Food and Environmental Virology最新文献

{"title":"Antiviral Activity of Natural Compounds for Food Safety","authors":"Irene Falcó,&nbsp;Walter Randazzo,&nbsp;Gloria Sánchez","doi":"10.1007/s12560-024-09605-3","DOIUrl":"10.1007/s12560-024-09605-3","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 3","pages":"280 - 296"},"PeriodicalIF":4.1,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11422275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330031","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":"Hepatitis E Virus RNA Detection in Liver and Muscle Tissues Sampled from Home Slaughtered Domestic Pigs in Central Italy","authors":"Gianluigi Ferri,&nbsp;Giorgia Giantomassi,&nbsp;Daniele Tognetti,&nbsp;Alberto Olivastri,&nbsp;Alberto Vergara","doi":"10.1007/s12560-024-09606-2","DOIUrl":"10.1007/s12560-024-09606-2","url":null,"abstract":"<div><p>Hepatitis E virus is a worldwide emerging foodborne pathogen; raw or undercooked meats and liver pork products can cause infection through the orofecal route. In Central-Southern Italy, small traditional farming method, associated with the possibility of environmental sharing with wild species, can facilitate HEV diffusion and persistence. The aim of this study was to determine HEV genotype and subtype in Marche region from home slaughtered domestic pigs involved in small and traditional food chains. A total of 236 liver and muscle tissues and 6 pooled salami samples were screened. Laboratory workflow started with homogenization, followed by RNA extraction. Nested reverse transcription PCR and qRT-PCR were used to amplify specific parts of overlapping open reading frames belonging to the HEV genome. A total of 42/236 (17.79%) liver and 8/236 (3.39%) diaphragm specimens were positive; none of the pooled salami specimens showed positive HEV signal. The discovered HEV3c presented high nucleotide similarities with ones amplified from wild boar populations hunted in the same province. Extensive farming methods and environmental sharing with wild animal species support cross-infection infections, as observed in the present study. Although salami resulted negative for HEV RNA detection, the effects of food technologies on viral loads remain unclear. Therefore, further scientific investigations coupled with efficacious standardized laboratory procedures will be the next challenge.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 4","pages":"438 - 448"},"PeriodicalIF":4.1,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-024-09606-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305144","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":"Isolation and Identification of Postharvest Rot Pathogens in Citrus × tangelo and Their Potential Inhibition with Acidic Electrolyzed Water","authors":"Ying Ji,&nbsp;Jieqiong Wang,&nbsp;Ye Liu,&nbsp;Shaoyan Liu,&nbsp;Xuanjing Jiang,&nbsp;Huaming Huang","doi":"10.1007/s12560-024-09604-4","DOIUrl":"10.1007/s12560-024-09604-4","url":null,"abstract":"<div><p>This study focused on the identification of rot-causing fungi in <i>Citrus</i> × <i>tangelo</i> (tangelo) with a particular emphasis on investigating the inhibitory effects of acidic electrolyzed water on the identified pathogens. The dominant strains responsible for postharvest decay were isolated from infected tangelo fruits and characterized through morphological observation, molecular identification, and pathogenicity detection. Two strains were isolated from postharvest diseased tangelo fruits, cultured and morphologically characterized, and had their gene fragments amplified using primers ITS1 and ITS4. The results revealed the rDNA-ITS sequence of two dominant pathogens were 100% homologous with those of <i>Penicillium citrinum</i> and <i>Aspergillus sydowii</i>. These isolated fungi were confirmed to induce tangelo disease, and subsequent re-isolation validated their consistency with the inoculum. Antifungal tests demonstrated that acidic electrolyzed water (AEW) exhibited a potent inhibitory effect on <i>P. citrinum</i> and <i>A. sydowii</i>, with EC₅₀ values of 85.4 μg/mL and 60.12 μg/mL, respectively. The inhibition zones of 150 μg/mL AEW to 2 kinds of pathogenic fungi were over 75 mm in diameter. Furthermore, treatment with AEW resulted in morphological changes such as bending and shrinking of the fungal hyphae surface. In addition, extracellular pH, conductivity, and absorbance at 260 nm of the fungi hypha significantly increased post-treatment with AEW. Pathogenic morphology and IST sequencing analysis confirmed <i>P. citrinum</i> and <i>A. sydowii</i> as the primary pathogenic fungi, with their growth effectively inhibited by AEW.