{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:27:02Z","timestamp":1787009222195,"version":"build-2736575974"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"7-8","funder":[{"DOI":"10.13039\/100000181","name":"Air Force Office of Scientific Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000181","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009898","name":"Defense Health Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009898","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020163","name":"Skoll Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000181","name":"Air Force Office of Scientific Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000181","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009898","name":"Defense Health Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009898","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020163","name":"Skoll Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020163","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Wastewater surveillance is an important technique to monitor public health and is being studied extensively for pandemic prevention, force health protection and readiness, and as a potential early warning system for chem-bio defense. Wastewater surveillance has traditionally relied on techniques such as quantitative PCR or targeted sequencing, both of which are microbe- or disease-specific tools. Newer pan-viral metagenomics strategies may provide higher specificity for pathogens of interest, resulting in a lower false negative rate and reduced sequencing of undesired background nucleic acids. One such system, VirCapSeq-VERT, has been developed to target\u00a0all vertebrate virus pathogens; until recently, its application has been limited to clinical samples. The objective of this study was to use VirCapSeq-VERT to interrogate wastewater samples from the U.S. Air Force Academy (USAFA), Colorado Springs, Colorado, to determine its utility in assessing complex samples and its potential application in public health surveillance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and Methods<\/jats:title>\n                    <jats:p>Biweekly samples were analyzed from February 2022 through May 2023. Samples were collected from the wastewater treatment facility at USAFA before treatment and stored at \u221220\u2009\u00b0C until total nucleic acid (tNA: DNA and RNA) extraction. tNA was then subject to the probe-based capture system, VirCapSeq, and run through a collection of public bioinformatics pipelines to identify captured viral pathogens and perform phylogenetic analysis. It was determined by the USAFA IRB that the study was non-human subject research and was deemed exempt.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In total, 68 families of viruses were identified, comprising thousands of individual strains. This study focused on viruses responsible for gastrointestinal dysfunction as a test of the use of the VirCapSeq-VERT to identify human pathogenic viruses within a complex and highly enriched biological sample. Four enteric viruses dominated the wastewater samples, with Adenoviridae most prevalent before the cadet winter recess (December 17, 2022-January 4, 2023) and Astroviridae most abundant thereafter.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Although gastroenteritis outbreaks at USAFA are commonly attributed to norovirus because of clinical presentation and the acute nature of the illness\u2014often diagnosed and treated without confirmatory stool testing\u2014this virus was not found in high prevalence in these wastewater samples. Among adenoviruses, F serotype 41 predominated, suggesting a role in gastrointestinal infections among the cadet population. Phylogenetic investigation of adenovirus and norovirus exposed common variants with seasonal distributions. These findings may prompt correlational studies to assess the clinical predictive capability of VirCapSeq-VERT and to determine the utility of wastewater monitoring as an outbreak early warning system.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/milmed\/usae518","type":"journal-article","created":{"date-parts":[[2024,10,18]],"date-time":"2024-10-18T15:23:00Z","timestamp":1729264980000},"page":"e1570-e1577","source":"Crossref","is-referenced-by-count":5,"title":["Application of Pan-Viral Metagenomic Sequencing on United States Air Force Academy Wastewater to Uncover Potential Causes of Acute Gastroenteritis"],"prefix":"10.1093","volume":"190","author":[{"given":"Michael A","family":"Mechikoff","sequence":"first","affiliation":[{"name":"Department of Biology, Life Sciences Research Center, United States Air Force Academy , USAF Academy, CO 80840,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P","family":"Collins","sequence":"additional","affiliation":[{"name":"Global Alliance for Preventing Pandemics, Center for Infection and Immunity, Mailman School of Public Health, Columbia University , New