{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T15:18:54Z","timestamp":1789399134062,"version":"build-2803163510"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,12,1]],"date-time":"2016-12-01T00:00:00Z","timestamp":1480550400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Rationale<\/jats:title>\n                    <jats:p>Little is known about the epidemiology of severe acute respiratory infection (SARI) or influenza in sub-Saharan Africa. Characterization of influenza transmission dynamics and risk factors for severe disease and mortality is critical to inform prevention and mitigation strategies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To characterize the epidemiology and transmission dynamics of influenza and risk factors for influenza-associated severe respiratory infection in Uganda.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Clinicians at 12 sentinel surveillance sites prospectively collected clinical data and upper respiratory tract samples from consecutive patients who met criteria for SARI and influenza-like illness (ILI). Samples were tested for influenza A and B viruses using real-time reverse transcription\u2013polymerase chain reaction. Spatial and spatiotemporal cluster modeling was performed to identify loci of increased influenza transmission. Morbidity and mortality were assessed through chart review in a defined subset of patients. Univariable and multivariable analyses were used to identify risk factors for severe respiratory infection, prolonged hospitalization, and in-hospital mortality.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Measurements and Main Results<\/jats:title>\n                    <jats:p>From October 2010 to June 2015, 9,978 patients met case definitions for SARI and ILI and had samples tested for influenza A and B. Of the 9,978 patient samples tested, 1,113 (11.2%) were positive for influenza. Among 6,057 patients with ILI, 778 samples (12.8%) were positive, and among 3,921 patients with SARI, 335 samples (8.5%) were positive. Significant clustering of influenza cases was observed in urban and periurban areas and during rainy seasons. Among 1,405 cases of SARI with available outcome data, in-hospital mortality was 1.6%. Infection with the 2009 pandemic A\/H1N1 subtype and prolonged time to presentation were independently associated with SARI among influenza cases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Influenza is associated with a substantial proportion of acute respiratory infection in Uganda. As influenza vaccination programs are developed in East Africa, timing campaigns to confer protection during rainy seasons should be considered, particularly among high-risk urban populations.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1513\/annalsats.201607-561oc","type":"journal-article","created":{"date-parts":[[2016,9,9]],"date-time":"2016-09-09T17:39:40Z","timestamp":1473442780000},"page":"2159-2168","source":"Crossref","is-referenced-by-count":30,"title":["Epidemiologic and Spatiotemporal Characterization of Influenza and Severe Acute Respiratory Infection in Uganda, 2010-2015"],"prefix":"10.1093","volume":"13","author":[{"given":"Matthew J.","family":"Cummings","sequence":"first","affiliation":[{"name":"Department of Medicine and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barnabas","family":"Bakamutumaho","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Kayiwa","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy","family":"Byaruhanga","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Owor","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Namagambo","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda"}],"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, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph F.","family":"Wamala","sequence":"additional","affiliation":[{"name":"Epidemiology and Surveillance Division, Ministry of Health, Kampala, Uganda"},{"name":"South Sudan Country Office, World Health Organization, Juba, South Sudan; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen S.","family":"Morse","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julius J.","family":"Lutwama","sequence":"additional","affiliation":[{"name":"National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda"}],"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, New York"},{"name":"Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,12,1]]},"reference":[{"key":"2026020502562344600_bib1","volume-title":"Acute respiratory infections atlas.","author":"World Lung Foundation","year":"2010"},{"key":"2026020502562344600_bib2","author":"World Health