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 3","pages":"409 - 421"},"PeriodicalIF":4.1,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11422426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141282607","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":"Urban Wastewater-Based Surveillance of SARS-CoV-2 Virus: A Two-Year Study Conducted in City of Patras, Greece","authors":"Zoi Anastopoulou,&nbsp;Zoi Kotsiri,&nbsp;Eleftheria Chorti-Tripsa,&nbsp;Rafail Fokas,&nbsp;Apostolos Vantarakis","doi":"10.1007/s12560-024-09601-7","DOIUrl":"10.1007/s12560-024-09601-7","url":null,"abstract":"<div><p>Wastewater-based epidemiology, during the COVID-19 pandemic years, has been applied as a complementary approach, worldwide, for tracking SARS-CoV-2 virus into the community and used as an early warning of the prevalence of COVID-19 infection. The present study presents the results of the 2-year surveillance project, in the city of Patras, Greece. The purpose of the study was to monitor SARS-CoV-2 and implement WBE as an early warning method of monitoring Public Health impact. The presence of SARS-CoV-2 was determined and quantified in 310 samples using RT-qPCR assays. For the years 2022 and 2023, 93.5% and 78.7% of samples were found positive, respectively. Comparison of detection methods have been conducted to select the method with the highest recovery of the viral load. A seasonal variation of the virus was recorded, showing a recession in summer months confirming the country's epidemiological data as indicated by positive correlation of wastewater viral load with registered cases of COVID-19 infections during these years (<i>p</i> &lt; 0.05) and moreover sealed with a significant negative correlation observed with Daily Average (<i>p</i> &lt; 0.01) and Daily Maximum Temperature (<i>p</i> &lt; 0.01). More research was carried out to elucidate a possible association of physicochemical characteristics of wastewater with viral load showing positive correlation with Chlorides (<i>p</i> &lt; 0.01) advocating possible increased use of chlorine-based disinfectants and Electrical Conductivity (<i>p</i> &lt; 0.01) indicates that wastewater during periods of increased infections is more heavily loaded with ions from chemical and biological pollutants. No correlation found with rainfall and physicochemical indicators, such as COD, BOD₅, Total Phosphorus, Total Nitrogen, and Total Suspended Solids. According to the findings, WBE represents a useful tool in the management of epidemics based on an environmental approach and it can also shed light on the interacting parameters that capture Public Health since any infections that may lead to epidemics lead to a parallel change in the use of pharmaceuticals, antimicrobials, disinfectants, and microbial load in urban wastewater.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 3","pages":"398 - 408"},"PeriodicalIF":4.1,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199156","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":"Monitoring an Emergent Pathogen at Low Incidence in Wastewater Using qPCR: Mpox in Switzerland","authors":"Timothy R. Julian,&nbsp;Alexander J. Devaux,&nbsp;Laura Brülisauer,&nbsp;Sheena Conforti,&nbsp;Johannes C. Rusch,&nbsp;Charles Gan,&nbsp;Claudia Bagutti,&nbsp;Tanja Stadler,&nbsp;Tamar Kohn,&nbsp;Christoph Ort","doi":"10.1007/s12560-024-09603-5","DOIUrl":"10.1007/s12560-024-09603-5","url":null,"abstract":"<div><p>Wastewater-based epidemiology offers a complementary approach to clinical case-based surveillance of emergent diseases and can help identify regions with infected people to prioritize clinical surveillance strategies. However, tracking emergent diseases in wastewater requires reliance on novel testing assays with uncertain sensitivity and specificity. Limited pathogen shedding may cause detection to be below the limit of quantification or bordering the limit of detection. Here, we investigated how the definition of limit of detection for quantitative polymerase chain reaction (qPCR) impacts epidemiological insights during an mpox outbreak in Switzerland. 