastewater. The optimal conditions for the MO method were determined to be a concentration of MO extract at the UV280 value of 0.308 cm-1 and an elution buffer (0.05 M KH2PO4, 1 M NaCl, 0.1 % Tween80 [v/v]) for recovering the tested viruses in wastewater. Compared to other commonly used virus concentration methods such as InnovaPrep, HA, PEG, and Centricon, the MO method was found to be more efficient and cost-effective in recovering the tested viruses. Moreover, the MO method was successfully applied to detect various types of viruses (PMMoV, AiV, norovirus of genotype II [NoV II], enterovirus [EV], influenza A virus [matrix gene] [IAV], and SARS-CoV-2) in raw wastewater. Thus, the developed MO method could offer a simple, low-cost, and efficient tool to concentrate viruses in wastewater.

Temporal variations of human and animal Rotavirus A genotypes in surface water used for drinking water production

Rotavirus is a major cause of gastroenteritis among infants and children. In this study, nested PCR assays were developed to amplify partial regions of the VP7, VP4, and VP6 genes of Rotavirus A (RVA) for amplicon-based Illumina MiSeq sequencing to investigate RVA genotypes in environmental water samples. Eight sets of inner primers were first designed and screened for use in the nested PCR assays, and four sets of them could produce amplicons. Six sets of outer primers were then designed and combined with the four sets of inner primers that worked. The assays were evaluated for sensitivity using raw water samples collected from one drinking water treatment plant between April 2019 and March 2020 (Sample Set 1; N = 12) and seven DWTPs between 2018 and 2020 (Sample Set 2; N = 18). In total, 43 amplicons from Set 1 were sequenced and diverse sequences from human, porcine, bovine, equine, and feline RVA were observed. Human G8, G3, and G2 genotypes were obtained, with G8 predominant (relative abundance, 36–87%) in samples taken during the rotavirus epidemic season between April and June. Porcine G5, G11, and G4, and bovine G10 and G6 genotypes were also detected. VP4 sequence analysis revealed that the human P[8] genotype was present throughout the year, whereas P[4] and P[9] were present only in the epidemic season. The vaccine strains P[5] and P[8] (RotaTeq®) were also detected. Our approach enables the identification of prevalent human and animal RVA genotypes and their host species that potentially caused fecal contamination in water sources.

Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal

The applicability of wastewater-based epidemiology (WBE) has been extensively studied throughout the world with remarkable findings. This study reports the presence and reduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at two wastewater treatment plants (WWTPs) of Nepal, along with river water, hospital wastewater (HWW), and wastewater from sewer lines collected between July 2020 and February 2021. SARS-CoV-2 RNA was detected in 50%, 54%, 100%, and 100% of water samples from WWTPs, river hospitals, and sewer lines, respectively, by at least one of four quantitative PCR assays tested (CDC-N1, CDC-N2, NIID_2019-nCOV_N, and N_Sarbeco). The CDC-N2 assay detected SARS-CoV-2 RNA in the highest number of raw influent samples of both WWTPs. The highest concentration was observed for an influent sample of WWTP A (5.5 ± 1.0 log10 genome copies/L) by the N_Sarbeco assay. SARS-CoV-2 was detected in 47% (16/34) of the total treated effluents of WWTPs, indicating that biological treatments installed at the tested WWTPs are not enough to eliminate SARS-CoV-2 RNA. One influent sample was positive for N501Y mutation using the mutation-specific qPCR, highlighting a need for further typing of water samples to detect Variants of Concern. Furthermore, crAssphage-normalized SARS-CoV-2 RNA concentrations in raw wastewater did not show any significant association with the number of new coronavirus disease 2019 (COVID-19) cases in the whole district where the WWTPs were located, suggesting a need for further studies focusing on suitability of viral as well as biochemical markers as a population normalizing factor. Detection of SARS-CoV-2 RNA before, after, and during the peaking in number of COVID-19 cases suggests that WBE is a useful tool for COVID-19 case estimation in developing countries.

Recovery of Nucleic Acids of Enteric Viruses and Host-Specific Bacteroidales from Groundwater by Using an Adsorption-Direct Extraction Method

In this study, the adsorption-elution method was modified to concentrate viral particles in water samples and investigate the contamination of groundwater with norovirus genogroup II (NoV GII), rotavirus A (RVA), and Pepper mild mottle virus (PMMoV). The mean recovery rate of a murine norovirus strain, which was inoculated into groundwater samples collected from a deep well, was the highest (39%) when the viral RNA was directly extracted from the membrane instead of eluting the adsorbed viral particles. This adsorption-direct extraction method was applied to groundwater samples (20 liters) collected from deep wells used for the public drinking water supply (n = 22) and private wells (n = 9). RVA (85 copies/liter) and NoV GII (35 copies/liter) were detected in water samples from a deep well and a private well, respectively. PMMoV was detected in 95% and 89% of water samples from deep wells and private wells, respectively, at concentrations of up to 990 copies/liter. The modified method was also used to extract bacterial DNA from the membrane (recovery rate of inoculated Escherichia coli K-12 was 22%). The Bacteroidales genetic markers specific to ruminants (BacR) and pigs (Pig2Bac) were detected in samples from a deep well and a private well, respectively. The modified virus concentration method has important implications for the management of microbiological safety in the groundwater supply. IMPORTANCE We investigated the presence of enteric viruses and bacterial genetic markers to determine fecal contamination in groundwater samples from deep wells used for the public drinking water supply and private wells in Japan. Groundwater is often subjected to chlorination; malfunctions in chlorine treatment result in waterborne disease outbreaks. The modified method successfully concentrated both viruses and bacteria in 20-liter groundwater samples. Norovirus genogroup II (GII), rotavirus A, Pepper mild mottle virus, and Bacteroidales genetic markers specific to ruminants and pigs were detected. Frequent flooding caused by increased incidences of extreme rainfall events promotes the infiltration of surface runoff containing livestock wastes and untreated wastewater into wells, possibly increasing groundwater contamination risk. The practical and efficient method developed in this study will enable waterworks and the environmental health departments of municipal/prefectural governments to monitor water quality. Additionally, the modified method will contribute to improving the microbiological safety of groundwater.

Estimating the minimum number of SARS-CoV-2 infected cases needed to detect viral RNA in wastewater: To what extent of the outbreak can surveillance of wastewater tell us?

There is increasing interest in wastewater-based epidemiology (WBE) of SARS-CoV-2 RNA to serve as an early warning system for a community. Despite successful detection of SARS-CoV-2 RNA in wastewaters sampled from multiple locations, there is still no clear idea on the minimal number of cases in a community that are associated with a positive detection of the virus in wastewater. To address this knowledge gap, we sampled wastewaters from a septic tank (n = 57) and biological activated sludge tank (n = 52) located on-site of a hospital. The hospital is providing treatment for SARS-CoV-2 infected patients, with the number of hospitalized patients per day known. It was observed that depending on which nucleocapsid gene is targeted by means of RT-qPCR, a range of 253-409 positive cases out of 10,000 persons are required prior to detecting RNA SARS-CoV-2 in wastewater. There was a weak correlation between N1 and N2 gene abundances in wastewater with the number of hospitalized cases. This correlation was however not observed for N3 gene. The frequency of detecting N1 and N2 gene in wastewater was also higher than that for N3 gene. Furthermore, nucleocapsid genes of SARS-CoV-2 were detected at lower frequency in the partially treated wastewater than in the septic tank. In particular, N1 gene abundance was associated with water quality parameters such as total organic carbon and pH. In instances of positive detection, the average abundance of N1 and N3 genes in the activated sludge tank were reduced by 50 and 70% of the levels detected in septic tank, suggesting degradation of the SARS-CoV-2 gene fragments already occurring in the early stages of the wastewater treatment process.

