Food and Environmental Virology最新文献

{"title":"In Vitro Efficacy of Foam Hand Sanitizers Against Enveloped and Non-Enveloped Viruses","authors":"Francis Torko,&nbsp;Kristen E. Gibson","doi":"10.1007/s12560-025-09640-8","DOIUrl":"10.1007/s12560-025-09640-8","url":null,"abstract":"<div><p>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 (<i>Emesvirus zinderi</i>) and Tulane virus (TuV) as surrogates for non-enveloped viruses. Significant differences in log reduction were observed among viruses (<i>P</i> ≤ 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 (<i>P</i> ≤ 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.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 2","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-025-09640-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143769879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Occurrence and Molecular Characterization of Human Astrovirus and Hepatitis A Virus in Bivalve Mollusks Marketed in Tourist Cities in Rio de Janeiro, Brazil","authors":"Natália Lourenço dos Santos,&nbsp;Fernanda Marcicano Burlandy,&nbsp;Andreza Soriano Figueiredo,&nbsp;Bruna Figueiredo Lopes,&nbsp;Livia Melo Villar,&nbsp;Adriana Gonçalves Maranhão,&nbsp;Caroline Roberta Soares Salgado,&nbsp;Marcelo Luiz Lima Brandão,&nbsp;Marize Pereira Miagostovich,&nbsp;José Paulo Gagliardi Leite,&nbsp;Carina Pacheco Cantelli","doi":"10.1007/s12560-025-09639-1","DOIUrl":"10.1007/s12560-025-09639-1","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 2","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Navigating Uncertainties in RT-qPCR and Infectivity Assessment of Norovirus","authors":"Razieh Sadat Mirmahdi,&nbsp;Samantha L. Dicker,&nbsp;Nuradeen Garba Yusuf,&nbsp;Naim Montazeri","doi":"10.1007/s12560-024-09632-0","DOIUrl":"10.1007/s12560-024-09632-0","url":null,"abstract":"<div><p>Human norovirus (HuNoV) is the primary cause of gastroenteritis globally. Due to the lack of a reliable cultivation system, RT-qPCR is a gold standard technique for the detection and quantification of HuNoV. However, the inability of PCR to differentiate between infectious from non-infectious particles remains a significant limitation. This study aims to address this limitation by exploring the relationship between culture-based (plaque assay and TCID₅₀) and non-culture-based (RT-qPCR) methods for HuNoV quantification, using Tulane virus as a cultivable surrogate. The ultracentrifuge-purified Tulane virus at 6.7 log₁₀ PFU/ml or 5.8 log₁₀ TCID₅₀/ml in Tris–EDTA buffer (pH 7.2), was serially diluted and subjected to RNA extraction, with or without RNase pretreatment, followed by quantification with RT-qPCR. Further physical characterization of the virus stock was performed with dynamic light scattering and transmission electron microscopy. A strong correlation (Pearson’s Correlation Coefficient of 0.99) was observed between log₁₀ genome copies (GC) and log₁₀ plaque forming units (PFU) per PCR reaction for both RNase-pretreated and unpretreated samples. Beta distributions indicated a similar median GC:PFU ratio of ca. 3.7 log₁₀ for both RNase-pretreated and unpretreated samples. The high GC:PFU ratio may indicate the sensitive nature of RT-qPCR or the presence of intact, non-infectious virus particles. The outcomes of this study will contribute to the more accurate estimation of infectious norovirus particles in food and environmental matrices.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div><div><p>Created in BioRender. Mirmahdi, R. (2024) https://BioRender.com/l49a583</p></div></div></figure></div></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-024-09632-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimization of An Enveloped Virus Surrogate, Bacteriophage Phi6, Recovery from Hands","authors":"Francis Torko,&nbsp;Kristen E. Gibson","doi":"10.1007/s12560-025-09637-3","DOIUrl":"10.1007/s12560-025-09637-3","url":null,"abstract":"<div><p>Surfaces contaminated with enveloped viruses, such as severe acute respiratory syndrome coronavirus 2 and influenza virus, can potentially spread illness via hand contact. Often, the efficacy of hand hygiene interventions relies on virus recovery from hands. However, the recovery of bacteriophage phi6 (Φ6), a recommended surrogate for enveloped viruses, from the entire hands using the ASTM E2011-21 standard has not been optimized. For Φ6 recovery from the hands, three eluents [lysogeny broth (LC), tryptic soy broth (TSB), and 1.5% beef extract (BE)] and three recovery methods [glove juice method (GJM), hand rinsing, and modified dish method] were examined. The effects of inoculum application on either the palmar surface or the whole hand were compared, and virus