365 wastewater samples from three wastewater treatment plants in Switzerland from 9 March through 31 October 2022 were analyzed for mpox DNA using qPCR. We detected mpox DNA in 22% (79 of 365) wastewater samples based on a liberal definition of qPCR detection as any exponentially increasing fluorescence above the threshold. Based on a more restrictive definition as the lowest concentration at which there is 95% likelihood of detection, detection was 1% (5 of 365). The liberal definition shows high specificity (90%) and accuracy (78%), but moderate sensitivity (64%) when benchmarked against available clinical case reporting, which contrasts with higher specificity (98%) but lower sensitivity (10%) and accuracy (56%) of the 95% likelihood definition. Wastewater-based epidemiology applied to an emergent pathogen will require optimizing public health trade-offs between reporting data with high degrees of uncertainty and delaying communication and associated action. Information sharing with relevant public health stakeholders could couple early results with clear descriptions of uncertainty.</p><p><b>Impact Statement:</b> When a novel pathogen threatens to enter a community, wastewater-based epidemiology offers an opportunity to track its emergence and spread. However, rapid deployment of methods for to detect a novel pathogen may rely on assays with uncertain sensitivity and specificity. Benchmarking the detection of mpox DNA in Swiss wastewaters with reported clinical cases in 2022, we demonstrate how definitions of detection of a qPCR assay influence epidemiological insights from wastewater. The results highlight the need for information sharing between public health stakeholders that couple early insights from wastewater with descriptions of methodological uncertainty to optimize public health actions.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 3","pages":"269 - 279"},"PeriodicalIF":4.1,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11422434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141080145","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":"Tulane Virus Persistence and Microbial Stability in 3D Food Ink under Various Storage Conditions: A Pre- and Post-Printing Analysis","authors":"Allyson N. Hamilton,&nbsp;Kristen E. Gibson","doi":"10.1007/s12560-024-09597-0","DOIUrl":"10.1007/s12560-024-09597-0","url":null,"abstract":"<div><p>3D food printers facilitate novel customization of the physicochemical properties of food. This study aimed to investigate the impact of storage conditions on the inactivation of the human norovirus surrogate, Tulane virus (TuV), within 3D printed foods. TuV-inoculated protein cookie food ink (∽ 4 log PFU/g) was distributed into 18 3D food printer capsules (50 g each); half immediately underwent extrusion. Storage of the capsules and printed food products at 20 °C (0, 6, 12, and 24 h), 4 °C (0, 1, 3, and 5d), and − 18 °C (0, 1, 3, and 5d) was completed before analysis for TuV via plaque assays in addition to aerobic plate count, yeast and mold counts, and pH and water activity (a_w) measurements. A significant 3-way interaction effect was observed between time, temperature, and storage method (capsule/print) (<i>p</i> = 0.006). Significant findings include: (1) A greater reduction in virions was observed in capsules after 24 h at 20 °C and (2) a substantial reduction in virions at 4 °C from day 0 to day 1 was observed, independent of storage method. Microbial indicators remained steady across temperatures, with storage temperature significantly impacting pH and a_w. A significant two-way interaction effect (<i>p</i> = 0.006) was found between microorganism type (yeast/aerobic counts) and temperature. This research seeks to provide insights for the food industry and regulatory bodies in crafting guidelines for the safe storage and handling of 3D printed foods and inks.