A Robust, Safe, and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Wastewater Samples

Molecular diagnosis and surveillance of pathogens such as SARS-CoV-2 depend on nucleic acid isolation. Pandemics at the scale of COVID-19 can cause a global shortage of proprietary commercial reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. An open-source method, magnetic-nanoparticle-aided viral RNA isolation from contagious samples (MAVRICS), built upon readily available reagents, and easily assembled in any basically equipped laboratory, is thus developed. The performance of MAVRICS is evaluated using validated pathogen detection assays and real-world and contrived samples. Unlike conventional methods, MAVRICS works directly in samples inactivated in phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. MAVRICS allows wastewater biomass immobilized on membranes to be directly inactivated and lysed in TRIzol followed by RNA extraction by magnetic nanoparticles, thereby greatly reducing biohazard risk and simplifying processing procedures. Using 39 COVID-19 patient samples and two wastewater samples, it is shown that MAVRICS rivals commercial kits in detection of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. Therefore, MAVRICS is safe, fast, and scalable. It is field-deployable with minimal equipment requirements and could become an enabling technology for widespread testing and wastewater monitoring of diverse pathogens.

Concentration and Quantification of SARS-CoV-2 RNA in Wastewater Using Polyethylene Glycol-Based Concentration and qRT-PCR

Wastewater-based epidemiology has become an important tool for the surveillance of SARS-CoV-2 outbreaks. However, the detection of viruses in sewage is challenging and to date there is no standard method available which has been validated for the sensitive detection of SARS-CoV-2. In this paper, we describe a simple concentration method based on polyethylene glycol (PEG) precipitation, followed by RNA extraction and a one-step quantitative reverse transcription PCR (qRT-PCR) for viral detection in wastewater. PEG-based concentration of viruses is a simple procedure which is not limited by the availability of expensive equipment and has reduced risk of disruption to consumable supply chains. The concentration and RNA extraction steps enable 900-1500× concentration of wastewater samples and sufficiently eliminates the majority of organic matter, which could inhibit the subsequent qRT-PCR assay. Due to the high variation in the physico-chemical properties of wastewater samples, we recommend the use of process control viruses to determine the efficiency of each step. This procedure enables the concentration and the extraction the DNA/RNA of different viruses and hence can be used for the surveillance of different viral targets for the comprehensive assessment of viral diseases in a community.

Isolation and Identification of a Murine Norovirus Persistent Infection Strain in China

Murine Norovirus (MNV) is one of the most known viruses among viruses in mice. Because of the high prevalence of MNV in frequently used laboratory animals in biomedical researches, there is a significant impact of MNV. There may be different prevalence degrees and molecular characteristics of MNV in different regions around the world. Here, we reported an MNV strain "designated HBTS-1806" isolation from commercial mice's feces that caused a detectable cytopathic effect (CPE) in RAW264.7 cells. According to electron microscopy, the virus was 50-70 nm in diameter. The complete genome of HBTS-1806 is 7383 nucleotides with a structure similar to that of MNV reference strains. According to phylogenetic analysis on the basis of the whole genome, HBTS-1806 shared nucleotide sequence identities of 90.2-95.4% with other Chinese isolates reported. Analysis of amino acid sequence on the basis of ORF1 and ORF2 suggested that the isolated strain may be derived from recombination. Although no gross lesions or histopathological changes were found from mice infected with 5 × 105 TCLD50 of MNV by oral gavage inoculation, the intestinal virus loads lasted 12 weeks, suggesting a persistent infection strain of MNV isolate in China.

Dynamic rotation of the protruding domain enhances the infectivity of norovirus

Norovirus is the major cause of epidemic nonbacterial gastroenteritis worldwide. Lack of structural information on infection and replication mechanisms hampers the development of effective vaccines and remedies. Here, using cryo-electron microscopy, we show that the capsid structure of murine noroviruses changes in response to aqueous conditions. By twisting the flexible hinge connecting two domains, the protruding (P) domain reversibly rises off the shell (S) domain in solutions of higher pH, but rests on the S domain in solutions of lower pH. Metal ions help to stabilize the resting conformation in this process. Furthermore, in the resting conformation, the cellular receptor CD300lf is readily accessible, and thus infection efficiency is significantly enhanced. Two similar P domain conformations were also found simultaneously in the human norovirus GII.3 capsid, although the mechanism of the conformational change is not yet clear. These results provide new insights into the mechanisms of non-enveloped norovirus transmission that invades host cells, replicates, and sometimes escapes the hosts immune system, through dramatic environmental changes in the gastrointestinal tract.

Virucidal Efficacy of Olanexidine Gluconate as a Hand Antiseptic Against Human Norovirus

Human noroviruses are the major cause of non-bacterial acute gastroenteritis worldwide. Since no therapeutic agent has been proven to prevent human norovirus infection yet, preventive healthcare interventions to block the infection routes play an important role in infection control. One of the possible infection routes of human noroviruses are through contaminated hands, but no hand antiseptics have been proven effective. Olanexidine gluconate is a new biguanide compound that has already been approved for sale as an antiseptic for the surgical field in Japan. A new hand antiseptic was developed using olanexidine gluconate in this study, and its virucidal efficacy against human noroviruses was evaluated using modified RT-qPCR that can account for genome derived from intact viruses using RNase A and photo-reactive intercalators. We tested the virucidal efficacy of five materials; two olanexidine gluconate antiseptics (hand rub formulation and surgical field formulation), two kinds of ethanol solutions at different pH (approx. 3 or 7), and a base component of olanexidine gluconate hand rub formulation against 11 human norovirus genotypes by culture-independent methods. The infectivity of murine norovirus (MNV), a surrogate for human norovirus, was significantly reduced after use of the antiseptics. The olanexidine gluconate hand rub demonstrated the strongest virucidal efficacy against human norovirus among the five tested materials. This study showed that olanexidine gluconate has the potential to become a strong tool for the prevention of human norovirus infection.

How Fiber Breakage Reduces Microorganism Removal in Ultrafiltration for Wastewater Reclamation

Ultrafiltration (UF) membranes are increasingly being used for wastewater reclamation treatment for their high removal of pathogens and suspended solids. However, breakage of UF membrane fibers could allow leakage of pathogens into the permeate and create health risks in the use of reclaimed water. Here, we assessed the log₁₀ reduction value (LRV) of human enteric viruses and microbial indicators of new and aged UF modules in a pilot-scale UF process to evaluate the influence of fiber breakage. Norovirus genotypes I and II, Aichi virus, and Escherichia coli were not detected in any permeate samples of intact UF modules, but were detected in samples of damaged UF modules. LRVs of all microorganisms assayed decreased as fiber breakage of new UF modules increased, with maximum decreases of > 3.3 log₁₀. Fiber breakage in the aged UF modules did not decrease LRVs of somatic coliphages and MS2, but breakage in the new UF modules did decrease them. Intact new UF modules gave higher LRVs than intact aged UF modules. When the LRV of intact UF module was assumed to be 1 or 2 log₁₀, increasing fiber breakage did not significantly decrease the predicted LRV, but when it was ≥ 3 log₁₀, it did decrease LRV, in good agreement with measured LRVs in the degraded UF modules. These results suggest that the LRV of intact UF modules affects the decrease in LRV and confirm the leakage of human enteric viruses following fiber breakage in UF modules of different ages in the UF process of wastewater reclamation.