recovery was assessed under wet and dry conditions to identify the optimal combinations for maximizing Φ6 recovery. Statistical differences among methods, inoculum application, and recovery types were identified. While no statistical difference was observed among the eluents (<i>P</i> = 0.281), LC demonstrated the highest Φ6 recovery efficiency, while TSB and BE had comparable recoveries. Two-way interaction effects were observed between method type vs. application type (<i>P</i> ≤ 0.05), method type vs. recovery type (<i>P</i> ≤ 0.05), and application type vs. recovery type (<i>P</i> ≤ 0.05), indicating these factors influencing one another. Additionally, no Φ6 recovery was obtained for the dry basis recovery type and the GJM method type. Based on the present study, to maximize Φ6 recovery from the hands during hand hygiene studies, inoculum should be applied to the palmar surface and recovered while it is still wet using LC.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-025-09637-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering the Prevalence and Genetic Characterization of Rabbit-Derived Paslahepevirus Balayani (Hepatitis E Virus) in Hebei Province, China","authors":"Xinyue Hu,&nbsp;Jinfeng Wang,&nbsp;Yinuo Wang,&nbsp;Libing Liu,&nbsp;Junjie Miao,&nbsp;Huan Ren,&nbsp;Jianchang Wang,&nbsp;Xiangdong Xu","doi":"10.1007/s12560-025-09636-4","DOIUrl":"10.1007/s12560-025-09636-4","url":null,"abstract":"<div><p><i>Paslahepevirus balayani</i> (hepatitis E virus) is a zoonotic pathogen, with rabbit <i>Paslahepevirus balayani</i> (HEV-3ra) being widely distributed among global rabbit populations. Notably, in China, rabbits constitute a significant HEV host, second only to swine. Emerging evidence suggests that HEV-3ra possesses the capability to cross species barriers and infect humans. Against this backdrop, our investigation aimed to delineate the HEV infection status and epidemiological patterns in the commercial rabbits of Hebei Province, China. We collected 386 liver and 100 fecal samples across four regions in Hebei Province. Detection of HEV RNA in these specimens was achieved by employing reverse transcription quantitative polymerase chain reaction (RT-qPCR) and reverse transcription nested PCR (RT-Nested PCR), focusing on the amplification of a segment of the open reading frame 2 (ORF2) and the complete genome. Among the 486 samples, 73 were tested positive for HEV RNA, resulting in an overall positive rate of 15.0%. The positive rates for liver and fecal samples were 11.7% (45/386) and 28.0% (28/100), respectively. The study successfully obtained 38 partial ORF2 sequences and 5 complete genome sequences. Sequence analysis revealed that the complete genome sequences shared 86.0–94.5% nucleotide identity with HEV-3ra sequences in GenBank. Phylogenetic analysis confirmed that all strains belonged to HEV-3ra and were closely related to previously reported sequences from China. This study provides the first comprehensive genomic overview of circulating HEV-3ra strains in Hebei, offering valuable insights into the infection dynamics and prevalence of HEV-3ra among commercial rabbits, which can inform public health strategies.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantification of Particle-Associated Viruses in Secondary Treated Wastewater Effluent","authors":"Huiyun Wu,&nbsp;Keegan Brighton,&nbsp;Jiahao Chen,&nbsp;Danmeng Shuai,&nbsp;Tiong Gim Aw","doi":"10.1007/s12560-025-09634-6","DOIUrl":"10.1007/s12560-025-09634-6","url":null,"abstract":"<div><p>Viruses can interact with a broad range of inorganic and organic particles in water and wastewater. These associations can protect viruses from inactivation by quenching chemical disinfectants or blocking ultraviolet light transmission, and a much higher dosage of disinfectants is required to inactivate particle-associated viruses than free viruses. There have been only few studies of the association of viruses with particles in wastewater, particularly in secondary treated effluent. As secondary effluent is the source water to the reclaimed water treatment system, this study quantified indigenous enteric viruses, and viral indicators associated with particles in secondary effluents collected from five full-scale water reclamation facilities in the United States. Particle-associated viruses were enumerated using a sequential filtration followed by microfluidic digital PCR. This study showed that enteric viruses and viral indicators (crAssphage and pepper mild mottle virus, PMMoV) were attached to particles of different sizes in secondary effluent. Significantly higher concentrations of RNA viruses including PMMoV, norovirus, and enterovirus were detected in filtrate of the sequential filtration, which contained particles &lt; 0.45 µm. DNA viruses including adenovirus and crAssphage were found to be more associated with larger particles in secondary effluent. Overall, high correlations were observed between viral indicators and enteric viruses, supporting the use of crAssphage and PMMoV to evaluate virus removal efficiency in water and wastewater treatment processes. The association of viruses with particles in wastewater has significant implications on wastewater treatment and disinfection processes as well as virus enumeration in wastewater.