Food and Environmental Virology最新文献

Since molecular typing method of enterovirus was introduced, many new types have been discovered. However, due to the low epidemic potential, the information on newer enteroviruses remains limited globally. This study aims to investigate the diversity and phylogeny of newer enterovirus types through environmental surveillance utilizing next-generation sequencing (NGS) technology. Sixty-six wastewater samples were collected from two cities in eastern China between 2019 and 2021 and concentrated 100-fold using a negatively charged membrane method. After cell culture, 388 enterovirus isolates representing 14 serotypes were recovered, including Sabin-like poliovirus type 1 (n = 22) and type 3 (n = 57). Concurrently, RNA extraction was performed on all 66 sewage concentrates, and VP1 semi-nested RT-PCR yielded 56 amplicons, which were subsequently subjected to NGS. The NGS analysis identified a total of 33 serotypes, with echovirus 11, coxsackievirus A10, echovirus 18, coxsackievirus B4, and coxsackievirus B5 being the most prevalent, accounting for 29.11%, 9.87%, 8.27%, 8.14%, and 6.10% of the total reads, respectively. Newer identified enterovirus types A76, A89, A90, and C113 were detected in 1 (1.52%), 17 (25.76%), 5 (7.58%), and 6 (9.09%) sewage samples, respectively. Phylogenetic analysis based on the partial VP1 coding region indicated that these local enteroviruses formed distinct lineages separate from previously identified strains. These findings demonstrate that sewage contains enteroviruses with considerable diversity. NGS-based sewage surveillance offers a significant advantage in data output compared to the cell culture method and can be effectively utilized for monitoring newer enterovirus strains.

Graphical Abstract

Norovirus and rotavirus are the major causes of acute gastroenteritis in humans worldwide. Due to their small size, these enteric viruses present in wastewater become aerosolized. The objective of this study was to assess the presence and concentrations of norovirus and rotavirus in aerosol samples collected from wastewater treatment plants (WWTPs) in Thailand. A developed method for concentrating viruses and performing molecular detection was used to determine naturally occurring enteric viruses. Of the 24 collected aerosol samples, 8 (33.3%) and 2 (8.3%) tested positive for norovirus RNA using RT-qPCR and RT-nested PCR, respectively. Based on RT-qPCR, norovirus GII RNA was detected more frequently in aerosol samples (7/24, 29.2%) compared to norovirus GI RNA (2/24, 8.3%). The norovirus GI concentrations were 9.8 × 10² and 3.2 × 10³ genome copies/m³. The norovirus GII concentrations ranged from 1.5 × 10² to 5.5 × 10³ genome copies/m³. RT-nested PCR detected norovirus GII RNA and the rare GII.21 norovirus strains were identified in the two aerosol samples. However, rotavirus RNA was not detected in any of the aerosol samples using either RT-qPCR or RT-nested PCR. This study highlights the quantification and genotyping of norovirus in aerosol samples generated from wastewater, suggesting a potential effect of airborne transmission for WWTPs workers.

Hepatitis E virus (HEV) is a cause of enterically transmitted hepatitis around the world. Because of the high frequency of asymptomatic infections, the magnitude of HEV infection is underestimated. Wastewater monitoring could be useful to improve our knowledge on HEV epidemiology. In this study, we analyzed the capacity of wastewater surveillance to give an insight into the circulation and the diversity of HEV in two French cities. HEV RNA was detected and quantified by digital PCR in 115 untreated composite wastewater samples collected weekly at the inlet of wastewater treatment plants (WWTPs), 58 at Toulouse WWTP and 57 at Dunkerque WWTP. Plasma HEV RNA in blood donors was detected by a commercial assay (Roche Cobas) over the same period in the same area. HEV diversity was analyzed using long-read single-molecule real-time sequencing (Pacific Biosciences). HEV RNA was detected in 88% and 95% wastewater samples collected at Toulouse (Occitanie region, Southern France) and Dunkerque (Hauts-de-France region, Northern France) WWTPs, respectively. HEV RNA concentration ranged between 4.1 and 5.7 log copies/L and was almost similar between the two sites. A long orf2 fragment of HEV genome (1030 nucleotides) was obtained and sequenced in 45% and 70% of positive HEV RNA wastewater samples collected at Toulouse site and Dunkerque site, respectively. Out of 31 strains identified in Toulouse wastewater, 24 were HEV-3c (77%), 6 were HEV-3f (19%), and 1 was HEV-3h (3%). Out of 55 strains identified in Dunkerque, 30 were HEV-3c (55%) and 25 were HEV-3f (45%). All HEV RNA-positive samples from blood donors that could be genotyped during the study period contained HEV-3. Subtype distribution in 51 blood donors living in Toulouse did not differ from that in Toulouse wastewater. The HEV-3 subtype distribution in 51 Hauts-de-France region blood donors and in Dunkerque wastewater were different, but the predominant subtype was the same (HEV-3c). Lastly, we explored the link between the measurement of viral loads in wastewater and the extent of infection in the served population. Although a good correlation between the peaks of positive HEV RNA estimated in wastewater samples and that observed in blood donors was observed with a lag of + 3 weeks for Toulouse, the correlation was weaker for Dunkerque. Wastewater surveillance system applied locally could be very useful for assessing the HEV infection status of a population.

