Food and Environmental Virology最新文献

{"title":"Evaluation of Methods and Processes for Robust Monitoring of SARS-CoV-2 in Wastewater","authors":"Olivera Maksimovic Carvalho Ferreira,&nbsp;Živa Lengar,&nbsp;Zala Kogej,&nbsp;Katarina Bačnik,&nbsp;Irena Bajde,&nbsp;Mojca Milavec,&nbsp;Anže Županič,&nbsp;Nataša Mehle,&nbsp;Denis Kutnjak,&nbsp;Maja Ravnikar,&nbsp;Ion Gutierrez-Aguirre","doi":"10.1007/s12560-022-09533-0","DOIUrl":"10.1007/s12560-022-09533-0","url":null,"abstract":"<div><p>The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 4","pages":"384 - 400"},"PeriodicalIF":3.4,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09533-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4882739","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":"Combining Community Wastewater Genomic Surveillance with State Clinical Surveillance: A Framework for SARS-CoV-2 Public Health Practice","authors":"Ted Smith,&nbsp;Rochelle H. Holm,&nbsp;Ray Yeager,&nbsp;Joseph B. Moore IV,&nbsp;Eric C. Rouchka,&nbsp;Kevin J. Sokoloski,&nbsp;Erin M. Elliott,&nbsp;Daymond Talley,&nbsp;Vaneet Arora,&nbsp;Sarah Moyer,&nbsp;Aruni Bhatnagar","doi":"10.1007/s12560-022-09531-2","DOIUrl":"10.1007/s12560-022-09531-2","url":null,"abstract":"<div><p>This study aimed to develop a framework for combining community wastewater surveillance with state clinical surveillance for the confirmation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants within the community and to provide recommendations on how to expand on such research and apply the findings in public health responses. Wastewater samples were collected weekly from 17 geographically resolved locations in Louisville/Jefferson County, Kentucky (USA), from February 10 to December 13, 2021. Genomic surveillance and quantitative reverse transcription PCR (RT-qPCR) platforms were used to screen for SARS-CoV-2 in wastewater, and state clinical surveillance was used for confirmation. The study results highlighted an increased epidemiological value of combining community wastewater genomic surveillance and RT-qPCR with conventional case-auditing methods. The spatial scale and temporal frequency of wastewater sampling provided promising sensitivity and specificity for gaining public health screening insights about SARS-CoV-2 emergence, seeding, and spread in communities. Improved national surveillance systems are needed against future pathogens and variants, and wastewater-based genomic surveillance exhibits great potential when coupled with clinical testing. This paper presents evidence that complementary wastewater and clinical testing are cost-effectively enhanced when used in combination, as they provide a strong tool for a joint public health framework. Future pathogens of interest may be examined in either a targeted fashion or using a more global approach where all pathogens are monitored. This study has also provided novel insights developed from evidence-based public health practices.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 4","pages":"410 - 416"},"PeriodicalIF":3.4,"publicationDate":"2022-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09531-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4710239","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":"Active Surveillance and Genetic Characterization of Prevalent Velogenic Newcastle Disease and Highly Pathogenic Avian Influenza H5N8 Viruses Among Migratory Wild Birds in Southern Egypt During 2015–2018","authors":"Serageldeen Sultan,&nbsp;Nahla Mohamed Ibrahim Eldamarany,&nbsp;Mohmed Wael Abdelazeem,&nbsp;Hanan Ali Fahmy","doi":"10.1007/s12560-022-09532-1","DOIUrl":"10.1007/s12560-022-09532-1","url":null,"abstract":"<div><p>A total of 1007 samples (910 fecal droplets and 97 cloacal swabs) were collected from 14 species of migratory wild birds in most wetlands during 3 successive migration seasons from September to March (2015–2018) in Southern Egypt. The samples were propagated in embryonated chicken eggs and positive allantoic fluids by hemagglutination test were tested for Newcastle disease virus (NDV) and avian influenza virus (AIV) prevalence using RT-PCR and specific primers targeting the NDV fusion (F) and AIV matrix genes. Further subtyping of the AIV hemagglutinin (HA) and neuraminidase (NA) was conducted, and representative isolates were selected and sequenced for full F gene of NDVs and HA and NA genes of the AIV. Overall isolation rate of hemagglutinating viruses was 5.56% (56/1007), from them 5.36% (3/56) AIV, 85.71% (48/56) NDV and 8.93% (5/56) co-infection of NDV and AIV was detected. The sequences analysis of full F genes of 10 NDV isolates revealed that they have multi-basic amino acid motifs ¹¹¹E/GRRQKR/F¹¹⁷ as velogenic strains with nucleotides and amino acids similarities of 96–100%. In addition, they phylogenetically clustered into groups and subgroups within genotype VII.1.1 and sub-genotype VIIj with a close relation to NDVs isolated from chickens in Egypt. The AIV H5N8 subtype was in clade 2.3.4.4b with a highly pathogenic nature and close relation to Egyptian domesticated H5N8 viruses rather than those from wild birds. The current data showed the contribution of migratory birds to the continuous circulation of virulent NDV and AIV H5N8 among domesticated chickens in Southern Egypt.