{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T22:22:30Z","timestamp":1789424550848,"version":"build-2803163510"},"reference-count":47,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2020,8,29]],"date-time":"2020-08-29T00:00:00Z","timestamp":1598659200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Wellcome Trust of Great Britain","award":["204904\/Z\/16\/Z"],"award-info":[{"award-number":["204904\/Z\/16\/Z"]}]},{"name":"Wellcome Trust of Great Britain","award":["106680\/B\/14\/Z"],"award-info":[{"award-number":["106680\/B\/14\/Z"]}]},{"name":"Wellcome Trust of Great Britain","award":["WT\/093724"],"award-info":[{"award-number":["WT\/093724"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol\/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.<\/jats:p>","DOI":"10.3390\/v12090960","type":"journal-article","created":{"date-parts":[[2020,8,30]],"date-time":"2020-08-30T06:06:22Z","timestamp":1598767582000},"page":"960","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5270-1181","authenticated-orcid":false,"given":"Nguyen","family":"Thi Kha Tu","sequence":"first","affiliation":[{"name":"Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"},{"name":"Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nguyen","family":"Thi Thu Hong","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nguyen","family":"Thi Han Ny","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tran","family":"My Phuc","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pham","family":"Thi Thanh Tam","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9807-1821","authenticated-orcid":false,"given":"H. Rogier van","family":"Doorn","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ha Noi 8000, Vietnam"},{"name":"Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ho","family":"Dang Trung Nghia","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dang","family":"Thao Huong","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duong","family":"An Han","sequence":"additional","affiliation":[{"name":"Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luu","family":"Thi Thu Ha","sequence":"additional","affiliation":[{"name":"Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xutao","family":"Deng","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA"},{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guy","family":"Thwaites","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"},{"name":"Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6296-4484","authenticated-orcid":false,"given":"Eric","family":"Delwart","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA"},{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2540-9171","authenticated-orcid":false,"given":"Anna-Maija K.","family":"Virtala","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olli","family":"Vapalahti","sequence":"additional","affiliation":[{"name":"Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Virology and Immunology, HUSLAB, Helsinki University Hospital, 00029 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Baker","sequence":"additional","affiliation":[{"name":"Cambridge Institute of Therapeutic Immunology &amp; Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1791-3901","authenticated-orcid":false,"given":"Le","family":"Van Tan","sequence":"additional","affiliation":[{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,8,29]]},"reference":[{"key":"ref_1","unstructured":"WHO (2013). 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