The effects of allyl isothiocyanate (AITC) on enteric viruses, specifically hepatitis A virus (HAV) and murine norovirus (MNV) as a norovirus surrogate, were evaluated at different concentrations, temperatures, and exposure time. AITC at 0.1 and 0.5% was mixed with each virus and incubated at 10, 25, and 37 °C for 2 h or overnight. AITC demonstrated a concentration-, temperature-, and time-dependent antiviral effect, with the lowest concentration resulting in a modest decrease in viral titer. However, at the highest concentration and 37 °C during overnight incubation, reductions of 3.75 log TCID50/mL for MNV and below the limit of detection for HAV were reported. Additionally, efficacy of AITC was evaluated on human norovirus (HuNoV) GI suspensions using an in situ capture quantitative reverse transcription polymerase chain reaction (RT-qPCR) method. The results indicated that HuNoVs are susceptible to AITC at 37 °C, which partially inhibits the interaction between the viral capsid and its receptor. Furthermore, AITC was tested as a natural disinfectant for produce with treatment times of 15 and 30 min, with no statistically significant changes in viral titers. Although further optimization of AITC application is required, these findings suggest that AITC has potential as a tool to reduce enteric virus contamination on food and food-contact surfaces.

This study presents a comprehensive assessment of viral contamination and antibiotic resistance genes (ARGs) presence in mussels (Mytilus galloprovincialis) (n = 60) collected from retail stores in the Campania region (Italy). High prevalence of human noroviruses (HuNoV) genogroup I (GI) (77%) and genogroup II (GII) (40%), rotaviruses (RV) (60%), and astroviruses (HAstV) (25%) was found, with average levels of 4.34, 5.09, 5.05, and 4.00 Log genome copies (GC)/g, respectively. All samples tested negative for hepatitis A and E viruses. Viral faecal contamination indicators, including somatic coliphages (88%, 3.62 mean Log plaque forming units (PFU)/100 g) and crAssphage (50%, 3.72 mean Log GC/g), showed strong correlations (ρ > 0.65, p-value < 0.05) with HuNoV GII, HAstV, and RV concentrations in mussels. The study also investigated the presence of respiratory viruses, with all samples testing negative for SARS-CoV-2, respiratory syncytial virus, and influenza A virus.

Furthermore, a capsid-integrity RT-qPCR assay was applied to selected positive samples, confirming the presence of potentially infectious viruses and underscoring the associated risks to consumers.

Additionally, ARGs were detected by qPCR, targeting beta-lactams, quinolones, and chloramphenicol resistance genes in both the total and the bacteriophage fractions of selected samples.

Overall, this study emphasizes the importance of continued surveillance and strategic interventions to mitigate public health risks associated with the consumption of contaminated bivalve molluscan shellfish (BMS), which may imply the dissemination of infectious enteric viruses and ARGs within communities.

Human papillomavirus (HPV) is primarily transmitted through sexual contact and is classified into high- and low-risk genotypes based on their association with cancer development. High-risk (HR) genotypes, such as 16 and 18, among others, have been identified as responsible for the development of cervical cancer while low-risk (LR) genotypes, such as 6 and 11, among others, cause anogenital warts. The aim of this study was to determine the presence of HPV genotypes in wastewater from the wastewater treatment plant of the city of Salto, Uruguay in order to analyze the circulating HPV strains in their population. These samples were subjected to qualitative PCR analysis, and genotypes were identified through sequencing of the DNA products. HPV 6, 16, 31, 66, 81, 84, and 145 were frequently detected in wastewater and HPV 6 and 16 were the prevalent in cytological samples. A great diversity of genotypes was evident in the wastewater of the city. The approach of wastewater-based epidemiology as a representation of the circulating HPV genotypes in the population is adequate and an important tool for molecular epidemiologic studies mainly in developing countries such as Uruguay where information concerning genotypes circulation is scarce.