Variable non-linear removal of viruses during transport through a saturated soil column

Reduction of viral surrogates (bacteriophage MS2 and murine norovirus-1 [MNV-1]) and viruses naturally present in wastewater (enteroviruses, adenoviruses, Aichi viruses, reovirus, pepper mild mottle virus) was studied in a long-term experiment simulating soil-aquifer treatment of a non-disinfected secondary treated wastewater effluent blend using a 4.4 m deep saturated soil column (95% sand, 4% silt, 1% clay) with a hydraulic residence time of 15.4 days under predominantly anoxic redox conditions. Water samples were collected over a four-week period from the column inflow and outflow as well as from seven intermediate sampling ports at different depths. Removal of MS2 was 3.5 log₁₀ over 4.4 m and removal of MNV-1 was 3 log₁₀ over 0.3 m. Notably, MNV-1 was removed to below detection limit within 0.3 m of soil passage. In secondary treated wastewater effluent, MNV-1 RNA and MS2 RNA degraded at a first-order rate of 0.59 day^-1 and 0.12 day^-1, respectively. In 15.4 days, the time to pass the soil column, the RNA-degradation of MS2 would amount to 0.8 log_10, and in one day that of MNV-1 0.3 log₁₀ implying that attachment of MNV-1 and MS2 to the sandy soil took place. Among the indigenous viruses, genome copies reductions were observed for Aichi virus (4.9 log₁₀) and for pepper mild mottle virus (4.4 log₁₀). This study demonstrated that under saturated flow and predominantly anoxic redox conditions MS2 removal was non-linear and could be described well by a power-law relation. Pepper mild mottle virus was removed less than all of the other viruses studied, which substantiates field studies at managed aquifer recharge sites, suggesting it may be a conservative model/tracer for enteric virus transport through soil.

Detection of Norovirus and Rotavirus Present in Suspended and Dissolved Forms in Drinking Water Sources

We investigated the present forms of genogroup II norovirus and group A rotavirus in surface water used for drinking water production. River water samples (N = 15) collected at a drinking water treatment plant (DWTP) monthly from June 2017 to August 2018 were fractioned by filtration through 10- and 0.45-μm-pore-size membranes, and viruses present in suspended and dissolved forms were quantitatively detected. Norovirus GII was present in > 10-μm- and 0.45-10-μm-suspended and dissolved forms with detection rates of 33%, 60%, and 87%, respectively. Rotavirus A was detected more frequently than norovirus GII in each form (> 10 μm suspended, 73%; 0.45-10 μm suspended, 93%; dissolved, 100%). We also analyzed surface water samples from 21 DWTPs all over Japan in non-epidemic and epidemic seasons of gastroenteritis. Norovirus GII was detected in 48% and 81% of samples with the concentrations of up to 4.1 and 5.3 log₁₀ copies/L in dissolved form in non-epidemic and epidemic seasons, respectively, and GII.4 Sydney 2012 was predominant genotype followed by GII.2. Rotavirus A was detected in 95% and 86% of samples with the maximum concentrations of 5.5 and 6.3 log₁₀ copies/L in dissolved form in respective seasons. Concentration of norovirus GII was similar in 0.45-10-μm suspended and dissolved forms, while there was a significant difference for rotavirus A (P < 0.01, pared t test), indicating that rotavirus A was less associated with suspended solids in the surface water samples compared to norovirus GII. Our observations provide important implications for understanding of viral behavior in environmental waters.

Occurrence and reduction of F-specific RNA bacteriophage genotypes as indicators of human norovirus at a wastewater treatment plant

F-specific RNA bacteriophages (FRNAPHs) have been suggested as good indicators of the presence of human enteric viruses in water treatment facilities. The occurrence and reduction of norovirus (NoV) and FRNAPH genotypes in wastewater treatment plants (WWTPs) have been well studied; however, the relationship between these genotypes in WWTPs has not been fully elucidated. Thus, we aimed to investigate the occurrence and reduction of FRNAPH genotypes in an attempt to identify NoV indicators in a WWTP via a 1-year survey. All FRNAPH and NoV genotypes were detected in WWTP influents at high rates (71-100%), including the infectious FRNAPH genotype IV (GIV), which has been rarely detected in previous studies. The reductions of FRNAPH GII and NoV GII during wastewater treatment indicated a relationship between the two (r = 0.69, P < 0.01), and the mean values were not significantly different. These results suggested that FRNAPH GII could be used as an appropriate indicator of NoV GII during wastewater treatment. FRNAPH GI was also found to be an appropriate indicator of viral reduction because of its high resistance to wastewater treatment compared with the other FRNAPH and NoV genotypes; therefore, it can be considered as a worst-case scenario organism.

Development and evaluation of a broadly reactive reverse transcription recombinase polymerase amplification assay for rapid detection of murine norovirus

Background

Murine norovirus (MNV) is recognized as the most prevalent viral pathogen in captive mouse colonies. The rapid detection assay for MNV would be a useful tool for monitoring and preventing MNV infection. A recombinase polymerase amplification (RPA) assay was established in this study to provide a solution for rapid and sensitive detection of MNV.

Results

The detection limit of the RT-RPA assay for the detection of MNV was 1 × 10² copies of RNA molecules per reaction. The assay was specific since there was no cross-reaction with other common murine viruses. In addition, the broad reactivity of the RT-RPA assay was validated using the synthesized template carrying seven point mutations among several MNV strains. The MNV RT-RPA assay could detect as few as 1 × 10² copies of the mutant per reaction, suggesting the assay could be broadly reactive against a large diversity of MNV strains. Forty eight clinical samples including 16 gastric tissue specimens, 16 cecal tissue specimens and 16 fecal specimens were tested for the validation of the new developed RT-RPA assay. The detection results of RT-RPA and RT-qPCR for clinical samples were very similar, except that a gastric tissue sample which was positive by RT-qPCR, with a RNA titer of 27 copies, was negative by RT-RPA.

Conclusions

A broadly reactive RT-RPA assay was successfully established for MNV detection.

A semi-nested RT-PCR assay for detection of norovirus in rat fecal samples

Norovirus is a highly prevalent pathogen that can infect a wide range of host species. Thus far, there have only been two reports of norovirus infection in rats. Diagnostic assays for the detection of norovirus are well established, but a specific molecular assay for the diagnosis of norovirus infection in laboratory rats has not yet been reported. In this study, we describe the development of a sensitive, semi-nested RT-PCR assay for detection of norovirus in fecal samples from Rattus norvegicus, reared in animal facilities under different sanitary barrier conditions. Additionally, we describe the first report of the presence of norovirus in rat colonies from Brazilian animal facilities.

Modelling of ultraviolet light inactivation kinetics of methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus, Clostridium difficile spores and murine norovirus on fomite surfaces

AIMS

Quantitative data on the doses needed to inactivate micro-organisms on fomites are not available for ultraviolet applications. The goal of this study was to determine the doses of UV light needed to reduce bacteria and murine norovirus (MNV) on hard surface fomites through experimentation and to identify appropriate models for predicting targeted levels of reduction.

METHODS AND RESULTS

Stainless steel and Formica laminate coupons were selected as they are common surfaces found in healthcare settings. Test organisms included methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), Clostridium difficile and MNV. The fomites were inoculated with 10⁵ -10⁷ bacteria or virus and exposed to a range of UV doses. The order of resistance to UV irradiation was virus, bacterial spore and vegetative cell. The best fitting inactivation curves suggested nonlinear responses to increasing doses after a 3-4 log reduction in the test organisms. The average UV doses required for a 3 log reduction in the C. difficile, MRSA and VRE were 16 000, 6164 and 11 228 (mJ-s cm^-2 ) for stainless steel, respectively, and 16 000, 11 727 and 12 441 (mJ-s cm^-2 ) for Formica laminate, respectively.