York, NY 10032,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Golder","sequence":"additional","affiliation":[{"name":"Department of Biology, Life Sciences Research Center, United States Air Force Academy , USAF Academy, CO 80840,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cullen M","family":"Ingersoll","sequence":"additional","affiliation":[{"name":"Department of Biology, Life Sciences Research Center, United States Air Force Academy , USAF Academy, CO 80840,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Riley E","family":"McGarry","sequence":"additional","affiliation":[{"name":"Department of Biology, Life Sciences Research Center, United States Air Force Academy , USAF Academy, CO 80840,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang-Jun","family":"Lu","sequence":"additional","affiliation":[{"name":"Global Alliance for Preventing Pandemics, Center for Infection and Immunity, Mailman School of Public Health, Columbia University , New York, NY 10032,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alper","family":"Gokden","sequence":"additional","affiliation":[{"name":"Global Alliance for Preventing Pandemics, Center for Infection and Immunity, Mailman School of Public Health, Columbia University , New York, NY 10032,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia","family":"Cuff","sequence":"additional","affiliation":[{"name":"Global Alliance for Preventing Pandemics, Center for Infection and Immunity, Mailman School of Public Health, Columbia University , New York, NY 10032,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryant J","family":"Webber","sequence":"additional","affiliation":[{"name":"10th Operational Medical Readiness Squadron, United States Air Force Academy , USAF Academy, CO 80840,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew B","family":"Wallace","sequence":"additional","affiliation":[{"name":"10th Operational Medical Readiness Squadron, United States Air Force Academy , USAF Academy, CO 80840,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Jordan","family":"Steel","sequence":"additional","affiliation":[{"name":"Department of Biology, Life Sciences Research Center, United States Air Force Academy , USAF Academy, CO 80840,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Kenneth","family":"Wickiser","sequence":"additional","affiliation":[{"name":"Global Alliance for Preventing Pandemics, Center for Infection and Immunity, Mailman School of Public Health, Columbia University , New York, NY 10032,","place":["USA"]},{"name":"Heilbrunn Department of Population and Family Health, Mailman School of Public Health, Columbia University , New York, NY10032,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2381-9911","authenticated-orcid":false,"given":"Armand L","family":"Balboni","sequence":"additional","affiliation":[{"name":"Department of Biology, Life Sciences Research Center, United States Air Force Academy , USAF Academy, CO 80840,","place":["USA"]},{"name":"U.S. Army Europe\u2014Africa (USAREUR-AF), Office of the Command Surgeon (OCSURG), Medical Security Cooperation Branch (MED-SC) , Wiesbaden 65205,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,11,15]]},"reference":[{"issue":"10","key":"2025070106314136400_R1","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1111\/j.1360-0443.2012.03887.x","article-title":"An analysis of ethical issues in using wastewater analysis to monitor illicit drug use","volume":"107","author":"Hall","year":"2012","journal-title":"Addiction"},{"issue":"2","key":"2025070106314136400_R2","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1111\/dar.12185","article-title":"Wastewater testing compared with random urinalyses for the surveillance of illicit drug use in prisons","volume":"35","author":"Brewer","year":"2016","journal-title":"Drug Alcohol Rev"},{"issue":"3","key":"2025070106314136400_R3","doi-asserted-by":"publisher","first-page":"44","DOI":"10.5864\/d2021-015","article-title":"Wastewater-based epidemiology: current uses and future opportunities as a public health surveillance tool","volume":"64","author":"O\u2019Keeffe","year":"2021","journal-title":"Environ Health Rev"},{"issue":"September","key":"2025070106314136400_R4","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijheh.2020.113621","article-title":"Metropolitan wastewater analysis for COVID-19 epidemiological surveillance","volume":"230","author":"Randazzo","year":"2020","journal-title":"Int J Hyg Environ Health"},{"issue":"June","key":"2025070106314136400_R5","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.coesh.2020.06.001","article-title":"Wastewater and public health: the potential of wastewater surveillance for monitoring COVID-19","volume":"17","author":"Farkas","year":"2020","journal-title":"Curr Opin Environ Sci Health"},{"issue":"4","key":"2025070106314136400_R6","doi-asserted-by":"publisher","first-page":"e01853","DOI":"10.1128\/aem.01853-22","article-title":"Monitoring enteroviruses and SARS-CoV-2 