Food and Environmental Virology最新文献

{"title":"Multi-virus Wastewater Surveillance in Heterogeneous Urban-Sewage Systems: Comparative Insights From Sewage Treatment Plants and Open Drains","authors":"Ambreen Shaikh,&nbsp;Shivam Nikam,&nbsp;Nerges Mistry","doi":"10.1007/s12560-026-09714-1","DOIUrl":"10.1007/s12560-026-09714-1","url":null,"abstract":"<div><p>Wastewater-based epidemiology (WBE) has been applied for public health surveillance for several decades but gained unprecedented global prominence during the COVID-19 pandemic, leading to its broader adoption for multi-pathogen surveillance. However, the impact of heterogeneous urban wastewater infrastructure on the detection and interpretation of pathogen signals remains inadequately characterised, particularly in settings such as Mumbai, with fragmented and partially connected sewer networks. This study systematically compared multi-pathogen wastewater surveillance from centralised sewage treatment plants (STPs) and decentralised open drains (ODs), which represent aggregated and localised population catchments, respectively. Wastewater was collected during two monitoring periods (2023 and 2024) and analysed by RT-qPCR for SARS-CoV-2, influenza viruses, and respiratory syncytial virus (RSV). Comparative analyses included detection frequency, temporal dynamics, and patterns of viral co-occurrence between node types. Viral detection rates were highest in STP influent, consistent with signal integration over larger populations and reduced short-term variability. Conversely, open drains exhibited greater temporal fluctuation, which may be consistent with localised, short-term changes but with reduced signal persistence. In the absence of concurrent clinical data, these node-level differences are interpreted as patterns in the wastewater signal rather than demonstrated gains in epidemiological sensitivity or earlier detection. SARS-CoV-2 was consistently detected across both node types, while influenza virus detection was more sporadic and exhibited marked variability, suggesting seasonal transmission dynamics. Co-detection of influenza A and B was observed in 2023, and influenza A subtyping revealed limited within-type diversity; source attribution for the detected subtypes could not be determined. Collectively, these findings indicate that wastewater signal profiles reflect an interplay between pathogen-specific characteristics and the structural configuration of the sampling network. Overall, the findings support integrated surveillance frameworks that leverage both centralised and decentralised nodes, while highlighting the need for extended temporal monitoring and independent clinical validation to strengthen epidemiological inference.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149316951","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":"Multi-Virus Surveillance Across Diverse Freshwater Systems in Tehran, Iran","authors":"Mohammad Tanhaei,&nbsp;Guangming Jiang,&nbsp;Seyed Masoud Hosseini,&nbsp;Maedeh Rafieepoor,&nbsp;Yaser Nikpeyman,&nbsp;Mahsa Saeedi Niasar,&nbsp;Shabnam Kazemian,&nbsp;Bahareh Nadalian,&nbsp;Abbas Yadegar,&nbsp;Hamed Mirjalali,&nbsp;Amir Ghaemi,&nbsp;Matthew D. Moore,&nbsp;Mohammad Reza Zali,&nbsp;Seyed Reza Mohebbi","doi":"10.1007/s12560-026-09712-3","DOIUrl":"10.1007/s12560-026-09712-3","url":null,"abstract":"<div><p>Environmental surveillance of viral contaminants in water systems is an essential tool for assessing exposure risk and supporting early-warning frameworks for emerging infectious diseases. In this study, a comprehensive one-year surveillance of SARS-CoV-2 and six enteric viruses was conducted across diverse freshwater systems in Tehran, Iran — including rivers, wells, and traditional qanat (underground aqueduct) infrastructures. Water quality parameters (turbidity, pH, Total Dissolved Solids, nitrate) and fecal bacterial indicators (total coliforms, fecal coliforms, and <i>E. coli</i>) were also measured to contextualize viral contamination within a broader environmental risk framework. Between September 2020 and August 2021, a total of 118 water samples were collected and analyzed using quantitative molecular detection methods. Overall, 61 of 118 samples (51.7%) tested positive for at least one virus. Surface water (rivers) showed substantially higher contamination rates (80.3%; 53/66 samples) compared to groundwater (15.4%; 8/52 samples). Among groundwater sources, qanat systems were markedly more vulnerable than conventional wells, with 25.0% (6/24) of qanat samples testing positive versus only 7.1% (2/28) of well samples. This elevated contamination in qanats was dominated by rotavirus (5/6 positive qanat samples, detection rate 20.8%) and was associated with higher fecal bacterial