Food and Environmental Virology最新文献

Currently, the predominant commercially available disinfectants and sanitizers are formulated with active ingredients including alcohol, halogenated compounds (e.g., sodium hypochlorite), surfactants, oxidizing agents (eg., hydrogen peroxide), and quaternary ammonium compounds. Natural products represent an alternative since they are often effective microbicides and are generally recognized as safe (GRAS) due to their long history of use. The purpose of this study was to evaluate the efficacy of several organic acids and plant essential oils against three bacteriophages (MS2, ΦX174, PR772) with different genome characteristics (e.g., RNA versus DNA, single-stranded versus double-stranded) and against an enveloped and non-enveloped mammalian virus (human coronavirus 229E and feline calicivirus, respectively). The active components of essential oils (carvacrol, cinnamaldehyde, eugenol, thymol) and organic acids (acetic, salicylic, tartaric) demonstrated virucidal activity against the three bacteriophages (typically 1.00 log₁₀ to > 5.00 log₁₀ reductions within 10 min); however, ΦX174 exhibited lesser susceptibility (< 1.0 log₁₀ reduction with all but salicylic acid) and PR772 was the most resistant to cinnamaldehyde. It is unclear why ΦX174, a ssDNA virus, was more resistant to these antimicrobials than the ssRNA (MS2) and dsDNA (PR772) viruses. Carvacrol, eugenol, and thymol were also highly effective against both mammalian viruses (≥ 1.49 and > 3.00 log₁₀ reductions within one and 10 min, respectively). Salicylic acid was the most effective antimicrobial tested with > 3.84 log₁₀ reductions observed with all the viruses in one minute. Based on these results, several of the organic acids and essential oil components included appear to be viable eco-friendly alternatives to currently used disinfectants/sanitizers that are effective against viruses possessing diverse genomic and morphological characteristics.

Hepatitis E virus (HEV), human astrovirus (HAstV), and sapovirus (SaV) are pathogens associated with foodborne disease outbreaks. We developed a rapid and sensitive quadruple real-time fluorescence quantitative PCR (RT-qPCR) method for the simultaneous detection of HEV, HAstV, and SaV, using MS2 phage as a process control virus. We optimized the experimental parameters, detection limits for HEV, HAstV, SaV, and MS2 RNA were 10³ copies/μL, 10³ copies/μL, 10² copies/μL, and 10³ copies/μL, respectively, with intra-method and inter-method coefficients of variation below 3.0%, indicating good reproducibility and a total detection time of less than 90 min. We collected 354 bivalve shellfish samples from various regions in Hebei Province. After optimizing the proteinase K-PEG 8000 precipitation-chloroform extraction method for viral nucleic acid extraction, we applied the quadruple real-time RT-qPCR for simultaneous detection. The positive rates were 9.60% (34/354) for HEV, 3.67% (13/354) for HAstV, and 6.78% (24/354) for SaV, with mixed contaminations observed for HEV and HAstV (0.28%), HEV and SaV (2.54%), and HAstV and SaV (0.56%). In addition, a single real-time RT-qPCR was performed on 200 randomly selected samples and showed an overall agreement with the quadruple method of 98.67%, 100% positive agreement, 98.54% negative agreement and a Kappa value of 0.922. In conclusion, this quadruple real-time RT-qPCR method offers rapid screening for HEV, HAstV, and SaV in bivalve shellfish.

Monitoring viral loads in sewage can reflect the prevalence of infections within communities to a certain extent. Methods for concentrating and enriching viruses in sewage are also rapidly evolving. The magnetic bead method has been widely adopted for nucleic acid extraction due to its simplicity and high efficiency. In this study, we designed three pre-treatment procedures (T1: sedimentation for 30 min; T2: low-speed centrifugation at 2500×g for 5 min; T3: high-speed centrifugation at 8000×g for 5 min) to identify the optimal pre-treatment for enhancing viral nucleic acid concentration efficiency using the magnetic bead method. Spiked recovery tests were employed to compare the concentration efficiency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in sewage between the magnetic bead method and the traditional polyethylene glycol (PEG) precipitation method. Real sewage samples were further used to evaluate both methods for enriching enveloped viruses (SARS-CoV-2, influenza virus) and non-enveloped viruses (Norovirus, Rotavirus, Adenovirus). Results demonstrated that low-speed centrifugation (T2) served as the optimal pre-treatment for the magnetic bead-based concentration. The high-throughput magnetic bead method achieved significantly higher recovery rates for SARS-CoV-2, Norovirus, and Adenovirus compared to PEG precipitation. Thus, the high-throughput magnetic bead method can be widely applied for the concentration and concentration of diverse viruses in sewage.