Organization","year":"2014"},{"key":"2026020502562344600_bib3","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1164\/rccm.201412-2272ED","article-title":"Global participation in core data sets for emerging pathogens","volume":"191","author":"Carson","year":"2015","journal-title":"Am J Respir Crit Care Med"},{"key":"2026020502562344600_bib4","article-title":"Limiting spread: limiting the spread of pandemic, zoonotic, and seasonal epidemic influenza","author":"World Health Organization","year":"2010"},{"key":"2026020502562344600_bib5","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1093\/infdis\/jis548","article-title":"Influenza in Africa: uncovering the epidemiology of a long-overlooked disease","volume":"206","author":"Katz","year":"2012","journal-title":"J Infect Dis"},{"key":"2026020502562344600_bib6","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.gheart.2014.08.004","article-title":"Global burden of influenza as a cause of cardiopulmonary morbidity and mortality","volume":"9","author":"Fischer","year":"2014","journal-title":"Glob Heart"},{"key":"2026020502562344600_bib7","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1093\/infdis\/jis606","article-title":"Influenza surveillance in 15 countries in Africa, 2006-2010","volume":"206","author":"Radin","year":"2012","journal-title":"J Infect Dis"},{"key":"2026020502562344600_bib8","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1111\/j.1750-2659.2011.00257.x","article-title":"Pandemic influenza in Africa, lessons learned from 1968: a systematic review of the literature","volume":"6","author":"Ortiz","year":"2012","journal-title":"Influenza Other Respi Viruses"},{"key":"2026020502562344600_bib9","first-page":"A20168","article-title":"Clinical epidemiology and seasonality of influenza-associated severe acute respiratory illness in Uganda, 2010-2015 [abstract]","volume":"193","author":"Cummings","year":"2016","journal-title":"Am J Respir Crit Care Med"},{"key":"2026020502562344600_bib10","doi-asserted-by":"crossref","first-page":"S87","DOI":"10.1093\/infdis\/jis578","article-title":"Clinic- and hospital-based sentinel influenza surveillance, Uganda 2007-2010","volume":"206","author":"Lutwama","year":"2012","journal-title":"J Infect Dis"},{"key":"2026020502562344600_bib11","author":"World Health Organization"},{"key":"2026020502562344600_bib12","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1080\/03610929708831995","article-title":"A spatial scan statistic","volume":"26","author":"Kulldorff","year":"1997","journal-title":"Commun Statist Theory Meth"},{"key":"2026020502562344600_bib13","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1164\/rccm.201205-0913OC","article-title":"Spatial clusters of nontuberculous mycobacterial lung disease in the United States","volume":"186","author":"Adjemian","year":"2012","journal-title":"Am J Respir Crit Care Med"},{"key":"2026020502562344600_bib14","author":"Uganda Bureau of Statistics"},{"key":"2026020502562344600_bib15","volume-title":"Climate change knowledge portal.","author":"World Bank","year":"2016"},{"key":"2026020502562344600_bib16","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.3201\/eid1508.081422","article-title":"Strategy to enhance influenza surveillance worldwide","volume":"15","author":"Ortiz","year":"2009","journal-title":"Emerg Infect Dis"},{"key":"2026020502562344600_bib17","doi-asserted-by":"crossref","first-page":"2211","DOI":"10.1016\/S0140-6736(06)69895-4","article-title":"Estimation of potential global pandemic influenza mortality on the basis of vital registry data from the 1918-20 pandemic: a quantitative analysis","volume":"368","author":"Murray","year":"2006","journal-title":"Lancet"},{"key":"2026020502562344600_bib18","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1111\/irv.12083","article-title":"Macroeconomic impact of pandemic influenza and associated policies in Thailand, South Africa and Uganda","volume":"7","author":"Smith","year":"2013","journal-title":"Influenza Other Respi Viruses"},{"key":"2026020502562344600_bib19","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1111\/irv.12374","article-title":"Seasonal influenza vaccine policy, use and effectiveness in the tropics and subtropics - a systematic literature review","volume":"10","author":"Hirve","year":"2016","journal-title":"Influenza Other Respi Viruses"},{"key":"2026020502562344600_bib20","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.3201\/eid1512.091232","article-title":"Pandemic influenza as 21st century urban public health crisis","volume":"15","author":"Bell","year":"2009","journal-title":"Emerg Infect Dis"},{"key":"2026020502562344600_bib21","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/S1473-3099(10)70223-1","article-title":"Urbanisation