Food and Environmental Virology最新文献

Human norovirus (HuNoV) is the leading cause of foodborne illness in the developed world and a major contributor to gastroenteritis globally. Its low infectious dose and environmental persistence necessitate effective disinfection protocols. Sodium hypochlorite (NaOCl) bleach is a widely used disinfectant for controlling HuNoV transmission via contaminated fomites. This study aimed to evaluate the susceptibility of HuNoV genotypes (n = 11) from genogroups I, II, and IV to NaOCl in suspension. HuNoV was incubated for 1 and 5 min in diethyl pyrocarbonate (DEPC) treated water containing 50 ppm, 100 ppm, or 150 ppm NaOCl, buffered to maintain a pH between 7.0 and 7.5. Neutralization was achieved by a tenfold dilution into 100% fetal bovine serum. RNase pre-treatment followed by RT-qPCR was used to distinguish between infectious and non-infectious HuNoV. Statistical methods, including imputation, machine learning, and generalized linear models, were applied to process and analyze the data. Results showed that NaOCl reduced viral loads across all genotypes, though efficacy varied. Genotypes GI.1, GII.4 New Orleans, and GII.4 Sydney were the least susceptible, while GII.6 and GII.13 were the most susceptible. All NaOCl concentrations above 0 ppm were statistically indistinguishable, and exposure duration did not significantly affect HuNoV reduction, suggesting rapid inactivation at effective concentrations. For instance, some genotypes were completely inactivated within 1 min, rendering extended exposure unnecessary, while other genotypes maintained the initial concentration at both 1 and 5 min, indicating a need for longer contact times. These findings underscore the critical role of HuNoV genotype selection in testing disinfection protocols and optimizing NaOCl concentrations. Understanding HuNoV susceptibility to NaOCl bleach informs better disinfection strategies, aiding public health and food safety authorities in reducing HuNoV transmission and outbreaks.

Noroviruses (NoVs) are the leading cause of non-bacterial gastroenteritis with societal costs of US$60.3 billion per annum. Development of a long amplicon nanopore-based method for dual-typing the RNA-dependent RNA polymerase (RdRp) and major structural protein (VP1) regions from a single RNA fragment could improve existing norovirus typing methods. Application to wastewater-based epidemiology (WBE) and environmental testing could enable the discovery of novel types and improve outbreak tracking and source apportionment. Here, we have developed such a method with a consensus-based bioinformatics pipeline and optimised reverse transcription (RT) and PCR procedures. Inhibitor removal and LunaScript® RT gave robust amplification of the ≈ 1000 bp RdRP + VP1 amplicon for both the GI and GII PCR assays. Platinum™ Taq polymerase showed good sensitivity and reduced levels non-specific amplification (NSA) when compared to other polymerases. Optimised PCR annealing temperatures significantly reduced NSA (51.3 and 42.4% for GI and GII), increased yield (86.5% for GII) and increased taxa richness (57.7%) for GII. Analysis of three NoV positive faecal samples showed 100% nucleotide similarity with Sanger sequencing. Eight GI genotypes, 11 polymerase types (p-types) and 13 combinations were detected in wastewater along with 4 GII genotypes, 4 p-types and 8 combinations; highlighting the diversity of norovirus taxa present in wastewater in England. The most common genotypes detected in clinical samples were all detected in wastewater while we also frequently detected several GI genotypes not reported in the clinical data. Application of this method into a WBE scheme, therefore, may allow for more accurate measurement of norovirus diversity within the population.

Hepatitis E virus (HEV) is currently recognized as an emerging problem and a growing concern for public health in developed countries, with HEV infections mainly attributable to foodborne transmission of HEV-3. The zoonotic HEV genotype 3 infects a wide range of mammalian hosts, with swine considered as the primary host. This study investigates the occurrence of HEV among small ruminants in Portugal. The primary aim of the present research was to evaluate the circulation and the potential for HEV infection among sheep and goats. A total of 400 bile samples and 493 blood samples were collected from sheep and goats at a slaughterhouse in the center region of Portugal, between January 2022 and March 2023. The HEV RNA detection in bile samples was performed using a nested broad-spectrum RT-PCR targeting the ORF1 region. Serological analysis to detect anti-HEV antibodies was conducted using a commercial double-antigen sandwich multi-species ELISA. The HEV RNA was not detected in any bile samples using the nested broad-spectrum RT-PCR. Serological analysis revealed an overall HEV antibody seroprevalence of 2% (10/493, 95% CI: 0.98–3.70) among the small ruminants, namely 2.2% in goats and 2.0% in sheep. Curiously, no statistically significant association among the factors, age, sex and species and HEV seroprevalence was observed. Although HEV RNA was not detected in the bile of sheep and goats, this study the evidence of seroprevalence in these small ruminant species. Further research could provide additional insights into the factors influencing HEV transmission dynamics in small ruminants in Portugal and its potential implications for public health.

