{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T08:18:51Z","timestamp":1790756331911,"version":"4.1.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2018,8,7]],"date-time":"2018-08-07T00:00:00Z","timestamp":1533600000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["UL1TR000040"],"award-info":[{"award-number":["UL1TR000040"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["K23AI098479"],"award-info":[{"award-number":["K23AI098479"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Albany Medical College"},{"DOI":"10.13039\/100003442","name":"Stony Wold-Herbert Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100003442","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["107743"],"award-info":[{"award-number":["107743"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Precision public health is a novel set of methods to target disease prevention and mitigation interventions to high-risk subpopulations. We applied a precision public health strategy to syndromic surveillance for severe acute respiratory infection (SARI) in Uganda by combining spatiotemporal analytics with genomic sequencing to detect and characterize viral respiratory pathogens with epidemic potential.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Using a national surveillance network we identified patients with unexplained, influenza-negative SARI from 2010 to 2015. Spatiotemporal analyses were performed retrospectively to identify clusters of unexplained SARI. Within clusters, respiratory viruses were detected and characterized in naso- and oropharyngeal swab samples using a novel oligonucleotide probe capture (VirCapSeq-VERT) and high-throughput sequencing platform. Linkage to conventional epidemiologic strategies further characterized transmission dynamics of identified pathogens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Among 2901 unexplained SARI cases, 9 clusters were detected, accounting for 301 (10.4%) cases. Clusters were more likely to occur in urban areas and during biannual rainy seasons. Within detected clusters, we identified an unrecognized outbreak of measles-associated SARI; sequence analysis implicated cocirculation of endemic genotype B3 and genotype D4 likely imported from England. We also detected a likely nosocomial SARI cluster associated with a novel picobirnavirus most closely related to swine and dromedary viruses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Using a precision approach to public health surveillance, we detected and characterized the genomics of vaccine-preventable and zoonotic respiratory viruses associated with clusters of severe respiratory infections in Uganda. Future studies are needed to assess the feasibility, scalability, and impact of applying similar approaches during real-time public health surveillance in low-income settings.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/cid\/ciy656","type":"journal-article","created":{"date-parts":[[2018,8,6]],"date-time":"2018-08-06T15:12:20Z","timestamp":1533568340000},"page":"1118-1125","source":"Crossref","is-referenced-by-count":24,"title":["Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda"],"prefix":"10.1093","volume":"68","author":[{"given":"Matthew J","family":"Cummings","sequence":"first","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafal","family":"Tokarz","sequence":"additional","affiliation":[{"name":"Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barnabas","family":"Bakamutumaho","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Kayiwa","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy","family":"Byaruhanga","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Owor","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Namagambo","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allison","family":"Wolf","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barun","family":"Mathema","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, Columbia University Mailman School of Public Health, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julius J","family":"Lutwama","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neil W","family":"Schluger","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York"},{"name":"Department of Epidemiology, Columbia University Mailman School of Public Health, New York"},{"name":"Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W Ian","family":"Lipkin","sequence":"additional","affiliation":[{"name":"Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max R","family":"O\u2019Donnell","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York"},{"name":"Department of Epidemiology, Columbia University Mailman School of Public Health, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,8,7]]},"reference":[{"key":"2019121022390852200_CIT0001","volume-title":"Accelerating progress on HIV, tuberculosis, malaria, hepatitis, and neglected tropical diseases","author":"World Health Organization","year":"2015"},{"key":"2019121022390852200_CIT0002","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1016\/S1473-3099(17)30396-1","article-title":"Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the Global Burden of Disease Study 2015","volume":"17","author":"Troeger","year":"2017","journal-title":"Lancet Infect 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