CONCLUSIONS

Higher UV light doses are required to inactivate bacteria and viruses on hard surfaces than in suspension. Greater doses are needed to inactivate bacterial spores and MNV compared to vegetative bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

Quantitative data and models on UV light doses needed to inactivate bacteria and MNV on hard surfaces are now available. The generalizable results of this study can be used to estimate required UV dosages to achieve targeted levels of inactivation based on estimated levels of contamination or to support quantitative microbial risk assessments.

Persistence of Viruses by qPCR Downstream of Three Effluent-Dominated Rivers in the Western United States

This study was designed to determine the quantitative polymerase chain reaction (qPCR) signal persistence of viruses in three effluent-dominated streams. Samples were collected from the effluent outfall of three wastewater treatment plants in the Western United States and downstream at different locations. All samples were tested for the presence of pepper mild mottle virus (PMMoV), adenoviruses, norovirus GI and GII, Aichi virus, and enteroviruses using qPCR. PMMoV was detected most frequently in 54/57 (94.7%) samples, followed by adenoviruses which was detected in 21/57 (36.8%) samples. PMMoV was detected at all locations downstream and up to 32 km from the discharge point. This study demonstrated that the detection signal of PMMoV was able to persist in wastewater discharges to a greater degree than human enteric viruses in effluent-dominated rivers.

Free-Chlorine Disinfection as a Selection Pressure on Norovirus

Human noroviruses are excreted in feces from infected individuals and included in wastewater. It is critical to remove/inactivate them in wastewater treatment processes, particularly in the disinfection step, before release to aquatic environments. However, the high mutation rates of human noroviruses raise concerns about the emergence of strains that are less susceptible to disinfectants and can survive even after wastewater treatment. This study aimed to demonstrate the strain-dependent susceptibility of norovirus to free chlorine. A population originated from the murine norovirus strain S7-PP3, a surrogate for human noroviruses in environmental testing, was exposed to free chlorine and then propagated in a host cell. This cycle of free chlorine exposure followed by propagation in cells was repeated 10 times, and populations with lower susceptibility to free chlorine were obtained from two independent trials of chlorine exposure cycles. Open reading frame 2 (ORF2) and ORF3 of the murine norovirus genome were analyzed by next-generation sequencing, and a unique nonsynonymous mutation (corresponding to a change from phenylalanine to serine) at nucleotide (nt) 7280 in ORF3, which encodes the minor capsid protein VP2, was found in chlorine-exposed populations from both trials. It was confirmed that all of the clones from the chlorine-treated population had lower susceptibility to free chlorine than those from the control population. These results indicate that exposure to free chlorine and dilution exert different driving forces to form murine norovirus (MNV) quasispecies, and that there is a selective force to form MNV quasispecies under free chlorine exposure.IMPORTANCE This study showed that free chlorine disinfection exerted a selection pressure for murine norovirus (MNV). The strain-dependent viral susceptibility to the disinfectant elucidated in this study highlights the importance of employing less susceptible strains as representative viruses in disinfection tests, because the disinfection rate values obtained from more susceptible strains would be less useful in predicting the virus inactivation efficiency of circulating strains under practical disinfection conditions.

Tissue Distribution and Visualization of Internalized Human Norovirus in Leafy Greens

Lettuce has been implicated in human norovirus (HuNoV) outbreaks. The virus is stable on the leaf surface for at least 2 weeks; however, the dynamics of virus internalization have not been fully investigated. The purpose of this study was to assess the internalization and distribution of HuNoV and two surrogate viruses, porcine sapovirus (SaV) and Tulane virus (TV), in lettuce and spinach. Viral inoculations through the roots of seedlings and the petiole of leaves from mature plants were performed, and the viruses were tracked on days 1 and 6 post-root inoculation and at 16 h and 72 h post-petiole inoculation. Confocal microscopy was used to visualize root-internalized HuNoV. In both lettuce and spinach, (i) HuNoV was internalized into the roots and leaves at similar RNA titers, whereas surrogate viruses were more restricted to the roots, (ii) all three viruses were stable inside the roots and leaves for at least 6 days, and (iii) HuNoV disseminated similarly inside the central veins and leaf lamina, whereas surrogate viruses were more restricted to the central veins. Infectious TV, but not SaV, was detectable in all tissues, suggesting that TV has greater stability than SaV. HuNoV was visualized inside the roots' vascular bundle and the leaf mesophyll of both plants. In conclusion, using surrogate viruses may underestimate the level of HuNoV internalization into edible leaves. The internalization of HuNoV through roots and cut leaves and the dissemination into various spinach and lettuce tissues raise concerns of internal contamination through irrigation and/or wash water.IMPORTANCE Human noroviruses are the leading cause of foodborne outbreaks, with lettuce being implicated in the majority of outbreaks. The virus causes acute gastroenteritis in all age groups, with more severe symptoms in children, the elderly, and immunocompromised patients, contributing to over 200,000 deaths worldwide annually. The majority of deaths due to HuNoV occur in the developing world, where limited sanitation exists along with poor wastewater treatment facilities, resulting in the contamination of water resources that are often used for irrigation. Our study confirms the ability of lettuce and spinach to internalize HuNoV from contaminated water through the roots into the edible leaves. Since these leafy greens are consumed with minimal processing that targets only surface pathogens, the internalized HuNoV presents an added risk to consumers. Thus, preventive measures should be in place to limit the contamination of irrigation water. In addition, better processing technologies are needed to inactivate internalized viral pathogens.

Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro

Human norovirus (HuNoV) is a major cause of nonbacterial gastroenteritis worldwide, yet despite its impact on society, vaccines and antivirals are currently lacking. A HuNoV replicon system has been widely applied to the evaluation of antiviral compounds and has thus accelerated the process of drug discovery against HuNoV infection. Rupintrivir, an irreversible inhibitor of the human rhinovirus 3C protease, has been reported to inhibit the replication of the Norwalk virus replicon via the inhibition of the norovirus protease. Here we report, for the first time, the generation of rupintrivir-resistant human Norwalk virus replicon cells in vitro Sequence analysis revealed that these replicon cells contained amino acid substitutions of alanine 105 to valine (A105V) and isoleucine 109 to valine (I109V) in the viral protease NS6. The application of a cell-based fluorescence resonance energy transfer (FRET) assay for protease activity demonstrated that these substitutions were involved in the enhanced resistance to rupintrivir. Furthermore, we validated the effect of these mutations using reverse genetics in murine norovirus (MNV), demonstrating that a recombinant MNV strain with a single I109V substitution in the protease also showed reduced susceptibility to rupintrivir. In summary, using a combination of different approaches, we have demonstrated that, under the correct conditions, mutations in the norovirus protease that lead to the generation of resistant mutants can rapidly occur.