</p><h3>Graphic Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-025-09634-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of Enrichment Approaches for the Study of the Viromes in Mollusk Species","authors":"Tongling Chen,&nbsp;Tiantian Wu,&nbsp;Yunyi Hu,&nbsp;Zifeng Zhu,&nbsp;Ji Wu,&nbsp;Datao Lin,&nbsp;Xi Sun,&nbsp;Zhongdao Wu,&nbsp;Yi-Ping Li","doi":"10.1007/s12560-024-09625-z","DOIUrl":"10.1007/s12560-024-09625-z","url":null,"abstract":"<div><p>Invasive alien species such as freshwater snails have significantly affected the food, environment, and the health of humans and animals, which have unfortunately received insufficient attention. To facilitate the study of viromes in snail species, we compared the enrichment effect of cesium chloride (CsCl) and sucrose density gradient ultracentrifugations in the recovery of diverse viruses in <i>Pomacea canaliculata</i> and <i>Achatina fulica</i>. First, we showed that CsCl-based ultracentrifugation enriched more virus contigs and reduced the nucleic acid background of the <i>Pomacea canaliculata</i> and was thus beneficial for virus recovery. Further studies comparing CsCl- and sucrose-based density gradient ultracentrifugations revealed that the former enriched more viral contigs and viral families of RNA viruses, while the latter yielded more DNA viruses from both <i>Pomacea canaliculata</i> and <i>Achatina fulica</i>. Certain RNA virus families, such as <i>Rhabdoviridae, Arenaviridae, Hepeviridae, Astroviridae,</i> and <i>Alphatetraviridae</i>, were exclusively enriched by CsCl-based ultracentrifugation. Conversely, several DNA virus families including <i>Bacilladnaviridae</i>, <i>Nudiviridae</i>, <i>Malacoherpesviridae</i>, and <i>Adintoviridae</i> were solely identified using the sucrose-based method. Therefore, the selection of viral enrichment technique (either CsCl or sucrose density gradient ultracentrifugation) should be carefully considered based on the specific virome (DNA or RNA viruses) being studied in mollusk species.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Metagenomic Survey of Virological Hazards in Market-Ready Oysters","authors":"René A. M. Dirks,&nbsp;Nils P. Sosef,&nbsp;Johanna T. M. Zwartkruis-Nahuis,&nbsp;Marijke M. A. Thijssen,&nbsp;Claudia C. C. Jansen,&nbsp;Ingeborg L. A. Boxman","doi":"10.1007/s12560-024-09630-2","DOIUrl":"10.1007/s12560-024-09630-2","url":null,"abstract":"<div><p>Viral contamination of bivalve molluscs, such as oysters, is a well-recognized food safety risk. The aim of this study was to assess virological hazards in market-ready oysters on the Dutch market. Non-targeted metagenome analysis was first performed on norovirus spiked-in samples showing linear and sensitive detection of norovirus GI.2 and GII.4 down to 14 and 5 genome copies per reaction, respectively. Subsequently, metagenomic measurements were performed to detect vertebrate viral genomes present in 24 undepurated B-area samples and 144 market-ready oyster samples taken in November up to and including February of the years 2015–2021. Genome sequences from fifteen viral species were identified in market-ready oysters which are associated with infections in humans and were detected above the genomic coverage threshold (5%) applied. Among these, the two genera from the <i>Caliciviridae</i> family, norovirus and sapovirus were detected at high prevalence (44 and 30%). Additionally, adeno-associated dependoparvovirus A and B as well as Aichi virus A and B (ribo)nucleic acids were detected (42, 33, 6, and 11%). Nucleic acids from virus species in oysters included potentially hazardous <i>Picobirnavirus, Anellovirus,</i> and multiple <i>Circoviridae</i> and <i>Genomoviridae</i> species. By integrating metagenome analysis into the monitoring process, researchers, food producers and regulatory bodies can gain valuable insights into the viral communities present in the food chain. This allows for the detection of potential pathogenic hazards at an early stage, providing an opportunity for tailored monitoring programs and targeted interventions to maintain the sanitary quality of the production area and safeguard public health.