Cosavirus (CoSV) and Salivirus (SalV) are two novel picornaviruses that are associated with human diseases. However, epidemiological data on these viruses in China remain limited. In this study, we conducted the first simultaneous investigation of CoSV and SalV in a city of eastern China by wastewater-based epidemiology (WBE) method. From 2021 to 2023, a total of 21 influent wastewater samples were collected. After virus concentration and molecular detection, 71.43% (15/21) and 80.95% (17/21) of samples tested positive for CoSV and SalV, respectively. The sequences of CoSV were determined to be CoSV-A and CoSV-D, and SalV were all genotyped to be SalV-A1. Phylogenetic analysis showed that UTR region of CoSV-D and 3D region of CoSV-A can be divided into several clusters. UTR region of CoSV-A, UTR and 3D region of SalV-A1 were not clustered. Furthermore, the sequences in this study were closely related to some strains from human samples in China and wastewater samples in other countries. These findings reveal that CoSV and SalV circulated at a high prevalence in the local population and demonstrate that WBE is an effective method for novel picornaviruses research.

Viruses are key components of soils, influencing microbial dynamics and biogeochemical cycles. Here, we used shotgun metagenomics to analyze the virome of hydrocarbon-contaminated and uncontaminated soils from King George Island, Antarctica. Viral sequences were obtained from metagenomes of all soils; however, the relative abundance of viruses was higher in hydrocarbon-contaminated soils compared to uncontaminated soils. Our results indicate that viral distribution correlates with polycyclic aromatic hydrocarbons (PAHs) in King George Island soil (p = 0.05). Taxonomic analysis of viral contigs revealed viruses from realms Duplodnaviria, Varidnaviria, Monodnaviria, and Riboviria. While Caudoviricetes (realm Duplodnaviria) represented more than 90% of the relative abundance of viruses found in hydrocarbon-contaminated soils, this class represented less than 62% of the viruses of uncontaminated soils. Most viral hosts detected in King George Island soils belonged to hydrocarbon-degrading bacterial genera from the phyla Pseudomonadota and Actinomycetota. Hydrocarbon contamination resulted in the enrichment of well-characterized viruses at the expense of previously uncharacterized viral taxa, which were predominantly detected in non-contaminated soils. Among them, Gordonia-related Stormageddonvirus was the most abundant viral entity identified in King George Island soil. Viral auxiliary metabolic genes (AMGs) associated with nitrogen and phosphate cycles were found in different Caudoviricetes-related contigs. Our results further indicate that Caudoviricetes abundance is correlated with the carbon: phosphate (C:P) ratio in King George Island soils. We propose the Caudoviricetes may actively contribute to microbial competition for phosphorus in hydrocarbon-contaminated soils. These findings shed light on the intricate interplay between viruses, microbial hosts, and environmental contamination in Antarctic soils.

Hepatitis E is an emerging zoonosis caused by the hepatitis E virus (HEV) and is recognised worldwide. Wild boars are considered one of the main reservoirs of the zoonotic HEV-3 genotype. However, HEV-3 has also been detected in many other wildlife species. In this study, we investigated 284 liver and muscle tissue samples from wild boars and 107 liver and muscle tissue samples from four different wild ruminant species (red deer, roe deer, European mouflon and fallow deer) across 35 hunting areas in Slovakia. HEV RNA was detected in 14.2% (95% CI 9.8–18.6%) of the liver and 10.5% (95% CI 0.4–20.6%) of the muscle tissue samples from wild boars but in none of the samples from the wild ruminant species. Phylogenetic analysis based on partial ORF1 and ORF2 of the HEV genome revealed that the Slovak wild boar HEV sequences clustered within the zoonotic genotype HEV-3. Depending on their geographical origin, the obtained sequences clustered into three HEV-3 subtypes: HEV-3a, HEV-3i and HEV-3e. Our findings confirm the circulation of HEV in the wild boar population in the Slovak Republic but not in wild ruminant species.