in wastewater using the polio environmental surveillance system in Japan","volume":"89","author":"Kazuhiro","year":"2023","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"2025070106314136400_R7","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1038\/s44221-023-00083-8","article-title":"A world of wastewater-based epidemiology","volume":"1","author":"Singer","year":"2023","journal-title":"Nat Water"},{"issue":"4","key":"2025070106314136400_R8","doi-asserted-by":"publisher","DOI":"10.1289\/EHP8572","article-title":"Developing a flexible national wastewater surveillance system for COVID-19 and beyond","volume":"129","author":"Aparna","year":"2021","journal-title":"Environ Health Perspect"},{"issue":"11","key":"2025070106314136400_R9","doi-asserted-by":"publisher","first-page":"2201","DOI":"10.1021\/acsestwater.2c00094","article-title":"Rapid implementation of high-frequency wastewater surveillance of SARS-CoV-2","volume":"2","author":"Holst","year":"2022","journal-title":"ACS ES&T Water"},{"key":"2025070106314136400_R10","first-page":"55","volume-title":"Wastewater-Based Disease Surveillance for Public Health Action","author":"National Academies of Sciences, Engineering, Health and Medicine Division, Division on Earth and Life Studies, Board on Population Health and Public Health Practice, Water Science and Technology Board, and Committee on Community Wastewater-based Infectious Disease Surveillance","year":"2023"},{"issue":"36","key":"2025070106314136400_R11","doi-asserted-by":"publisher","first-page":"1242","DOI":"10.15585\/mmwr.mm7036a2","article-title":"Using wastewater surveillance data to support the COVID-19 response \u2014 United States, 2020\u20132021","volume":"70","author":"Kirby","year":"2021","journal-title":"MMWR"},{"issue":"6","key":"2025070106314136400_R12","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2020.100098","article-title":"Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater","volume":"1","author":"Nemudryi","year":"2020","journal-title":"Cell Rep Med"},{"key":"2025070106314136400_R13","article-title":"About Small Wastewater Systems","volume-title":"Overviews and Factsheets","author":"US EPA, OW"},{"issue":"2","key":"2025070106314136400_R14","doi-asserted-by":"publisher","DOI":"10.1097\/PHH.0000000000001511","article-title":"Wastewater surveillance provides a powerful tool for monitoring and controlling communicable diseases","volume":"28","author":"Bethel","year":"2022","journal-title":"J Public Health Manage Pract"},{"issue":"January-December","key":"2025070106314136400_R15","doi-asserted-by":"publisher","DOI":"10.1177\/1849454417712666","article-title":"A novel method for the isolation of extracellular vesicles and RNA from urine","volume":"6","author":"Markowska","year":"2017","journal-title":"J Circ Biomark"},{"issue":"August","key":"2025070106314136400_R16","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2021.149405","article-title":"Development of a reproducible method for monitoring SARS-CoV-2 in wastewater","volume":"799","author":"Palmer","year":"2021","journal-title":"Sci Total Environ"},{"issue":"1","key":"2025070106314136400_R17","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1007\/s12560-017-9311-7","article-title":"Improvement of the bag-mediated filtration system for sampling wastewater and wastewater-impacted waters","volume":"10","author":"Fagnant","year":"2018","journal-title":"Food Environ Virol"},{"issue":"5","key":"2025070106314136400_R18","first-page":"9","article-title":"Review of por RT-PCR and minion nanopore sequencing as a proof-of-concept SARS-CoV-2 biosurveillance in wastewater","volume":"30","author":"Pavlyuk","year":"2023","journal-title":"Med Surveillance Mon Rep"},{"issue":"9","key":"2025070106314136400_R19","doi-asserted-by":"publisher","first-page":"4616","DOI":"10.1128\/JCM.43.9.4616-4622.2005","article-title":"Reduced PCR sensitivity due to impaired DNA recovery with the MagNA Pure LC total nucleic acid isolation kit","volume":"43","author":"Schuurman","year":"2005","journal-title":"J Clin Microbiol"},{"issue":"10","key":"2025070106314136400_R20","doi-asserted-by":"publisher","first-page":"3888","DOI":"10.21037\/tlcr-21-564","article-title":"A large-scale, multicentered trial evaluating the sensitivity and specificity of digital PCR versus ARMS-PCR for detecting CtDNA-Based EGFR p.T790M in non-small-cell lung cancer patients","volume":"10","author":"Jiachen","year":"2021","journal-title":"Transl Lung Cancer Res"},{"key":"2025070106314136400_R21","doi-asserted-by":"publisher","DOI":"10.4172\/jngsa.1000106","article-title":"Accuracy of next generation sequencing platforms","volume":"1","author":"Fox","year":"2014","journal-title":"Next Gen Seq App"},{"issue":"1","key":"2025070106314136400_R22","doi-asserted-by":"publisher","first-page":"4","DOI":"10.20892\/j.issn.2095-3941.2018.0055","article-title":"Next-generation sequencing and its clinical application","volume":"16","author":"Qin","year":"2019","journal-title":"Cancer