loads (total coliform geometric mean: 245 MPN/100 mL in qanats vs. 28 MPN/100 mL in wells), consistent with the susceptibility of shallow horizontal collection channels to fecal infiltration. SARS-CoV-2 RNA was detected in 34.8% of river samples and 3.9% of groundwater samples, with concentrations reaching 1.28 × 10⁴ genome copies per liter (GC/L) in surface waters, demonstrating sustained fecal contamination across all seasons. The most prevalent viruses in river water were norovirus GII (45.5%), adenovirus (43.9%), rotavirus (42.4%), and norovirus GI (40.9%), with mean concentrations ranging from 1.26 × 10² to 3.76 × 10³ GC/L. Hepatitis A and E viruses were not detected in any sample. Seasonal variation in viral detection was observed for enteric viruses, while SARS-CoV-2 and adenovirus showed year-round persistence. Strong correlations between fecal indicators and viral contamination (Spearman <i>r</i> = 0.61–0.63) support the use of bacterial monitoring as a cost-effective screening proxy. The results highlight the particular vulnerability of qanat systems and underscore the value of integrated environmental surveillance for water safety management in arid, water-stressed urban environments.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149284738","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":"Longitudinal Surface Water Viral Surveillance Following the 2024 Extreme Flood: One-Year Monitoring in Porto Alegre, Brazil","authors":"Thales De Lima Bermann,&nbsp;Fernanda Mückler-Pereira,&nbsp;Bruno Aschidamini Prandi,&nbsp;Nicóle Verardo De Mattos,&nbsp;Vítor Felippi Tessele,&nbsp;Luis Gustavo Dos Santos Da Silva,&nbsp;Nicole Vieira Stone,&nbsp;Raíssa Gasparetto,&nbsp;Bruna Simone Paredes-Galarza,&nbsp;Martha Trindade Oliveira,&nbsp;Louidi Lauer Albornoz,&nbsp;Lucas Bohnenberger,&nbsp;Salatiel Wohlmuth da Silva,&nbsp;Ana Cláudia Franco","doi":"10.1007/s12560-026-09713-2","DOIUrl":"10.1007/s12560-026-09713-2","url":null,"abstract":"<div><p>Extreme flood events can overwhelm sanitation infrastructure and drive the widespread dispersal of viral pathogens into aquatic environments. In May 2024, Porto Alegre (southern Brazil) experienced an unprecedented flood that caused record-breaking overflow of the Guaíba hydrological system and prolonged urban inundation. Here we report a one-year longitudinal environmental viral surveillance study, comprising seven campaigns between May 2024 and April 2025. Surface waters were analyzed by RT-qPCR for SARS-CoV-2, norovirus genogroups I and II, hepatitis A virus (HAV) and hepatitis E virus (HEV). All five targets were detected simultaneously during the flood peak, reflecting widespread contamination possibly driven by sewage overflow and multi-site infrastructure failure. Thereafter, the number of targets detected per campaign was lower and fluctuating (two to four), tracing a transition from an initial multi-pathogen contamination pulse observed during the flood peak to persistent detection of viral genomic material in surface waters. SARS-CoV-2 was detected in every campaign, in a minority of sites in all campaigns except the last (C7, 14/22, 63.6%), where both detection frequency and viral load increased significantly (<i>p</i> &lt; 0.001 for both; median Ct 29.7 versus 36.8). HEV was detected only at the flood peak; norovirus GII was detected intermittently up to C6, without a significant temporal pattern (<i>p</i> = 0.13); and norovirus GI was absent between C2 and C5, reappearing in C6 and C7. HAV detection increased significantly over the monitoring period (Cochran–Armitage <i>p</i> &lt; 0.0005), temporally coincident with an officially declared hepatitis A outbreak. These findings demonstrate the value of longitudinal, multi-target environmental surveillance for capturing both the acute virological impact of extreme flooding and the persistent contamination dynamics that follow, pointing to chronic vulnerabilities in urban wastewater infrastructure that outlast the emergency.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13710650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149260268","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":"Long-Term Wastewater Genomic Surveillance Reveals SARS-CoV-2 Variant Dynamics in Italy from 2021 to 2025","authors":"C. Veneri,&nbsp;G. Bonanno Ferraro,&nbsp;P. Mancini,&nbsp;D. Brandtner,&nbsp;M. Iaconelli,&nbsp;D. Congiu,&nbsp;A. Franco,&nbsp;L. Lucentini,&nbsp;C. Del Giudice,&nbsp;M. Rossi,&nbsp;G. D’Avenio,&nbsp;P. Stefanelli,&nbsp;L. Ambrosio,&nbsp;A. Mammone,&nbsp;E. Suffredini,&nbsp;The SARI Network,&nbsp;G. La Rosa","doi":"10.1007/s12560-026-09711-4","DOIUrl":"10.1007/s12560-026-09711-4","url":null,"abstract":"<div><p>Long-term genomic surveillance of SARS-CoV-2 remains