Presence of Human Enteric Viruses, Protozoa, and Indicators of Pathogens in the Bagmati River, Nepal

Quantification of waterborne pathogens in water sources is essential for alerting the community about health hazards. This study determined the presence of human enteric viruses and protozoa in the Bagmati River, Nepal, and detected fecal indicator bacteria (total coliforms, Escherichia coli, and Enterococcus spp.), human-fecal markers (human Bacteroidales and JC and BK polyomaviruses), and index viruses (tobacco mosaic virus and pepper mild mottle virus). During a one-year period between October 2015 and September 2016, a total of 18 surface water samples were collected periodically from three sites along the river. Using quantitative polymerase chain reaction, all eight types of human enteric viruses tested—including adenoviruses, noroviruses, and enteroviruses, were detected frequently at the midstream and downstream sites, with concentrations of 4.4–8.3 log copies/L. Enteroviruses and saliviruses were the most frequently detected enteric viruses, which were present in 72% (13/18) of the tested samples. Giardia spp. were detected by fluorescence microscopy in 78% (14/18) of the samples, with a lower detection ratio at the upstream site. Cryptosporidium spp. were detected only at the midstream and downstream sites, with a positive ratio of 39% (7/18). The high concentrations of enteric viruses suggest that the midstream and downstream regions are heavily contaminated with human feces and that there are alarming possibilities of waterborne diseases. The concentrations of enteric viruses were significantly higher in the dry season than the wet season (p < 0.05). There was a significant positive correlation between the concentrations of human enteric viruses and the tested indicators for the presence of pathogens (IPP) (p < 0.05), suggesting that these IPP can be used to estimate the presence of enteric viruses in the Bagmati River water.

Virological Quality of Irrigation Water Sources and Pepper Mild Mottle Virus and Tobacco Mosaic Virus as Index of Pathogenic Virus Contamination Level

Irrigation water is a doorway for the pathogen contamination of fresh produce. We quantified pathogenic viruses [human adenoviruses, noroviruses of genogroups I and II, group A rotaviruses, Aichi virus 1 (AiV-1), enteroviruses (EnVs), and salivirus (SaliV)] and examined potential index viruses [JC and BK polyomaviruses (JCPyVs and BKPyVs), pepper mild mottle virus (PMMoV), and tobacco mosaic virus (TMV)] in irrigation water sources in the Kathmandu Valley, Nepal. River, sewage, wastewater treatment plant (WWTP) effluent, pond, canal, and groundwater samples were collected in September 2014, and in April and August 2015. Viruses were concentrated using an electronegative membrane-vortex method and quantified using TaqMan (MGB)-based quantitative PCR (qPCR) assays with murine norovirus as a molecular process control to determine extraction-reverse transcription-qPCR efficiency. Tested pathogenic viruses were prevalent with maximum concentrations of 5.5-8.8 log₁₀ copies/L, and there was a greater abundance of EnVs, SaliV, and AiV-1. Virus concentrations in river water were equivalent to those in sewage. Canal, pond, and groundwater samples were found to be less contaminated than river, sewage, and WWTP effluent. Seasonal dependency was clearly evident for most of the viruses, with peak concentrations in the dry season. JCPyVs and BKPyVs had a poor detection ratio and correspondence with pathogenic viruses. Instead, the frequently proposed PMMoV and the newly proposed TMV were strongly predictive of the pathogen contamination level, particularly in the dry season. We recommend utilizing canal, pond, and groundwater for irrigation to minimize deleterious health effects and propose PMMoV and TMV as indexes to elucidate pathogenic virus levels in environmental samples.

Temporal variations in genotype distribution of human sapoviruses and Aichi virus 1 in wastewater in Southern Arizona, United States

AIMS

To investigate the molecular epidemiology, especially temporal variations in genotype distribution, of sapoviruses and Aichi virus 1 (AiV-1) in Arizona, United States, by examining wastewater.

METHODS AND RESULTS

A total of 26 wastewater samples (13 influent and 13 effluent) were collected monthly from a wastewater treatment plant and viral strains were identified through nested reverse transcription-PCR followed by cloning and sequencing analysis. Identified sapovirus strains were classified into seven genotypes belonging to three genogroups (GI, GII, and GV): GI.1, GI.2, GI.3, GII.1, GII.2, GII.8 and GV.1, with a clear temporal shift. The majority of AiV-1 strains identified from the wastewater samples were classified into genotype B, and genotype A strains were identified in only two samples.

CONCLUSIONS

We identified a number of sapovirus and AiV-1 strains belonging to multiple genotypes in wastewater samples collected over a 13-month period. Our results suggested a temporal shift in prevalent genotypes in the community.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study elucidating the genotype distribution of human sapoviruses and AiV-1 in wastewater in the United States. Wastewater surveillance is especially useful for understanding molecular epidemiology of viruses that are less commonly tested in clinical diagnosis, including sapoviruses and AiV-1.

Attempts to grow human noroviruses, a sapovirus, and a bovine norovirus in vitro

Noroviruses (NoVs) and Sapoviruses (SaVs) are enteric caliciviruses that have been detected in multiple mammalian species, including humans. Currently, efficient cell culture systems have been established only for murine NoVs and porcine SaV Cowden strain. Establishment of an efficient in vitro cell culture system for other NoVs and SaVs remains challenging; however, human NoV (HuNoV) replication in 3D cultured Caco-2 cells and a clone of Caco-2 cells, C2BBe1, human enteroids and in human B cells has been reported. In this study, we tested various cells and culture conditions to grow HuNoVs and a human SaV (HuSaV) to test the possibility of the propagation in different cells and culture conditions. We also attempted to grow a bovine NoV (BoNoV) in ex vivo organ cultures. We did not observe significant RNA level increases for HuSaV and BoNoV under our test conditions. HuNoV RNA levels increased to a maximum of ~600-fold in long-term Caco-2 cells that were cultured for 1–2 months in multi-well plates and inoculated with HuNoV-positive and bacteria-free human stool suspensions using serum-free medium supplemented with the bile acid, GCDCA. However, this positive result was inconsistent. Our results demonstrated that HuNoVs, BoNoV and HuSaV largely failed to grow in vitro under our test conditions. Our purpose is to share our findings with other researchers with the goal to develop efficient, reproducible simplified and cost-effective culture systems for human and animal NoVs and SaVs in the future.

Evaluation of Virus Reduction by Ultrafiltration with Coagulation-Sedimentation in Water Reclamation

The evaluation of virus reduction in water reclamation processes is essential for proper assessment and management of the risk of infection by enteric viruses. Ultrafiltration (UF) with coagulation-sedimentation (CS) is potentially effective for efficient virus removal. However, its performance at removing indigenous viruses has not been evaluated. In this study, we evaluated the reduction of indigenous viruses by UF with and without CS in a pilot-scale water reclamation plant in Okinawa, Japan, by measuring the concentration of viruses using the real-time polymerase chain reaction (qPCR). Aichi virus (AiV) and pepper mild mottle virus (PMMoV) were targeted in addition to the main enteric viruses of concern for risk management, namely, norovirus (NoV) genogroups I and II (GI and GII) and rotavirus (RoV). PMMoV, which is a plant pathogenic virus and is present at high concentrations in water contaminated by human feces, has been suggested as a useful viral indicator. We also investigated the reduction of a spiked model virus (F-specific RNA bacteriophage MS2) to measure the effect of viral inactivation by both qPCR and plaque assay. Efficiencies of removal of NoV GI, NoV GII, RoV, and AiV by UF with and without CS were >0.5 to 3.7 log₁₀, although concentrations were below the detection limit in permeate water. PMMoV was the most prevalent virus in both feed and permeate water following UF, but CS pretreatment could not significantly improve its removal efficiency (mean removal efficiency: UF, 3.1 log₁₀; CS + UF, 3.4 log₁₀; t test, P > 0.05). CS increased the mean removal efficiency of spiked MS2 by only 0.3 log₁₀ by qPCR (t-test, P > 0.05), but by 2.8 log₁₀ by plaque assay (t-test, P < 0.01). This difference indicates that the virus was inactivated during CS + UF. Our results suggest that PMMoV could be used as an indicator of removal efficiency in water reclamation processes, but cultural assay is essential to understanding viral fate.