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 3","pages":"280 - 294"},"PeriodicalIF":3.4,"publicationDate":"2022-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09532-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4414049","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":"Investigation of the Presence of DNA of Highly Pathogenic Human Papillomaviruses in Water Bodies of the Lake Baikal Natural Territory","authors":"A. S. Stolbikov,&nbsp;R. K. Salyaev,&nbsp;V. N. Nurminsky,&nbsp;M. Yu. Chernyshov","doi":"10.1007/s12560-022-09529-w","DOIUrl":"10.1007/s12560-022-09529-w","url":null,"abstract":"<div><p>Human papillomaviruses (HPVs) are extremely widespread throughout the world. There are more than 100 types of HPVs, of which at least 14 types represent high oncogenic risk viruses (World Health Organization, 2020). Numerous attempts were made to analyze various water sources in order to (i) reveal the presence of DNA of pathogenic human papillomaviruses in them and (ii) assess the potential risks of occurrence of epidemics caused by HPV. With time, the necessity to solve these important problems stimulated the formation of a new direction in the world medical and environmental investigations.</p><p>This paper contains the investigation of the presence of DNA of highly dangerous types of human papillomaviruses (HPV6, HPV11, HPV16 and HPV18) in water bodies of the Baikal natural territory, in particular in the water reservoirs in and near the villages of Listvyanka, Bolshiye Koty, Kultuk and the cities of Baikalsk and Slyudyanka. In course of our work, the conditions good for the study of the biological material obtained from water samples by the PCR technique to reveal the presence of DNA of HPV6, HPV11, HPV16 and HPV18 papillomaviruses were chosen. PCR analysis was conducted with the aid of both the already well-known universal primers GP5 + /6 + and the primers developed by our team to be applied to the conservative domains of nucleotide sequences encoding the main capsid protein L1 of human papillomaviruses HPV6, HPV11 (these types of the virus contribute to the occurrence of anogenital condylomatosis and the development of respiratory papillomatosis) and HPV16, HPV16 (these types of virus contribute to the occurrence of cervical cancer).</p><p>The analyzes conducted by our team have revealed the presence of DNA of the four types of HPVs (6, 11, 16 and 18) in the samples taken from various water sources of the Baikal natural territory.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 3","pages":"258 - 266"},"PeriodicalIF":3.4,"publicationDate":"2022-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4238655","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 2019 Outbreak Investigation of Hepatitis A Virus Infections in the United States Linked to Imported Fresh Blackberries","authors":"Monica McClure,&nbsp;Johnson Nsubuga,&nbsp;Martha P. Montgomery,&nbsp;Erin Jenkins,&nbsp;Alvin Crosby,&nbsp;Daniela Schoelen,&nbsp;Colin Basler,&nbsp;Sumathi Ramachandran,&nbsp;Yulin Lin,&nbsp;Guo-liang Xia,&nbsp;Yury Khudaykov,&nbsp;Vilasini Suktankar,&nbsp;Angela Wagley,&nbsp;Vincent Thomas,&nbsp;Jacquelina Woods,&nbsp;Leslie Hintz,&nbsp;Janete Oliveira,&nbsp;Ana Lilia Sandoval,&nbsp;Justin Frederick,&nbsp;Blake Hendrickson,&nbsp;Laura Gieraltowski,&nbsp;Stelios Viazis","doi":"10.1007/s12560-022-09527-y","DOIUrl":"10.1007/s12560-022-09527-y","url":null,"abstract":"<div><p>Globally, hepatitis A virus (HAV) is one of the most common agents of acute viral hepatitis and causes approximately 1.4 million cases and 90,000 deaths annually despite the existence of an effective vaccine. In 2019, federal, state, and local partners investigated a multi-state outbreak of HAV infections linked to fresh blackberries sourced from multiple suppliers in Michoacán, Mexico. A total of 20 individuals with outbreak-related HAV infection were reported in seven states, including 11 hospitalizations, and no deaths. The Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and Nebraska State and Douglas County Health Departments conducted a traceback investigation for fresh blackberries reportedly purchased by 16 ill persons. These individuals reported purchasing fresh blackberries from 11 points of service from September 16 through 29, 2019 and their clinical isolates assessed through next-generation sequencing and phylogenetic analysis were genetically similar. The traceback investigation did not reveal convergence on a common grower or packing house within Mexico, but all of the blackberries were harvested from growers in Michoacán, Mexico. FDA did not detect the pathogen after analyzing fresh blackberry samples from four distributors, one consumer, and from nine importers at the port of entry as a result of increased screening. Challenges included gaps in traceability practices and the inability to recover the pathogen from sample testing, which prohibited investigators from determining the source of the implicated blackberries. This multi-state outbreak illustrated the importance of food safety practices for fresh produce that may contribute to foodborne illness outbreaks.