Tick-borne encephalitis virus (TBEV) is a neuroinvasive arbovirus that is primarily transmitted to humans through the bites of Ixodes ricinus ticks. Consumption of unpasteurised milk and dairy products from infected ruminants can also cause infection in humans. In the majority of food-borne TBE (FB-TBE) cases, goat milk and/or cheese has been identified as the source of infection. The aim of the present study was to analyse the persistence of the infectious strain TBEV_Ain_2020 virus in spiked goat and cow raw milks under different storage conditions, and following pasteurisations performed at 63 °C/30 min or 72 °C/15 s. The total genome of TBEV was stable up to 48 h in goat and cow’s milks at 4 °C and 21 °C. In contrast, the viral titre was significantly lower in goat milk from T + 2 h post-contamination up to 17 h compared to culture cell medium and cow milk at 4 °C. At 21 °C, viral titres were lower than in DMEM in both milks up to T + 12 h. Thermal inactivations were effective in goat milk, but were not sufficient to eliminate all infective virus particles in cow milk. These unexpected findings highlighted that pasteurisation processes should be adapted to the species of origin of the milk and to the initial viral load to ensure food safety.

Iron is a cofactor in various biological processes, primarily obtained through dietary intake and also through oral or intravenous supplementation. Elevated iron levels are associated with increased production of reactive oxygen species, causing cellular damage. Additionally, iron influences the body’s response to infections and participates in the synthesis of genetic material and cellular functions. Therefore, this review aims to explore the complex interplay between iron homeostasis and viral infections, analyzing how iron availability affects viral replication, possible mutations, and pathogenesis. The interaction between viruses and iron, although less explored in the literature, indicates the influence of host iron bioavailability on parasite–host interactions. Furthermore, iron absorption is regulated by hepcidin, a peptide hormone produced by the liver, which reduces blood iron levels by inhibiting ferroportin function. Iron is important in viral growth and activities, potentially promoting replication, possible mutations, and increased virulence as seen in some studies with respiratory, enteric, and other viral models. Thus, iron chelators can be a promising preventive therapeutic strategy to limit iron availability and thereby reduce viral infectivity.

Enveloped and non-enveloped virus transmission can occur via person-to-person contact and potentially through contaminated surfaces with human hands. Establishing the efficacy of hand sanitizers, including gel and foam formats, is crucial in reducing the transmission of viruses of human health concern, yet foam hand sanitizers are generally underexplored despite being widely used. Following American Society for Testing and Materials (ASTM) E1052-20, the efficacy of foam-based hand sanitizers—one non-alcohol-based hand sanitizer and four alcohol-based hand sanitizers with benzalkonium chloride and ethanol as active ingredients, respectively—were explored using bacteriophage phi6 (Φ6) as a surrogate for enveloped viruses and bacteriophage MS2 (Emesvirus zinderi) and Tulane virus (TuV) as surrogates for non-enveloped viruses. Significant differences in log reduction were observed among viruses (P ≤ 0.05). After a 10 s exposure, a 5.23 ± 1.64 log reduction was observed for Φ6 while MS2 remained resistant (0.04 ± 0.08 log₁₀ reduction). Conversely, significant log reductions (P ≤ 0.05) were observed for TuV across all foam-based hand sanitizer products ranging from 0.07 ± 0.1 to 1.09 ± 0.22. An exposure time of 10 s (i.e., the typical rubbing time in real-world scenarios following hand sanitizer application) is likely sufficient for enveloped virus inactivation based on the inactivation of bacteriophage Φ6 by the tested commercially available products. However, longer exposure times or different hand sanitizer formulations may be required to achieve similar log reductions against non-enveloped viruses such as human norovirus based on the surrogates (MS2, TuV) tested.

This study investigated the prevalence and genetic diversity of human astrovirus (HAstV), hepatitis A virus (HAV), and hepatitis E virus (HEV) in bivalve mollusks (mussels and oysters) marketed in three tourist cities in the State of Rio de Janeiro, Brazil, from January to December 2022. One hundred and thirty-four samples were processed according to the ISO 15216-1:2017 (Microbiology of food a chain—horizontal method for determination of hepatitis A virus and norovirus in food using real-time RTPCR—Part 1: method for quantification, vol 2017. International Organization for Standardization, Geneva, pp 1–48, 2017), and viral screening was performed by the TaqMan real-time RT-qPCR. HAstV RNA was detected in 13.9% (10/72) of the oyster samples and 14.5% (9/62) of the mussel samples. HAV RNA was detected in 8.1% (5/62) of the mussels, while HEV RNA was not detected in any of the analyzed bivalves. The molecular characterization revealed that HAstV strains detected in live oysters belonged to both classical (HAstV-1) and non-classical (MLB-1) genotypes. The HAV-IA genotype was detected in mussel samples and segregated into two subclusters. This study reports the presence of HAstV and HAV in oysters and mussels marketed in Brazil for the first time. The findings indicate local water contamination in the bivalve sampling areas, highlighting the importance of environmental monitoring and surveillance improvements, particularly in shellfish production areas.