Quantification of multiple waterborne pathogens in drinking water, drainage channels, and surface water in Kampala, Uganda, during seasonal variation

Longitudinal water quality monitoring is important for understanding seasonal variations in water quality, waterborne disease transmission, and future implications for climate change and public health. In this study, microfluidic quantitative polymerase chain reaction (MFQPCR) was used to quantify genes from pathogens commonly associated with human intestinal infections in water collected from protected springs, a public tap, drainage channels, and surface water in Kampala, Uganda, from November 2014 to May 2015. The differences in relative abundance of genes during the wet and dry seasons were also assessed. All water sources tested contained multiple genes from pathogenic microorganisms, with drainage channels and surface waters containing a higher abundance of genes as compared to protected spring and the public tap water. Genes detected represented the presence of enterohemorrhagic Escherichia coli, Shigella spp., Salmonella spp., Vibrio cholerae, and enterovirus. There was an increased presence of pathogenic genes in drainage channels during the wet season when compared to the dry season. In contrast, surface water and drinking water sources contained little seasonal variation in the quantity of microbes assayed. These results suggest that individual water source types respond uniquely to seasonal variability and that human interaction with contaminated drainage waters, rather than direct ingestion of contaminated water, may be a more important contributor to waterborne disease transmission. Furthermore, future work in monitoring seasonal variations in water quality should focus on understanding the baseline influences of any one particular water source given their unique complexities.

Discovery and Synthesis of Heterocyclic Carboxamide Derivatives as Potent Anti-norovirus Agents

There is an urgent need for structurally novel anti-norovirus agents. In this study, we describe the synthesis, anti-norovirus activity, and structure-activity relationship (SAR) of a series of heterocyclic carboxamide derivatives. Heterocyclic carboxamide 1 (50% effective concentration (EC50)=37 µM) was identified by our screening campaign using the cytopathic effect reduction assay. Initial SAR studies suggested the importance of halogen substituents on the heterocyclic scaffold and identified 3,5-di-boromo-thiophene derivative 2j (EC50=24 µM) and 4,6-di-fluoro-benzothiazole derivative 3j (EC50=5.6 µM) as more potent inhibitors than 1. Moreover, their hybrid compound, 3,5-di-bromo-thiophen-4,6-di-fluoro-benzothiazole 4b, showed the most potent anti-norovirus activity with a EC50 value of 0.53 µM (70-fold more potent than 1). Further investigation suggested that 4b might inhibit intracellular viral replication or the late stage of viral infection.

Antiviral effect of theaflavins against caliciviruses

Caliciviruses are contagious pathogens of humans and various animals. They are the most common cause of viral gastroenteritis in humans, and can cause lethal diseases in domestic animals such as cats, rabbits and immunocompromised mice. In this study, we conducted cytopathic effect-based screening of 2080 selected compounds from our in-house library to find antiviral compounds against three culturable caliciviruses: feline calicivirus, murine norovirus (MNV) and porcine sapovirus (PoSaV). We identified active six compounds, of which two compounds, both related to theaflavins, showed broad antiviral activities against all three caliciviruses; three compounds (abamectin, a mixture of avermectin B1a and B1b; avermectin B1a; and (-)-epigallocatechin gallate hydrate) were effective against PoSaV only; and a heterocyclic carboxamide derivative (BFTC) specifically inhibited MNV infectivity in cell cultures. Further studies of the antiviral mechanism and structure-activity relationship of theaflavins suggested the following: (1) theaflavins worked before the viral entry step; (2) the effect of theaflavins was time- and concentration-dependent; and (3) the hydroxyl groups of the benzocycloheptenone ring were probably important for the anti-calicivirus activity of theaflavins. Theaflavins could be used for the calicivirus research, and as potential disinfectants and antiviral reagents to prevent and control calicivirus infections in animals and humans.

Genetically distinct genogroup IV norovirus strains identified in wastewater

We investigated the prevalence and genetic diversity of genogroup IV norovirus (GIV NoV) strains in wastewater in Arizona, United States, over a 13-month period. Among 50 wastewater samples tested, GIV NoVs were identified in 13 (26 %) of the samples. A total of 47 different GIV NoV strains were identified, which were classified into two genetically distinct clusters: the GIV.1 human cluster and a unique genetic cluster closely related to strains previously identified in Japanese wastewater. The results provide additional evidence of the considerable genetic diversity among GIV NoV strains through the analysis of wastewater containing virus strains shed from all populations.

Enteric and indicator virus removal by surface flow wetlands

We investigated the occurrence and attenuation of several human enteric viruses (i.e., norovirus, adenovirus, Aichi virus 1, polyomaviruses, and enterovirus) as well as a plant virus, pepper mild mottle virus (PMMoV), at two surface flow wetlands in Arizona. The retention time in one of the wetlands was seven days, whereas in the other wetland it could not be defined. Water samples were collected at the inlet and outlet from the wetlands over nine months, and concentration of viral genomes was determined by quantitative polymerase chain reaction (qPCR). Of the human enteric viruses tested, adenovirus and Aichi virus 1 were found in the greatest prevalence in treated wastewater (i.e., inlet of the wetlands). Reduction efficiencies of enteric viruses by the wetlands ranged from 1 to 3 log10. Polyomaviruses were generally removed to below detection limit, indicating at least 2 to 4 log10 removal. PMMoV was detected in a greater concentration in the inlet of both wetlands for all the viruses tested (10(4) to 10(7) genome copies/L), but exhibited little or no removal (1 log10 or less). To determine the factors associated with virus genome attenuation (as determined by qPCR), the persistence of PMMoV and poliovirus type 1 (an enterovirus) was studied in autoclaved and natural wetland water, and deionized water incubated under three different temperatures for 21 days. A combination of elevated water temperature and biological activities reduced poliovirus by 1 to 4 log10, while PMMoV was not significantly reduced during this time period. Overall, PMMoV showed much greater persistence than human viruses in the wetland treatment.

Abiotic Stress and Phyllosphere Bacteria Influence the Survival of Human Norovirus and Its Surrogates on Preharvest Leafy Greens

Foodborne outbreaks of human noroviruses (HuNoVs) are frequently associated with leafy greens. Because there is no effective method to eliminate HuNoV from postharvest leafy greens, understanding virus survival under preharvest conditions is crucial. The objective of this study was to evaluate the survival of HuNoV and its surrogate viruses, murine norovirus (MNV), porcine sapovirus (SaV), and Tulane virus (TV), on preharvest lettuce and spinach that were subjected to abiotic stress (physical damage, heat, or flood). We also examined the bacteria culturable from the phyllosphere in response to abiotic stress and in relation to viral persistence. Mature plants were subjected to stressors 2 days prior to inoculation of the viruses on leaves. We quantified the viral RNA, determined the infectivity of the surrogates, and performed bacterial counts on postinoculation days (PIDs) 0, 1, 7, and 14. For both plant types, time exerted significant effects on HuNoV, MNV, SaV, and TV RNA titers, with greater effects being seen for the surrogates. Infectious surrogate viruses were undetectable on PID 14. Only physical damage on PID 14 significantly enhanced HuNoV RNA persistence on lettuce, while the three stressors differentially enhanced the persistence of MNV and TV RNA. Bacterial counts were significantly affected by time and plant type but not by the stressors. However, bacterial counts correlated significantly with HuNoV RNA titers on spinach and with the presence of surrogate viruses on both plant types under various conditions. In conclusion, abiotic stressors and phyllosphere bacterial density may differentially influence the survival of HuNoV and its surrogates on lettuce and spinach, emphasizing the need for the use of preventive measures at the preharvest stage.