Wastewater-based epidemiology (WBE) is a well-established tool for monitoring enteric and respiratory viruses. However, its potential application to vector-borne diseases, including dengue virus (DENV), remains largely underexplored. This study investigated the feasibility of using WBE to detect DENV serotype 2 RNA during the largest dengue outbreak recorded to date in Italy (216 confirmed and probable cases), that occurred in the Marche Region (central Italy) from August to October 2024. From 1 to 30 October, during the decline of the epidemic (30 reported cases), 27 wastewater samples were collected from wastewater treatment plants in the affected municipality of Fano and in the nearby urban center of Pesaro. Four viral RNA concentration methods were tested: polyethylene glycol/sodium chloride precipitation, Nanotrap^® Magnetic Virus Particles, electropositive membrane filtration, and solid fraction analysis. Only solid fraction analysis detected DENV-2 RNA in 9 samples, with digital RT-PCR showing greater sensitivity than Real-time RT-PCR. Virus concentrations ranged from 6.1 × 10¹ to 7.9 × 10² genome copies per gram of solid material. This study highlights the feasibility of WBE as a complementary surveillance tool for vector-borne diseases. Future efforts should focus on refining detection methods and in exploring surveillance strategies for timely wastewater sampling to improve early warning and/or outbreak management.

Waterborne pathogens pose a serious threat to public health, emphasizing the need for reliable and efficient water treatment technologies. Wastewater treatment plants employ a range of processes to reduce microbial contamination, with membrane filtration emerging as a promising solution due to its ability to physically remove pathogens without the production of harmful chemical by-products. This study investigates the effectiveness of a gravity-driven membrane (GDM) filtration system for pathogen removal from wastewater and evaluates the associated public health risks with and without treatment. A quantitative microbial risk assessment model was employed to estimate infection probabilities for various waterborne pathogens. The results demonstrated a significant decrease in pathogen concentrations following treatment, with up to a 10⁴-fold reduction in norovirus infection risk. Three critical factors influencing membrane performance were identified: membrane integrity, pore size characteristics, and membrane fouling. Maintaining membrane integrity was found to be essential for ensuring consistent pathogen removal. While nominal pore size is commonly used to predict rejection efficiency, the overall pore size distribution was found to have a greater influence on virus retention. Additionally, although membrane fouling is often considered detrimental, it was shown to enhance virus removal by up to two orders of magnitude. These findings underscore the potential of GDM systems for effective virus removal and highlight the importance of proper membrane design, maintenance, and monitoring in ensuring long-term operational efficiency and maximizing public health protection in wastewater treatment applications.

This study focuses on the characterization of human viral diversity within a major Wastewater Treatment Plant (WWTP) in the central area of Tianjin, China, with a particular emphasis on adenoviruses due to their robust survivability and potential health implications. By employing metagenomic sequencing, targeted sequencing, quantitative polymerase chain reaction (qPCR) analysis, and cell culture methodologies, we identified a broad spectrum of human viruses, encompassing 25 viral families and 45 viral genera, including enteric, respiratory, and contact viruses. Our findings demonstrate that adenoviruses were stably present in sewage from January to May and retained their infectious activity. The temporal analysis of viral loads across different months revealed no significant changes, suggesting a consistent risk of exposure. Additionally, our phylogenetic analysis of adenoviruses isolated from A549 cell cultures provides insights into their genotypic diversity and potential transmission dynamics. This comprehensive assessment underscores the critical need for improved viral surveillance in urban wastewater systems to mitigate public health risks and highlights the importance of advanced treatment technologies to address the challenges posed by adenoviruses and other pathogenic viruses in municipal wastewater.

Surveillance in wild birds is essential for the timely detection of high pathogenicity avian influenza (HPAI) strains. As flocks congregate in large numbers in wetlands and may potentially contaminate the environment with pathogens, the monitoring of such water bodies represents an attractive opportunity to complement animal testing and to improve surveillance for avian influenza. To increase sensitivity, water concentration is often required but available methods based on (ultra)filtration and precipitation are mostly limited by the use of pumping equipment and by the need to identify the representative sample volumes. In contrast, passive samplers (PS) offer a cost-effective and scalable solution that requires basic devices for the deployment of adsorbent materials and minimal training for their installation in the field. This study evaluated nine materials for their virus adsorption efficiency in brackish and freshwater. Cotton gauze, nitrocellulose, and nylon showed the best performance across different deployment times, with the highest recovery after 24 h. Shorter (3 h) and longer (7 days) deployments also proved effective, accommodating different sampling regimens according to the logistical needs. Importantly, PS revealed their efficacy in adsorbing also deteriorated virions or in dynamic ecosystems subjected to changes in water volumes. Field trials in wetlands corroborated laboratory findings and demonstrated that PS allowed detecting avian influenza virus (AIV, including HPAI strains) genome in water bodies, yielding consistent results with active surveillance in wild birds. By offering a simple, cost-effective, and versatile solution, PS represent a promising tool for environmental AI monitoring and can successfully complement existing avian influenza surveillance activities.