important as routine clinical testing and sequencing decline over time after the pandemic. We describe the temporal dynamics, methodological adaptation, and operational continuity of Italy’s national wastewater variant surveillance from October 2021 to December 2025. Across 51 monthly surveys, 6,278 wastewater samples collected from 167 wastewater treatment plants in 18 Regions and 2 Autonomous Provinces were analysed by RT-qPCR and targeted spike sequencing using short- and long-amplicon Sanger and Oxford Nanopore Technology approaches. Overall, 1,186 samples yielded a successful long amplicon and an interpretable Sanger sequence, while 248 regional pools were characterized by ONT during the funded surveillance phase from October 2021 to March 2023. The data documented the replacement of Delta by Omicron, followed by the circulation of BA.1*, BA.2* and BA.4/BA.5* and the subsequent emergence of BQ*, XBB*, EG.5*, and JN.1* lineages, with periods of persistence and co-circulation. The analytical workflow was adapted as lineage-defining mutations changed. Since March 2023, surveillance continued voluntarily through December 2025 using only long-amplicon Sanger sequencing. A qualitative comparison with national periodic flash surveys to estimate the prevalence of SARS-CoV-2 variants on biological samples showed that the two systems broadly captured the same succession of major lineage transitions, although the variant prevalence estimates and wastewater lineage proportions were not directly comparable. These findings support the feasibility of a targeted and adaptable strategy for sustaining nationwide wastewater genomic surveillance across emergency and post-emergency phases and for complementing clinical surveillance when routine testing and sequencing are reduced.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-026-09711-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149068802","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":"Long-Term Survival of Human Enteric Virus Surrogates (Murine Norovirus, Rhesus Rotavirus, and Porcine Sapovirus) in Bottled Drinking Water","authors":"Ziwei Zhao,&nbsp;Leena Maunula","doi":"10.1007/s12560-026-09710-5","DOIUrl":"10.1007/s12560-026-09710-5","url":null,"abstract":"<div><p>Enteric viruses are major causes of food- and waterborne diseases. Due to the limited cultivability of many human enteric viruses, surrogate viruses are commonly used to model their environmental persistence. This study aimed to evaluate the not-well-understood long-term survival of murine norovirus (MNV), rhesus rotavirus (RRV), and porcine sapovirus (PoSaV), used here as cultivable surrogate viruses for human enteric viruses, in bottled drinking water. Bottled water artificially inoculated with each virus was stored at 4 °C, 25 °C, and 37 °C for up to 365 days, and viral infectivity was quantified using TCID₅₀ and plaque assays, with the latter successfully applied for PoSaV quantification. The initial virus concentrations were 5.2 log₁₀ TCID₅₀/mL for MNV, 6.5 log₁₀ PFU/mL for RRV, and 4.0 log₁₀ PFU/mL for PoSaV. MNV and RRV remained infectious for at least one year at 4 °C, whereas PoSaV gradually declined and became undetectable by day 55. At 25 °C, the viral inactivation rate was accelerated: MNV became undetectable by day 160, RRV by day 320, and PoSaV by day 20. At 37 °C, a rapid inactivation rate was observed for all viruses, with MNV, RRV, and PoSaV becoming undetectable by days 20, 80, and 10, respectively. These results demonstrate the pronounced temperature-dependent survival of enteric viruses in bottled water. It is important to ensure the use of microbiologically clean source for bottled water as well as implement effective food and water safety management to minimise potential viral contamination.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-026-09710-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035113","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":"Stage-Specific Tulane Virus Replication in Zebrafish: Permissive in Embryos, Restricted in Larvae","authors":"Sahaana Chandran,&nbsp;Kristen E. Gibson","doi":"10.1007/s12560-026-09708-z","DOIUrl":"10.1007/s12560-026-09708-z","url":null,"abstract":"<div><p>Human norovirus (HuNoV), the leading cause of foodborne illness in the United States and acute gastroenteritis globally, replicates in the zebrafish embryo and larvae model. However, due to challenges in obtaining well-characterized HuNoV positive stool specimens for research, demonstrating replication of Tulane virus (TuV), a surrogate of HuNoV, in the zebrafish embryo and larvae model is valuable to study HuNoV infection mechanisms and subsequent prevention and control strategies. Three nL of TuV (9 log RNA copies/mL or 