Protective role of murine norovirus against Pseudomonas aeruginosa acute pneumonia

The murine norovirus (MNV) is a recently discovered mouse pathogen, representing the most common contaminant in laboratory mouse colonies. Nevertheless, the effects of MNV infection on biomedical research are still unclear. We tested the hypothesis that MNV infection could alter immune response in mice with acute lung infection. Here we report that co-infection with MNV increases survival of mice with Pseudomonas aeruginosa acute lung injury and decreases in vivo production of pro-inflammatory cytokines. Our results suggest that MNV infection can deeply modify the parameters studied in conventional models of infection and lead to false conclusions in experimental models.

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.

Removal properties of human enteric viruses in a pilot-scale membrane bioreactor (MBR) process

In order to evaluate removal properties of human enteric viruses from wastewater by a membrane bioreactor (MBR), influent, anoxic and oxic mixed liquor, and membrane effluent samples were collected in a pilot-scale anoxic-oxic MBR process for 16 months, and concentrations of enteroviruses, norovirus GII, and sapoviruses were determined by real-time PCR using murine norovirus as a process control. Mixed liquor samples were separated into liquid and solid phases by centrifugation, and viruses in the bulk solution and those associated with mixed liquor suspended solids (MLSS) were quantified. Enteroviruses, norovirus GII, and sapoviruses were detected in the influent throughout the sampling period (geometrical mean, 4.0, 3.1, and 4.4 log copies/mL, respectively). Enterovirus concentrations in the solid phase of mixed liquor were generally lower than those in the liquid phase, and the mean log reduction value between influent and anoxic mixed liquor was 0.40 log units. In contrast, norovirus GII and sapovirus concentrations in the solid phase were equal to or higher than those in the liquid phase, and higher log reduction values (1.3 and 1.1 log units, respectively) were observed between influent and anoxic mixed liquor. This suggested that enteroviruses were less associated with MLSS than norovirus GII and sapoviruses, resulting in lower enterovirus removal in the activated sludge process. Enteroviruses and norovirus GII were detected in the MBR effluent but sapoviruses were not in any effluent samples. When MLSS concentration was reduced to 50-60% of a normal operation level, passages of enteroviruses and norovirus GII through a PVDF microfiltration membrane were observed. Since rejection of viruses by the membrane was not related to trans-membrane pressure which was monitored as a parameter of membrane fouling, the results indicated that adsorption to MLSS plays an important role in virus removal by an MBR, and removal properties vary by viruses reflecting different adsorptive behavior to MLSS. Our observations suggested that sapoviruses are more associated with MLSS and removed more efficiently than enteroviruses and norovirus GII.

Culture-independent evaluation of nonenveloped-virus infectivity reduced by free-chlorine disinfection

The inability of molecular detection methods to distinguish disinfected virions from infectious ones has hampered the assessment of infectivity for enteric viruses caused by disinfection practices. In the present study, the reduction of infectivity of murine norovirus S7-PP3 and mengovirus vMC0, surrogates of human noroviruses and enteroviruses, respectively, caused by free-chlorine treatment was characterized culture independently by detecting carbonyl groups on viral capsid protein. The amount of carbonyls on viral capsid protein was evaluated by the proportion of biotinylated virions trapped by avidin-immobilized gel (percent adsorbed). This culture-independent approach demonstrated that the percent adsorbed was significantly correlated with the logarithm of the infectious titer of tested viruses. Taken together with the results of previous reports, the result obtained in this study indicates that the amount of carbonyls on viral capsid protein of four important families of waterborne pathogenic viruses, Astroviridae, Reoviridae, Caliciviridae, and Picornaviridae, is increased in proportion to the received oxidative stress of free chlorine. There was also a significant correlation between the percent adsorbed and the logarithm of the ratio of genome copy number to PFU, which enables estimation of the infectious titer of a subject virus by measuring values of the total genome copy number and the percent adsorbed. The proposed method is applicable when the validation of a 4-log reduction of viruses, a requirement in U.S. EPA guidelines for virus removal from water, is needed along with clear evidence of the oxidation of virus particles with chlorine-based disinfectants.

Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples

To secure food and water safety, quantitative information on multiple pathogens is important. In this study, we developed a microfluidic quantitative PCR (MFQPCR) system to simultaneously quantify 11 major human viral pathogens, including adenovirus, Aichi virus, astrovirus, enterovirus, human norovirus, rotavirus, sapovirus, and hepatitis A and E viruses. Murine norovirus and mengovirus were also quantified in our MFQPCR system as a sample processing control and an internal amplification control, respectively. River water contaminated with effluents from a wastewater treatment plant in Sapporo, Japan, was collected and used to validate our MFQPCR system for multiple viruses. High-throughput quantitative information was obtained with a quantification limit of 2 copies/μl of cDNA/DNA. Using this MFQPCR system, we could simultaneously quantify multiple viral pathogens in environmental water samples. The viral quantities obtained using MFQPCR were similar to those determined by conventional quantitative PCR. Thus, the MFQPCR system developed in this study can provide direct and quantitative information for viral pathogens, which is essential for risk assessments.

Plasmid-based human norovirus reverse genetics system produces reporter-tagged progeny virus containing infectious genomic RNA

Human norovirus (HuNoV) is the leading cause of gastroenteritis worldwide. HuNoV replication studies have been hampered by the inability to grow the virus in cultured cells. The HuNoV genome is a positive-sense single-stranded RNA (ssRNA) molecule with three open reading frames (ORFs). We established a reverse genetics system driven by a mammalian promoter that functions without helper virus. The complete genome of the HuNoV genogroup II.3 U201 strain was cloned downstream of an elongation factor-1α (EF-1α) mammalian promoter. Cells transfected with plasmid containing the full-length genome (pHuNoVU201F) expressed the ORF1 polyprotein, which was cleaved by the viral protease to produce the mature nonstructural viral proteins, and the capsid proteins. Progeny virus produced from the transfected cells contained the complete NoV genomic RNA (VP1, VP2, and VPg) and exhibited the same density in isopycnic cesium chloride gradients as native infectious NoV particles from a patient's stool. This system also was applied to drive murine NoV RNA replication and produced infectious progeny virions. A GFP reporter construct containing the GFP gene in ORF1 produced complete virions that contain VPg-linked RNA. RNA from virions containing the encapsidated GFP-genomic RNA was successfully transfected back into cells producing fluorescent puncta, indicating that the encapsidated RNA is replication-competent. The EF-1α mammalian promoter expression system provides the first reverse genetics system, to our knowledge, generalizable for human and animal NoVs that does not require a helper virus. Establishing a complete reverse genetics system expressed from cDNA for HuNoVs now allows the manipulation of the viral genome and production of reporter virions.

Relative abundance and treatment reduction of viruses during wastewater treatment processes--identification of potential viral indicators

Waterborne pathogenic viruses discharged from wastewater treatment plants (WWTPs) pose potential public health risks. In the present study, we investigated the relative abundance, occurrence, and reduction of eleven different viruses at two WWTPs in southern Arizona over a 12-month period, from August 2011 to July 2012. Influent and effluent samples from the two WWTPs were collected monthly. Viruses were concentrated using an electronegative filter method and quantified using TaqMan-based quantitative PCR (qPCR) assays for each of the virus types (i.e., genogroup I, II and IV noroviruses, sapovirus, enterovirus, group A rotavirus, Aichi virus, pepper mild mottle virus, adenovirus, and JC and BK polyomaviruses), with murine norovirus internal control for the monitoring of extraction-RT-qPCR efficiencies. The pepper mild mottle virus, a plant virus, was found to be the most prevalent virus in both influent and effluent wastewater (annual mean concentration of 3.7-4.4×10(6) copies/L and 4.6-6.3×10(5) copies/L in influent and effluent wastewater, respectively), showing a low reduction by the treatment processes (0.76-0.99 annual mean log10 reduction), and no significant seasonal change in concentration. Aichi virus, a human enteric virus, was also found in greater abundance, and showed lower reduction during wastewater treatment than other human enteric viruses. Our results suggest that these viruses could be used as potential indicators of wastewater reclamation system performance, with respect to virus occurrence and removal.