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 3","pages":"351 - 362"},"PeriodicalIF":4.1,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11422428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140849917","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":"A Pilot Study of Aerosolization of Infectious Murine Norovirus in an Experimental Setup","authors":"Roderik Purhonen,&nbsp;Nina S. Atanasova,&nbsp;Julija Salokas,&nbsp;Jonathan Duplissy,&nbsp;Emil Loikkanen,&nbsp;Leena Maunula","doi":"10.1007/s12560-024-09595-2","DOIUrl":"10.1007/s12560-024-09595-2","url":null,"abstract":"<div><p>Human norovirus is transmitted mainly via the faecal-oral route, but norovirus disease outbreaks have been reported in which airborne transmission has been suggested as the only explanation. We used murine norovirus (MNV) as a surrogate for human norovirus to determine the aerosolization of infectious norovirus in an experimental setup. A 3-l air chamber system was used for aerosolization of MNV. Virus in solution (6 log₁₀ TCID₅₀/ml) was introduced into the nebulizer for generating aerosols and a RAW 264.7 cell dish without a lid was placed in the air chamber. Cell culture medium samples were taken from the dishes after the aerosol exposure time of 30 or 90 min, and the dishes were placed in a 37 °C, 5% CO₂ incubator and inspected with a light microscope for viral cytopathic effects (CPEs). We determined both the infectious MNV TCID₅₀ titre and used an RT-qPCR assay. During the experiments, virus infectivity remained stable for 30 and 90 min in the MNV solution in the nebulizer. Infectious MNV TCID₅₀ values/ml of 2.89 ± 0.29 and 3.20 ± 0.49 log₁₀ were measured in the chamber in RAW 264.7 cell dish media after the 30-min and 90-min exposure, respectively. The MNV RNA loads were 6.20 ± 0.24 and 6.93 ± 1.02 log₁₀ genome copies/ml, respectively. Later, a typical MNV CPE appeared in the aerosol-exposed RAW cell dishes. We demonstrated that MNV was aerosolized and that it remained infectious in the experimental setup used. Further studies required for understanding the behaviour of MNV in aerosols can thus be performed.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 3","pages":"329 - 337"},"PeriodicalIF":4.1,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11422255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140855120","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":"Whole-Genome Sequencing-Based Confirmatory Methods on RT-qPCR Results for the Detection of Foodborne Viruses in Frozen Berries","authors":"Zhihui Yang,&nbsp;Michael Kulka,&nbsp;Qianru Yang,&nbsp;Efstathia Papafragkou,&nbsp;Christine Yu,&nbsp;Samantha Q. Wales,&nbsp;Diana Ngo,&nbsp;Haifeng Chen","doi":"10.1007/s12560-024-09591-6","DOIUrl":"10.1007/s12560-024-09591-6","url":null,"abstract":"<div><p>Accurate detection, identification, and subsequent confirmation of pathogens causing foodborne illness are essential for the prevention and investigation of foodborne outbreaks. This is particularly true when the causative agent is an enteric virus that has a very low infectious dose and is likely to be present at or near the limit of detection. In this study, whole-genome sequencing (WGS) was combined with either of two non-targeted pre-amplification methods (SPIA and SISPA) to investigate their utility as a confirmatory method for RT-qPCR positive results of foods contaminated with enteric viruses. Frozen berries (raspberries, strawberries, and blackberries) were chosen as the food matrix of interest due to their association with numerous outbreaks of foodborne illness. The hepatitis A virus (HAV) and human norovirus (HuNoV) were used as the contaminating agents. The non-targeted WGS strategy employed in this study could detect and confirm HuNoV and HAV at genomic copy numbers in the single digit range, and in a few cases, identified viruses present in samples that had been found negative by RT-qPCR analyses. However, some RT-qPCR-positive samples could not be confirmed using the WGS method, and in cases with very high Ct values, only a few viral reads and short sequences were recovered from the samples. WGS techniques show great potential for confirmation and identification of virally contaminated food items. The approaches described here should be further optimized for routine application to confirm the viral contamination in berries.