7 log PFU/mL) were microinjected into either fertilized zebrafish eggs (within 4-hours post-fertilization [hpf]) or the yolk of 3-day post-fertilization larvae. Daily, 10 embryos or larvae were pooled into a single sample, with two samples collected per day up to 5 days post-infection (dpi). Viral RNA was quantified using droplet digital PCR. While TuV replicated in zebrafish embryos, with a 2-log increase by 3 dpi, no replication was observed in zebrafish larvae. Developmental regulation of sialylated glycans in zebrafish was investigated as a potential explanation for the absence of TuV replication in larvae. Zebrafish embryos express α-2,6-linked sialic acid (SA) residues, which decrease from 6 to 48 hpf, while α-2,3 sialylation increases later. Because TuV specifically binds to α-2,6-linked SA but not to α-2,3-linked SA, these developmental changes in sialylation were hypothesized to contribute to the absence of replication in larvae. To test this hypothesis, zebrafish embryos were microinjected with 3 nL of <i>Sambucus nigra</i> lectin (100 mg/mL), which binds α-2,6-linked SA, followed by TuV microinjection. However, lectin treatment did not inhibit replication of TuV, suggesting TuV may utilize other receptors in zebrafish embryos. While TuV replicates exclusively in zebrafish embryos, the previous reports of HuNoV replication in both embryonic and larval stages reveal potential limitations of TuV as a surrogate for evaluating prevention and control strategies against HuNoV transmission through food and environmental routes.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-026-09708-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148974784","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":"Ultrasound-Treated Ethanolic Extracts of Endemic Mount Ida Plants (Sideritis trojana and Hypericum kazdaghensis) Show Antiviral and Antibacterial Potential Against Norovirus Surrogates and Foodborne Bacteria","authors":"Dilvin İpek,&nbsp;Irene Falcó,&nbsp;Gloria Sánchez,&nbsp;Necati Barış Tuncel","doi":"10.1007/s12560-026-09709-y","DOIUrl":"10.1007/s12560-026-09709-y","url":null,"abstract":"<div><p>Human noroviruses and persistent bacterial pathogens remain major food-safety concerns. This screening study compared 40% (v/v) ethanolic extracts (EE) and ultrasound-treated ethanolic extracts (UTE) of the endemic Mount Ida plants Sideritis trojana Ehrend. and Hypericum kazdaghensis Gemici &amp; Leblebici. Feline calicivirus (FCV) and murine norovirus (MNV) served as cultivable human-norovirus surrogates; four reference bacteria were examined by disc diffusion. Ultrasound treatment was associated with higher measured total phenolic content (approximately 2.2- to 3.8-fold) and antioxidant capacity (approximately 1.9- to 2.3-fold) than EE. The largest reduction was 4.71 log₁₀ TCID₅₀/mL for H. kazdaghensis-UTE against FCV after overnight exposure. For MNV, the largest reduction was 2.42 log₁₀ TCID₅₀/mL for S. trojana-EE after overnight exposure. Inhibition-zone diameters ranged from 6.25 to 11.75 mm, including the 6-mm disc. FRhK-4 viability ranged from approximately 56% to 100% across the tested conditions, precluding a general claim of low cytotoxicity. The results provide preliminary, surrogate- and assay-specific evidence of antiviral and antibacterial activity. Because solvent-only and positive controls were not included, causal attribution to plant constituents and comparison with established antimicrobials are not possible. Confirmatory controlled assays are required before practical food-safety use can be proposed.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148899934","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":"Shrimp Aquaculture Under Viral Threats: Insights into Pathogens and Control Strategies","authors":"Linh T. T. Le,&nbsp;Thuan Duc Lao,&nbsp;Phuong-Uyen Le,&nbsp;Hoang Anh Tran,&nbsp;Thuy Huyen Ai Le,&nbsp;Phuong Vy Nguyen","doi":"10.1007/s12560-026-09707-0","DOIUrl":"10.1007/s12560-026-09707-0","url":null,"abstract":"<div><p>Viral diseases are among the most serious threats to shrimp aquaculture, causing large-scale mortality and production losses. This review summarizes current knowledge on the major viral diseases affecting cultured penaeid shrimp and freshwater prawns, with particular emphasis on white spot syndrome virus (WSSV), yellow head virus (YHV), Taura syndrome virus (TSV), infectious hypodermal and hematopoietic necrosis virus (IHHNV), infectious myonecrosis virus (IMNV), and <i>Macrobrachium rosenbergii</i> nodavirus (MrNV), the causative agent of white tail disease. We present a comparative overview of their genomic features, transmission routes, host range, and pathogenesis. Particular attention is given to the genome organization of WSSV and TSV, including variable regions and structural genes commonly used in molecular detection and strain differentiation. We also discuss mechanisms that may contribute to viral persistence in host populations, such as vertical transmission, chronic infections, and viral integration into host genomes. Finally, the review outlines current disease management strategies, including biosecurity measures, environmental control, and selective breeding. By compiling and contextualizing virological and epidemiological data, this review serves as a reference for disease surveillance and control in shrimp aquaculture.