The zebrafish larvae/embryo model has been shown to support the replication of seven strains (G1.7[P7], GII.2[P16], GII.3[P16], GII.4[P4], GII.4[P16], GII.6[P7], and GII.17[P13]) of human norovirus (HuNoV). However, due to challenges in consistently obtaining HuNoV-positive stool samples from clinical sources, evaluating HuNoV surrogates in this model is highly valuable. This study assesses the potential of zebrafish embryos and larvae as a model for Tulane virus (TuV) replication. Three infection methods were examined: microinjection, immersion, and feeding. Droplet digital PCR was used to quantify viral RNA across all three infection methods. Microinjection of 3 nL of TuV into zebrafish embryos (< 6-h post-fertilization) resulted in significant replication, with viral RNA levels reaching 6.22 logs at 4-day post-infection. In contrast, the immersion method showed no replication after immersing 4-day post-fertilization (dpf) larvae in TuV suspension for 6 h. Similarly, no replication was observed with the feeding method, where Paramecium caudatum loaded with TuV were fed to 4 dpf larvae. The findings indicate that the zebrafish embryo model supports TuV replication through the microinjection method, suggesting that TuV may serve as a useful surrogate for studying HuNoV pathogenesis. Additionally, TuV can be utilized in place of HuNoV in method optimization studies using the zebrafish embryo model, circumventing the limited availability of HuNoV.

Test protocols have been developed to test water treatment devices/systems for use for treating drinking water that are used at the individual and home level to ensure the removal of waterborne viruses. Current test procedures call for the use of poliovirus type 1 and/or rotavirus SA11. Recently we suggested that selected coliphages could be used as surrogates for poliovirus for testing of point-of-use (POU) water treatment devices, however, rotavirus was not used in those studies. The purpose of this review was to compare studies of POU devices which were tested with poliovirus type 1, simian rotavirus SA11 and coliphage MS2 to determine if the behavior of rotavirus SA11 was significantly different. In addition, an attempt was made to compare the relative resistance of these viruses by various disinfectants used to treat drinking water. In all cases SA11 was removed to an equal or greater degree than poliovirus. SA11 was found to be less resistant to halogens, although one study found it to be more resistance to chloramines than poliovirus and MS2. Based on this review, use of coliphages for testing POU devices appear justified. Additionally, data on chloramines for these viruses would be useful to determine if rotavirus is more resistant than poliovirus and MS2.

Aquatic habitats provide a bridge for influenza transmission among wild and domestic species. However, water sources pose highly variable physicochemical and ecological characteristics that affect avian influenza virus (AIV) stability. Therefore, the risk of survival or transmissibility of AIV in the environment is quite variable and has been understudied. In this study, we determine the risk of waterborne transmission and environmental persistence of AIV in a wild/domestic bird interface in the Central Mexico plateau (North America) during the winter season using a multi-criteria decision analysis (MCDA). A total of 13 eco-epidemiological factors were selected from public-access databases to develop the risk assessment. The MCDA showed that the Atarasquillo wetland presents a higher persistence risk in January. Likewise, most of the backyard poultry farms at this wild-domestic interface present a high persistence risk (50%). Our results suggest that drinking water may represent a more enabling environment for AIV persistence in contrast with wastewater. Moreover, almost all backyard poultry farms evidence a moderate or high risk of waterborne transmission especially farms close to water bodies. The wildlife/domestic bird interface on the Atarasquillo wetland holds eco-epidemiological factors such as the presence of farms in flood-prone areas, the poultry access to outdoor water, and the use of drinking-water troughs among multiple animal species that may enhance waterborne transmission of AIV. These findings highlight the relevance of understanding the influence of multiple factors on AIV ecology for early intervention and long-term control strategies.