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-024-09630-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effectiveness of Cold Smoking on Inactivating Murine Norovirus in Salami-Like Pork Sausages (Mettwurst), and Hepatitis E Virus and Murine Norovirus in Solution","authors":"Emil Loikkanen,&nbsp;Antti Mikkelä,&nbsp;Suvi Joutsen,&nbsp;Pirkko Tuominen,&nbsp;Leena Maunula","doi":"10.1007/s12560-024-09631-1","DOIUrl":"10.1007/s12560-024-09631-1","url":null,"abstract":"<div><p>Hepatitis E virus (HEV) is a zoonotic virus that infects humans when virus-containing pork products are consumed. This study aimed to explore MNV (murine norovirus) and HEV inactivation during cold smoking and ripening/fermentation treatments used for salami-like sausages (mettwurst). MNV inactivation was monitored in culture medium solution and in sausage while being subjected to a salami-like sausage manufacturing process. The inactivation of MNV in the solution was also monitored at room temperature (RT) for four weeks. HEV inactivation was monitored in solution during the cold smoking process and at RT. A TCID₅₀ assay was used to calculate the infectious MNV and HEV titres. MNV survival was modelled using Bayesian inference. MNV load in solution decreased by as much as 4.7 (SD 0.9) log₁₀ TCID₅₀/ml when it was subjected to the cold smoking process. Modelling revealed that 99.999% MNV might be inactivated during the treatment when observed at a level of 95% CI (Bayesian Confidence Interval). On the contrary, MNV load decreased by only 1.8 (0.2) log₁₀ when stored at RT. The low-titre HEV in solution was inactivated (&gt; 1.1 (0.2) log₁₀) when treated, and at RT. However, MNV was resistant in the sausage matrix during the cold smoking process (log₁₀ reduction of 1.9 (0.5) TCID₅₀/ml). Based on modelling, a substantial amount of virus would remain in the product, even when the uncertainty was considered. Hence, viruses, here exemplified by MNV, may not be inactivated from salami-like pork sausages during manufacturing, which poses a risk for consumers in real-life situations.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-024-09631-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeted Enrichment Sequencing Utilizing a Respiratory Pathogen Panel for Genomic Wastewater-Based Viral Epidemiology in Uruguay","authors":"Florencia Cancela,&nbsp;Andrés Lizasoain,&nbsp;Yanina Panzera,&nbsp;Elena Fernández-López,&nbsp;Joaquín Lozano,&nbsp;Lucia Calleros,&nbsp;Sofia Grecco,&nbsp;Ana Eugenia Marandino,&nbsp;María Noel Cortinas,&nbsp;Gisela Masachessi,&nbsp;Silvia Nates,&nbsp;Romina Icasuriaga,&nbsp;Rodney Colina,&nbsp;Santiago Mirazo","doi":"10.1007/s12560-024-09629-9","DOIUrl":"10.1007/s12560-024-09629-9","url":null,"abstract":"<div><p>Human respiratory and enteric viruses are responsible for substantial morbidity and mortality worldwide. Wastewater-based epidemiology utilizing next-generation sequencing serves as an effective tool for monitoring viral circulation dynamics at the community level. However, these complex environmental samples are often laden with other microorganisms and host genomic material, which can hinder the sensitivity of viral detection. To address this limitation, targeted enrichment sequencing is emerging as a preferred strategy, facilitating the acquisition of a more comprehensive understanding of specific pathogens. In this study, we evaluated the performance of a targeted enrichment sequencing panel for 42 excreted respiratory viruses (including <i>Picornaviridae, Adenoviridae, Coronaviridae, Paramyxoviridae, Orthomyxoviridae, Orthoherpesviridae, Pneumoviridae</i>, and <i>Parvoviridae</i> families), known as the Respiratory Pathogen ID/AMR enrichment panel (RPIP), coupled with Explify bioinformatics analysis in 3 sewage samples from Uruguay. RPIP panel successfully identified sequences from frequently circulating viruses, along with some that had not been documented previously. We identified and characterized various viruses, including human Enterovirus (Coxsackievirus A1 and A19), Influenza A-H1N1, and full-length sequences of SARS-CoV-2. Additionally, several other viral pathogens were detected, such as human Bocavirus, human Parechovirus, Enterovirus A71, and Enterovirus D68; however, for these viruses further analysis was limited due to the small genomic regions or low-read coverage obtained. While the RPIP panel necessitates substantial sequencing depth and may introduce bias towards the more predominant strains present in the samples, this approach suggests its viability as a genomic epidemiological tool for assessing respiratory and enteric viruses in wastewater.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}