and infectious diseases in a globalised world","volume":"11","author":"Alirol","year":"2011","journal-title":"Lancet Infect Dis"},{"key":"2026020502562344600_bib22","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/j.jinf.2011.03.011","article-title":"The clustering and transmission dynamics of pandemic influenza A (H1N1) 2009 cases in Hong Kong","volume":"63","author":"Lee","year":"2011","journal-title":"J Infect"},{"key":"2026020502562344600_bib23","author":"Uganda Bureau of Statistics"},{"key":"2026020502562344600_bib24","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1186\/1471-2458-14-624","article-title":"Descending the sanitation ladder in urban Uganda: evidence from Kampala Slums","volume":"14","author":"Kwiringira","year":"2014","journal-title":"BMC Public Health"},{"key":"2026020502562344600_bib25","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1371\/journal.pmed.0040295","article-title":"Slum health: from understanding to action","volume":"4","author":"Unger","year":"2007","journal-title":"PLoS Med"},{"key":"2026020502562344600_bib26","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1289\/ehp.1002383","article-title":"Global influenza seasonality: reconciling patterns across temperate and tropical regions","volume":"119","author":"Tamerius","year":"2011","journal-title":"Environ Health Perspect"},{"key":"2026020502562344600_bib27","doi-asserted-by":"crossref","first-page":"e1003194","DOI":"10.1371\/journal.ppat.1003194","article-title":"Environmental predictors of seasonal influenza epidemics across temperate and tropical climates","volume":"9","author":"Tamerius","year":"2013","journal-title":"PLoS Pathog"},{"key":"2026020502562344600_bib28","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/S1473-3099(11)70295-X","article-title":"Efficacy and effectiveness of influenza vaccines: a systematic review and meta-analysis","volume":"12","author":"Osterholm","year":"2012","journal-title":"Lancet Infect Dis"},{"key":"2026020502562344600_bib29","author":"World Health Organization"},{"key":"2026020502562344600_bib30","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1093\/infdis\/jit316","article-title":"Patients hospitalized with laboratory-confirmed influenza during the 2010-2011 influenza season: exploring disease severity by virus type and subtype","volume":"208","author":"Chaves","year":"2013","journal-title":"J Infect Dis"},{"key":"2026020502562344600_bib31","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.3201\/eid2007.131869","article-title":"Epidemiology of influenza virus types and subtypes in South Africa, 2009-2012","volume":"20","author":"Cohen","year":"2014","journal-title":"Emerg Infect Dis"},{"key":"2026020502562344600_bib32","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1086\/657314","article-title":"Elevated influenza-related excess mortality in South African elderly individuals, 1998-2005","volume":"51","author":"Cohen","year":"2010","journal-title":"Clin Infect Dis"},{"key":"2026020502562344600_bib33","doi-asserted-by":"crossref","first-page":"332","DOI":"10.2471\/BLT.07.049353","article-title":"Delayed care seeking for fatal pneumonia in children aged under five years in Uganda: a case-series study","volume":"86","author":"K\u00e4llander","year":"2008","journal-title":"Bull World Health Organ"},{"key":"2026020502562344600_bib34","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1093\/cid\/cis549","article-title":"Influenza-related mortality among adults aged 25-54 years with AIDS in South Africa and the United States of America","volume":"55","author":"Cohen","year":"2012","journal-title":"Clin Infect Dis"}],"container-title":["Annals of the American Thoracic Society"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/annalsats\/article-pdf\/13\/12\/2159\/66768577\/annalsats_13_12_2159.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/annalsats\/article-pdf\/13\/12\/2159\/66768577\/annalsats_13_12_2159.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T07:56:32Z","timestamp":1770278192000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/annalsats\/article\/13\/12\/2159\/8449345"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,12,1]]},"references-count":34,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2016,12,1]]},"published-print":{"date-parts":[[2016,12,1]]}},"URL":"https:\/\/doi.org\/10.1513\/annalsats.201607-561oc","relation":{},"ISSN":["2329-6933","2325-6621"],"issn-type":[{"value":"2329-6933","type":"print"},{"value":"2325-6621","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2016,12]]},"published":{"date-parts":[[2016,12,1]]}}}