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148856888","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":"Simplified Inhouse Nanoweb Membrane Enrichment Coupled Viral Whole Genome Shotgun Metagenomics Approach for Waste Water Surveillance","authors":"Shashi Sharma,&nbsp;Pushpendra Kumar Sharma,&nbsp;Ekta Gupta,&nbsp;Paban Kumar Dash,&nbsp;Ambuj Srivastava","doi":"10.1007/s12560-026-09706-1","DOIUrl":"10.1007/s12560-026-09706-1","url":null,"abstract":"<div><p>Wastewater/sewage represents a highly complex environmental matrix and harbors various viruses including viruses of epidemic and pandemic potential like Influenza A and, SARS-CoV-2. The limitations of available methods for sample concentration are cost, efficiency and time. NGS- metagenomics offer sample to virus genomic characterization for even non-cultivable viruses at highest resolution. In this study, we have collected samples from sewage treatment plants located in Gwalior region of Central India (December 2023 to March 2025). In this study a novel in house nanoweb membrane-based sample enrichment followed by magnetic bead based nucleic acid extraction was optimized in conjunction to shotgun whole genome metagenomics on Nanopore and ion torrent NGS. Both the methods were found comparable with commercially available methods by virus specific TaqMan qPCR. Both the methods were found successful in virus recovery at two log through 10²GC/50 ml feline calicivirus, Influenza A virus, Zika virus, SARS-CoV-2 spiked in sewage matrix alone or in mixture), suggesting the optimized protocol found working for virus characterization at strain level. Here, we have standardized a simple field amenable waste water sample enrichment followed by nucleic acid extraction protocol, that can easily be integrated with latest onsite downstream molecular diagnostic platforms. The developed method is very simple, cost effective and field deployable. This will help to develop a suitable strategic plan for sewage surveillance towards early warning/microbial forensics and future decisions for prevention and therapeutic interventions.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148719923","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":"Simultaneous Detection of Human Norovirus GI, GII and Hepatitis A Virus Using CRISPR-Cas12a-Based RT-RPA and Lateral Flow Strip Method","authors":"Yihan Wang,&nbsp;Mengya Chen,&nbsp;Yongjie Wang,&nbsp;Yongxin Yu","doi":"10.1007/s12560-026-09705-2","DOIUrl":"10.1007/s12560-026-09705-2","url":null,"abstract":"<div><p>Human norovirus (HuNoV) and hepatitis A virus (HAV) are highly prevalent and contagious foodborne pathogens that pose a significant threat to global public health. Current molecular detection methods such as RT-qPCR and RT-ddPCR are highly sensitive and specific but time-consuming, require specialized equipment, and are unsuitable for on-site detection. We developed a multiplex reverse transcription recombinase polymerase amplification (RT-RPA) assay coupled with CRISPR-Cas12a and lateral flow detection for rapid, simultaneous identification of HuNoV GI, GII, and HAV. Through rigorous in silico design and experimental validation, we optimized primer pools and crRNAs to ensure broad genotype coverage and high specificity. Using 2 µL of input per target per 50 µL reaction, the assay achieved limits of detection of 10¹ copies/µL (2 × 10¹ copies/reaction) for HAV, 10³ copies/µL (2 × 10³ copies/reaction) for GI HuNoV, and 10² copies/µL (2 × 10² copies/reaction) for GII HuNoV, with a total assay time of 50 min from purified RNA to final readout. No cross-reactivity occurred with other common foodborne viruses. Validation using total RNA extracted from shellfish digestive glands artificially spiked with RNA standards provided preliminary evidence supporting the feasibility of the method under laboratory conditions. This portable system shows strong potential as a rapid multiplex molecular detection platform.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"18 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148380563","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}