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 3","pages":"236 - 245"},"PeriodicalIF":3.4,"publicationDate":"2022-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09527-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4899365","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":"Assessment of Surface Disinfection Effectiveness of Decontamination System COUNTERFOG® SDR-F05A+ Against Bacteriophage ɸ29","authors":"Cristina del Álamo,&nbsp;Ángela Vázquez-Calvo,&nbsp;Antonio Alcamí,&nbsp;Juan Sánchez-García-Casarrubios,&nbsp;José Luis Pérez-Díaz","doi":"10.1007/s12560-022-09526-z","DOIUrl":"10.1007/s12560-022-09526-z","url":null,"abstract":"<div><p>The experience of COVID19 pandemic has demonstrated the real concern of biological agents dispersed in the air and surfaces environments. Therefore, the need of a fast and large-scale disinfection method has arisen for prevention of contagion. COUNTERFOG® is an innovative technology developed for large-scale decontamination of air and surfaces. The objective of this study is to assess experimentally the effectiveness of COUNTERFOG® in disinfecting viral-contaminated surfaces. We also aim to measure the necessary time to disinfect said surfaces. Stainless steel surfaces were contaminated with bacteriophage φ29 and disinfected using COUNTERFOG® SDR-F05A+, which uses a sodium hypochlorite solution at different concentrations and for different exposure times. A log reduction over 6 logs of virus titer is obtained in 1 min with 1.2% sodium hypochlorite when the application is direct; while at a radial distance of 5 cm from the point of application the disinfection reaches a reduction of 5.5 logs in 8 min. In the same way, a higher dilution of the sodium hypochlorite concentration (0.7% NaOCl) requires more exposure time (16 min) to obtain the same log reduction (&gt; 6 logs). COUNTERFOG® creates, in a short time and at a distance of 2 m from the point of application, a thin layer of disinfectant that covers the surfaces. The selection of the concentration and exposure time is critical for the efficacy of disinfection. These tests demonstrate that a concentration between 0.7- 1.2% sodium hypochlorite is enough for a fast and efficient ɸ29 phage inactivation. The fact that ɸ29 phage is more resistant to disinfection than SARS-CoV-2 sustains this disinfection procedure.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 3","pages":"304 - 313"},"PeriodicalIF":3.4,"publicationDate":"2022-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09526-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4753333","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":"Transmission of SARS-CoV-2 on Cold-Chain Food: Precautions Can Effectively Reduce the Risk","authors":"Meiyue Guo,&nbsp;Junfeng Yan,&nbsp;Yuan Hu,&nbsp;Lu Xu,&nbsp;Jinling Song,&nbsp;Kun Yuan,&nbsp;Xiangru Cheng,&nbsp;Sui Ma,&nbsp;Jie Liu,&nbsp;Xianbing Wu,&nbsp;Liegang Liu,&nbsp;Shuang Rong,&nbsp;Di Wang","doi":"10.1007/s12560-022-09521-4","DOIUrl":"10.1007/s12560-022-09521-4","url":null,"abstract":"<div><p>The COVID-19 pandemic has generated a new era in the world, also in the food safety. Up to now, there is no evidence to suggest that people can infect COVID-19 via food contaminated by SARS-CoV-2. Here, we analyzed the results of regular SARS-CoV-2 nucleic acid testing of considerable cold-chain food practitioners, cold-chain food surfaces, and their internal or external packaging as well as their associated environments, aiming to explore the risk of cold-chain food being contaminated by SARS-CoV-2 and the probability of people infecting COVID-19 through contaminated cold-chain food in the context of COVID-19 epidemic. This study found that only two batches of cold-chain food were contaminated by SARS-CoV-2, none of the cold-chain food handler were infected due to effective regulatory measures for cold-chain food. Therefore, effective supervision and preventive methods could effectively reduce the transmission risk of SARS-CoV-2 on cold-chain food.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 3","pages":"295 - 303"},"PeriodicalIF":3.4,"publicationDate":"2022-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09521-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5118192","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":"Infectious Pepper Mild Mottle Virus and Human Adenoviruses as Viral Indices in Sewage and Water Samples","authors":"Mohammed Kamal Rashed,&nbsp;Waled Morsy El-Senousy,&nbsp;ElSayed Tarek Abd ElSalam Sayed,&nbsp;Maha AlKhazindar","doi":"10.1007/s12560-022-09525-0","DOIUrl":"10.1007/s12560-022-09525-0","url":null,"abstract":"<div><p>The objective of this study was to compare human adenoviruses (HAdVs) genome and infectivity, polyomaviruses (JC and BK) genome (JCPyVs) and (BKPyVs), Pepper Mild Mottle Virus (PMMoV) genome and infectivity, and infectious bacteriophages as viral indices for sewage and water samples. One hundred and forty-four