Biol Med"},{"key":"2025070106314136400_R23","article-title":"Review report - corman-drosten et\u00a0al., eurosurveillance 2020","author":"Borger","year":"2020"},{"issue":"5","key":"2025070106314136400_R24","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/mBio.01491-15","article-title":"Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis","volume":"6","author":"Thomas","year":"2015","journal-title":"MBio"},{"issue":"4","key":"2025070106314136400_R25","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/msphere.00311-18","article-title":"Investigation of the plasma virome from cases of unexplained febrile illness in Tanzania from 2013 to 2014: a comparative analysis between unbiased and VirCapSeq-VERT high-throughput sequencing approaches","volume":"3","author":"Williams","year":"2018","journal-title":"MSphere"},{"issue":"4","key":"2025070106314136400_R26","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1016\/j.jinf.2021.12.042","article-title":"Viral capture sequencing detects unexpected viruses in the cerebrospinal fluid of adults with meningitis","volume":"84","author":"McGill","year":"2022","journal-title":"J Infect"},{"issue":"4","key":"2025070106314136400_R27","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1007\/s13311-014-0288-8","article-title":"Next generation sequencing and the future of genetic diagnosis","volume":"11","author":"Lohmann","year":"2014","journal-title":"Neurotherapeutics"},{"issue":"11\u201312","key":"2025070106314136400_R28","doi-asserted-by":"publisher","first-page":"e3675","DOI":"10.1093\/milmed\/usad239","article-title":"Designing a wastewater-based epidemiology study at the U.S. air force academy: using severe acute respiratory syndrome coronavirus 2 to test a sentinel system for early disease outbreak detection","volume":"188","author":"Goodwin","year":"2023","journal-title":"Mil Med"},{"issue":"2","key":"2025070106314136400_R29","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/s1473-3099(04)00928-4","article-title":"Rotavirus infection in adults","volume":"4","author":"Anderson","year":"2004","journal-title":"Lancet Infect Dis"},{"issue":"3","key":"2025070106314136400_R30","doi-asserted-by":"publisher","DOI":"10.1099\/jgv.0.001721","article-title":"ICTV virus taxonomy profile: adenoviridae 2022","volume":"103","author":"Benk\u0151","year":"2022","journal-title":"J Gen Virol"},{"issue":"7","key":"2025070106314136400_R31","doi-asserted-by":"publisher","DOI":"10.3390\/v15071541","article-title":"Significantly longer shedding of norovirus compared to rotavirus and adenovirus in children with acute gastroenteritis","volume":"15","author":"Qiu","year":"2023","journal-title":"Viruses"},{"key":"2025070106314136400_R32","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/b978-0-12-384947-2.00727-3","article-title":"Foodborne viruses of human health concern","author":"D\u2019Souza","year":"2016","journal-title":"Encyclopedia Food Health"},{"issue":"10","key":"2025070106314136400_R33","doi-asserted-by":"publisher","first-page":"e01468","DOI":"10.1128\/mbio.01468-23","article-title":"Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater","volume":"15","author":"Child","year":"2023","journal-title":"mBio"},{"key":"2025070106314136400_R34","article-title":"Norovirus Burden and Trends","volume-title":"Centers for Disease Control and Prevention","author":"Centers for Disease Control and Prevention"},{"issue":"11","key":"2025070106314136400_R35","first-page":"2","article-title":"Norovirus outbreak associated with person-to-person transmission, U.S. Air Force Academy, July 2011","volume":"18","author":"Chapman","year":"2011","journal-title":"MSMR"},{"issue":"3","key":"2025070106314136400_R36","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofv120","article-title":"Changes in clinical presentation and epidemiology of respiratory pathogens associated with acute respiratory illness in military trainees after reintroduction of adenovirus vaccine","volume":"2","author":"Yun","year":"2015","journal-title":"Open Forum Infect Dis"}],"container-title":["Military Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/milmed\/article-pdf\/190\/7-8\/e1570\/60685342\/usae518.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/milmed\/article-pdf\/190\/7-8\/e1570\/60685342\/usae518.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T06:31:48Z","timestamp":1751351508000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/milmed\/article\/190\/7-8\/e1570\/7901174"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,15]]},"references-count":36,"journal-issue":{"issue":"7-8","published-online":{"date-parts":[[2024,11,15]]},"published-print":{"date-parts":[[2025,6,30]]}},"URL":"https:\/\/doi.org\/10.1093\/milmed\/usae518","relation":{},"ISSN":["0026-4075","1930-613X"],"issn-type":[{"value":"0026-4075","type":"print"},{"value":"1930-613X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7]]},"published":{"date-parts":[[2024,11,15]]}}}