Mechanisms of antiviral action of plant antimicrobials against murine norovirus

Numerous plant compounds have antibacterial or antiviral properties; however, limited research has been conducted with nonenveloped viruses. The efficacies of allspice oil, lemongrass oil, and citral were evaluated against the nonenveloped murine norovirus (MNV), a human norovirus surrogate. The antiviral mechanisms of action were also examined using an RNase I protection assay, a host cell binding assay, and transmission electron microscopy. All three antimicrobials produced significant reductions (P ≤ 0.05) in viral infectivity within 6 h of exposure (0.90 log10 to 1.88 log10). After 24 h, the reductions were 2.74, 3.00, and 3.41 log10 for lemongrass oil, citral, and allspice oil, respectively. The antiviral effect of allspice oil was both time and concentration dependent; the effects of lemongrass oil and citral were time dependent. Based on the RNase I assay, allspice oil appeared to act directly upon the viral capsid and RNA. The capsids enlarged from ≤ 35 nm to up to 75 nm following treatment. MNV adsorption to host cells was not significantly affected. Alternatively, the capsid remained intact following exposure to lemongrass oil and citral, which appeared to coat the capsid, causing nonspecific and nonproductive binding to host cells that did not lead to successful infection. Such contrasting effects between allspice oil and both lemongrass oil and citral suggest that though different plant compounds may yield similar reductions in virus infectivity, the mechanisms of inactivation may be highly varied and specific to the antimicrobial. This study demonstrates the antiviral properties of allspice oil, lemongrass oil, and citral against MNV and thus indicates their potential as natural food and surface sanitizers to control noroviruses.

MNV primarily surveillance by a recombination VP1-derived ELISA in Beijing area in China

Murine norovirus (MNV) was first found as a surrogate for human norovirus study. However, MNV infection was mostly prevalent in laboratory mice, and its immunomodulatory properties may affect the outcome of animal experiments. MNV surveillance had been performed in Europe, North America and some other countries, but not in China. Nowadays, the complete MNV virions had been used as antigen in MNV serological detection. However, the complexity in the preparation of virions might affect the antigen stability, and the virulence recovery of virion antigen had also been detected. In this study, the caspid VP1 protein was proved to be the mostly predominant antigen in MNV virions. An ELISA method using the recombination VP1 as antigen was developed (rVP1 ELISA). The rVP1 ELISA is more sensitive and less specific than the MNV virion-derived IFA method. To address the prevalence of MNV in China, a totally 600 mouse serum samples from Beijing area were tested by rVP1 ELISA and confirmed by IFA and WB. The MNV infection rate was 11.67%, but most of the MNV-positive samples were from experimental facilities (MNV rate=30.94%), not from commercial vendors (MNV rate=0.27%). Collectively, a sensitive rVP1 ELISA was developed in the current study, and the MNV investigation by rVP1 ELISA showed that MNV infection was mostly prevalent in the laboratory mice, especially the mice from experimental facilities in Beijing area in China.

A broadly reactive one-step SYBR Green I real-time RT-PCR assay for rapid detection of murine norovirus

A one-step SYBR Green I real-time RT-PCR assay was developed for the detection and quantification of a broad range of murine noroviruses (MNVs). The primer design was based on the multiple sequence alignments of 101 sequences of the open reading frame (ORF)1−ORF2 junction of MNV. The broad reactivity and quantitative capacity of the assay were validated using 7 MNV plasmids. The assay was completed within 1 h, and the reliable detection limit was 10 copies of MNV plasmid or 0.063 median tissue culture infective doses per milliliter of RAW264 cell culture-propagated viruses. The diagnostic performance of the assay was evaluated using 158 mouse fecal samples, 91 of which were confirmed to be positive. The melting curve analysis demonstrated the diversity of MNV in the samples. This is the first report of a broadly reactive one-step SYBR Green I real-time RT-PCR assay for detecting of MNVs. The rapid and sensitive performance of this assay makes it a powerful tool for diagnostic applications.

Detection of murine norovirus by reverse transcription loop-mediated isothermal amplification

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RT-LAMP method with the potential to detect a broad range of MNV was developed.

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Sensitivity of RT-LAMP was 50-fold less than that of TaqMan RT-PCR.

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In a practical diagnostic test, RT-LAMP exhibited 96.4% and 94.7% sensitivity compared with TaqMan RT-PCR and nested RT-PCR.

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In a practical diagnostic test, RT-LAMP exhibited 100% specificity compared with both TaqMan RT-PCR and nested RT-PCR.

Murine norovirus (MNV) has considerable genetical and biological diversity and is recognized worldwide as the most common contaminant in laboratory mouse colonies. This study developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) method with the potential to detect a broad range of MNV. RT-LAMP, using a set of five primers containing mixed bases, obtained results under isothermal conditions at 62 °C for 90 min. Sensitivity of RT-LAMP was 50-fold less than that of two-step TaqMan real-time reverse transcription-polymerase chain reaction (TaqMan RT-PCR). Diagnostic performance of RT-LAMP on RNA extracted from mouse fecal specimens was compared with TaqMan RT-PCR and nested RT-PCR. MNV was detected in 54 of 120 mouse fecal specimens by RT-LAMP, and RT-LAMP had an estimated sensitivity and specificity of 96.4% and 100% compared with TaqMan RT-PCR, and 94.7% and 100% compared with nested RT-PCR. RT-LAMP, which does not require expensive instruments, might be useful for the screening of mice actively or persistently infected with MNV.

Antiviral efficacy and mechanisms of action of oregano essential oil and its primary component carvacrol against murine norovirus

AIMS

To investigate the antiviral efficacy of oregano oil and its primary active component, carvacrol, against the nonenveloped murine norovirus (MNV), a human norovirus surrogate.

METHODS AND RESULTS

Along with an observed loss in cell culture infectivity, the antiviral mechanisms of action were determined in side-by-side experiments including a cell-binding assay, an RNase I protection assay and transmission electron microscopy (TEM). Both antimicrobials produced statistically significant reductions (P ≤ 0·05) in virus infectivity within 15 min of exposure (c. 1·0-log10). Despite this, the MNV infectivity remained stable with increasing time exposure to oregano oil (1·07-log10 after 24 h), while carvacrol was far more effective, producing up to 3·87-log10 reductions within 1 h. Based on the RNase I protection assay, both antimicrobials appeared to act directly upon the virus capsid and subsequently the RNA. Under TEM, the capsids enlarged from ≤35 nm in diameter to up to 75 nm following treatment with oregano oil and up to 800 nm with carvacrol; with greater expansion, capsid disintegration could be observed. Virus adsorption to host cells did not appear to be affected by either antimicrobial.

CONCLUSIONS

Our results demonstrate that carvacrol is effective in inactivating MNV within 1 h of exposure by acting directly on the viral capsid and subsequently the RNA.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides novel findings on the antiviral properties of oregano oil and carvacrol against MNV and demonstrates the potential of carvacrol as a natural food and surface (fomite) sanitizer to control human norovirus.