samples were collected from inlets and outlets of water and wastewater treatment plants (WTPs), and WWTPs within Greater Cairo from October 2015 till March 2017. Two methods of viral concentration [Aluminium hydroxide (Al(OH)₃) precipitation method and adsorption-elution technique followed by organic flocculation method] were compared to determine which of them was the best method to concentrate viruses from sewage and water. Although samples with only one litre volume were concentrated using Al(OH)₃ precipitation method and the same samples with larger volumes (5–20 L) were concentrated using the adsorption-elution technique followed by the organic flocculation method, a non-significant difference was observed between the efficiency of the two methods in all types of samples except for the drinking water samples. Based on the qualitative prevalence of studied viruses in water and wastewater samples, the number of genome copies and infectious units in the same samples, resistance to treatment processes in water and wastewater treatment plants, higher frequency of both adenoviruses and PMMoV genomes as candidate viral indices in treated sewage and drinking water was observed. The problem of having a viral genome as indices of viral pollution is that it does not express the recent viral pollution because of the longer survivability of the viral genome than the infectious units in water and wastewater. Both infectious adenovirus and infectious phiX174 bacteriophage virus showed similar efficiencies as indices for viral pollution in drinking water and treated sewage samples. On the other hand, qualitative detection of infectious PMMoV failed to express efficiently the presence/absence of infectious enteric viruses in drinking water samples. Infectious adenoviruses and infectious bacteriophage phiX174 virus may be better candidates than adenoviruses genome, polyomaviruses genome, and PMMoV genome and infectivity as viral indices for water and wastewater.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 3","pages":"246 - 257"},"PeriodicalIF":3.4,"publicationDate":"2022-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09525-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4684759","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":"Air Surveillance for Viral Contamination with SARS-CoV-2 RNA at a Healthcare Facility","authors":"Amir Zahedi,&nbsp;Faezeh Seif,&nbsp;Masoumeh Golshan,&nbsp;Alireza Khammar,&nbsp;Mohammad Reza Rezaei Kahkha","doi":"10.1007/s12560-022-09524-1","DOIUrl":"10.1007/s12560-022-09524-1","url":null,"abstract":"<div><p>The transmission pathway of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 also called COVID-19 disease) in indoor environments are the main area of contention between health systems and scientists. In this context, little has been investigated about the collection of airborne viral shedding. Here, we collected air samples from 24 locations inside the sole COVID-19 patient care center in Zabol, Iran, for screening SARS-CoV-2 RNA from March to May 2021. Locations included the ICU, COVID-19 wards (CWs) rooms, corridors, nearby nurses’ stations, and toilets. We identified the SARS-CoV-2 RNA in breathing zone of CW, in room air, with the positivity rate of 2.5% at a concentration of 17 × 10³ virus genome copies/m³ air. It also investigates the relationship between local climate conditions [i.e., temperature and relative humidity] and COVID-19 transmission with the evolution of daily official data on the number of new cases, hospitalizations, and deaths. Current data explained that the difference of temperature and humidity may affect the behavior of virus along with other factors, i.e., population density, individual viral shedding, and infectious dose of SARS-CoV-2 (both indoor and outdoor). Our data support the potential SARS-CoV-2 airborne transmission indoors suggesting the specific safety assessment of building to improve ventilation solutions besides proper using face masks and extensive public health interventions.</p></div>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 4","pages":"374 - 383"},"PeriodicalIF":3.4,"publicationDate":"2022-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09524-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4944581","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":"Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform","authors":"Ahmed Donia,&nbsp;Muhammad Furqan Shahid,&nbsp;Sammer-ul Hassan,&nbsp;Ramla Shahid,&nbsp;Aftab Ahmad,&nbsp;Aneela Javed,&nbsp;Muhammad Nawaz,&nbsp;Tahir Yaqub,&nbsp;Habib Bokhari","doi":"10.1007/s12560-022-09522-3","DOIUrl":"10.1007/s12560-022-09522-3","url":null,"abstract":"<p>Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37–39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.</p>","PeriodicalId":563,"journal":{"name":"Food and Environmental Virology","volume":"14 4","pages":"364 - 373"},"PeriodicalIF":3.4,"publicationDate":"2022-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12560-022-09522-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4181467","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}