Pathogenic viruses in environmental water are usually present in levels too low for direct detection and thus, a concentration step is often required to increase the analytical sensitivity. The objective of this study was to evaluate an automated filtration device, the Innovaprep Concentrating Pipette Select (CP Select) for the rapid concentration of viruses in saline water samples, while considering duration of process and ease of use. Four bacteriophages (MS2, P22, Phi6, and PhiX174) and three animal viruses (adenovirus, coronavirus OC43, and canine distemper virus) were seeded in artificial seawater, aquarium water, and bay water samples, and processed using the CP Select. The recovery efficiencies of viruses were determined either using a plaque assay or droplet digital PCR (ddPCR). Using plaque assays, the average recovery efficiencies for bacteriophages ranged from 4.84 ± 3.8% to 82.73 ± 27.3%, with highest recovery for P22 phage. The average recovery efficiencies for the CP Select were 39.31 ± 26.6% for adenovirus, 19.04 ± 11.6% for coronavirus OC43, and 19.84 ± 13.6% for canine distemper virus, as determined by ddPCR. Overall, viral genome composition, not the size of the virus, affected the recovery efficiencies for the CP Select. The small sample volume size used for the ultrafilter pipette of the system hinders the use of this method as a primary concentration step for viruses in marine waters. However, the ease of use and rapid processing time of the CP Select are especially beneficial when rapid detection of viruses in highly contaminated water, such as wastewater or sewage-polluted surface water, is needed.

Graphical abstract

The emergence of new SARS-CoV-2 variants poses challenges to global surveillance efforts, necessitating swift actions in their detection, evaluation, and management. Among the most recent variants, Omicron BA.2.86 and its sub-lineages have gained attention due to their potential immune evasion properties. This study describes the development of a digital PCR assay for the rapid detection of BA.2.86 and its descendant lineages, in wastewater samples. By using this assay, we analyzed wastewater samples collected in Italy from September 2023 to January 2024. Our analysis revealed the presence of BA.2.86 lineages already in October 2023 with a minimal detection rate of 2% which then rapidly increased, becoming dominant by January 2024, accounting for a prevalence of 62%. The findings emphasize the significance of wastewater-based surveillance in tracking emerging variants and underscore the efficacy of targeted digital PCR assays for environmental monitoring.

Globally, rotavirus continues to be the leading etiology of severe pediatric gastroenteritis, and transmission of the disease via environmental reservoirs has become an emerging concern in developing countries. From August to October 2021, a total of 69 samples comprising 48 of raw and treated sewage, and 21 surface waters, were collected from four Durban wastewater treatment plants (DWWTP), and effluent receiving rivers, respectively. Rotaviruses recovered and identified from the samples were subjected to sequencing, genotyping, and phylogenetic analysis. Of the 65 (94.2%) rotavirus-positive samples, 33.3% were from raw sewage, 16% from activated sludge, 15.9% from final effluents, and 29.0% were from the receiving river samples. A total of 49 G and 41 P genotypes were detected in sewage while 15 G and 22 P genotypes were detected in river samples. G1 genotype predominated in sewage (24.5%) followed by G3 (22.4%), G2 (14.3%), G4 (12.2%), G12 (10.2%), G9 (8.2%), and G8 (6.1%). Similarly, G1 predominated in river water samples (33.3%) and was followed by G2, G4 (20.0% each), G3, and G12 (13.3% each). Rotavirus VP4 genotypes P[4], P[6], and P[8] accounted for 36.6%, 29.3%, and 9.8%, respectively, in sewage. Correspondingly, 45.5%, 31.8%, and 13.6% were detected in river samples. The G and P genotypes not identified by the methods used were 2.1% versus 24.3% and 0.1% versus 9.1% for sewage and river water samples, respectively. Sequence comparison studies indicated a high level of nucleotide identity in the G1, G2, G3, G4, G8 VP7, and P[4], P[6], and P[8] VP4 gene sequences between strains from the environment and those from patients in the region. This is the first environmental-based study on the G and P genotypes diversity of rotavirus in municipal wastewater and their receiving rivers in this geographical region. The high similarity between environmental and clinical rotavirus strains suggests both local circulation of the virus and potential exposure risks. In addition, it highlights the usefulness of sewage surveillance as an additional tool for an epidemiological investigation, especially in populations that include individuals with subclinical or asymptomatic infections that are precluded in case-based studies.

Gastroenteritis and hepatitis are the most common illnesses resulting from the consumption of food contaminated with human enteric viruses. Several natural compounds have demonstrated antiviral activity against human enteric viruses, such as human norovirus and hepatitis A virus, while little information is available for hepatitis E virus. Many in-vitro studies have evaluated the efficacy of different natural compounds against human enteric viruses or their surrogates. However, only few studies have investigated their antiviral activity in food applications. Among them, green tea extract, grape seed extract and carrageenans have been extensively investigated as antiviral natural compounds to improve food safety. Indeed, these extracts have been studied as sanitizers on food-contact surfaces, in produce washing solutions, as active fractions in antiviral food-packaging materials, and in edible coatings. The most innovative applications of these antiviral natural extracts include the development of coatings to extend the shelf life of berries or their combination with established food technologies for improved processes. This review summarizes existing knowledge in the underexplored field of natural compounds for enhancing the safety of viral-contaminated foods and underscores the research needs to be covered in the near future.