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 2","pages":"225 - 240"},"PeriodicalIF":4.1,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-024-09591-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140839690","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":"Environmental Surveillance of Poliovirus and Non-polio Enteroviruses in Iran, 2017–2023: First Report of Imported Wild Poliovirus Type 1 Since 2000","authors":"Ahmad Nejati,&nbsp;Seyed Mehdi Tabatabaei,&nbsp;Sussan Mahmoudi,&nbsp;Seyed Mohsen Zahraei,&nbsp;Hamideh Tabatabaie,&nbsp;Mohammad Razaghi,&nbsp;Farshad Khodakhah,&nbsp;Maryam Yousefi,&nbsp;Yaghoub Mollaei‑Kandelousi,&nbsp;Maryam Keyvanlou,&nbsp;Parastoo Soheili,&nbsp;Shayan Pouyandeh,&nbsp;Katayoon Samimi-Rad,&nbsp;Shohreh Shahmahmoodi","doi":"10.1007/s12560-024-09600-8","DOIUrl":"10.1007/s12560-024-09600-8","url":null,"abstract":"<div><p>In Iran, which is at high risk of the Wild Poliovirus (WPV) and Vaccine-Derived Poliovirus (VDPV) importation due to its neighborhood with two polio endemic countries, Pakistan and Afghanistan, Environmental Surveillance (ES) was established in November 2017. Sistan-Balouchestan province was chosen for the ES due to its vicinity with Pakistan and Afghanistan. Five sewage collection sites in 4 cities (Zahedan, Zabol, Chabahar and Konarak) were selected in the high-risk areas. Since the establishment of ES in November 2017 till the end of 2023, 364 sewage specimens were collected and analyzed. The ES detected polioviruses which have the highest significance for polio eradication program, that is, Wild Poliovirus type 1 (WPV1) and Poliovirus type 2 (PV2). In April and May 2019, three of 364 (0.8%) sewage specimens from Konarak were positive for imported WPV1. According to phylogenetic analysis, they were highly related to WPV1 circulating in Karachi (Sindh province) in Pakistan. PV2 was also detected in 5.7% (21/364) of the sewage specimens, most of which proved to be imported from the neighboring countries. Of 21 isolated PV2s, 7 were VDPV2, of which 5 proved to be imported from the neighboring countries as there was VDPV2 circulating in Pakistan at the time of sampling, and 2 were ambiguous VDPVs (aVDPV) with unknown source. According to the findings of this study, as long as WPV1 and VDPV2 outbreaks are detected in Iran’s neighboring countries, there is a definite need for continuation and expansion of the environmental surveillance.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"16 3","pages":"391 - 397"},"PeriodicalIF":4.1,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140662098","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":"Comparison of Three Viral Nucleic Acid\u0000 Preamplification Pipelines for Sewage Viral Metagenomics","authors":"Xavier Fernandez-Cassi,&nbsp;Tamar Kohn","doi":"10.1007/s12560-024-09594-3","DOIUrl":"10.1007/s12560-024-09594-3","url":null,"abstract":"<div><p>Viral metagenomics is a useful tool for detecting multiple human viruses in\u0000 urban sewage. However, more refined protocols are required for its effective use in\u0000 disease surveillance. In this study, we investigated the performance of three different\u0000 preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral\u0000 genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples\u0000 containing known concentrations of viruses. We found that compared to the pipeline\u0000 targeting all genome types, the RNA pipeline performed better in detecting RNA viruses\u0000 in both spiked and unspiked sewage samples, allowing the detection of various mammalian\u0000 viruses including members from the <i>Reoviridae</i>,\u0000 <i>Picornaviridae</i>, <i>Astroviridae</i> and <i>Caliciviridae</i>.\u0000 However, the DNA-specific pipeline did not improve the detection of mammalian DNA\u0000 viruses. We also measured viral recovery by quantitative reverse transcription\u0000 polymerase chain reaction and assessed the impact of genetic background (non-viral\u0000 genetic material) on viral coverage. Our results indicate that viral recoveries were\u0000 generally lower in sewage (average of 11.0%) and higher in Phosphate Buffered Saline\u0000 (average of 23.4%) for most viruses. Additionally, spiked-in viruses showed lower genome\u0000 coverage in sewage, demonstrating the negative effect of genetic background on\u0000 sequencing. Finally, correlation analysis revealed a relationship between virus\u0000 concentration and genome normalized reads per million, indicating that viral metagenomic\u0000 sequencing can be semiquantitative.</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":"16 3","pages":"1 - 22"},"PeriodicalIF":4.1,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-024-09594-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140636722","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}