{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:12:10Z","timestamp":1772169130293,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.17908.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T00:00:00Z","timestamp":1765411200000}},{"DOI":"10.12688\/wellcomeopenres.17908.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T00:00:00Z","timestamp":1765411200000}},{"DOI":"10.12688\/wellcomeopenres.17908.3","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T00:00:00Z","timestamp":1765411200000}}],"reference-count":27,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T00:00:00Z","timestamp":1765411200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000030","name":"U.S. Centers for Disease Control and Prevention","doi-asserted-by":"crossref","award":["#6U01GH002143"],"award-info":[{"award-number":["#6U01GH002143"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["102975"],"award-info":[{"award-number":["102975"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>Background Acute respiratory illnesses (ARI) are a major cause of morbidity and mortality globally. With (re)emergence of novel viruses and increased access to childhood bacterial vaccines, viruses have assumed greater importance in the aetiology of ARI. There are now promising candidate vaccines against some of the most common endemic respiratory viruses. Optimal delivery strategies for these vaccines, and the need for interventions against other respiratory viruses, requires geographically diverse data capturing temporal variations in virus circulation. Methods We leveraged three health facility-based respiratory illness surveillance platforms operating in 11 sites across Kenya. Nasopharyngeal (NP) and\/or oropharyngeal (OP) specimens, patient demographic, and clinical characteristics were collected in 2014 from individuals of various ages presenting with respiratory symptoms at the surveillance facilities. Real time multiplex polymerase chain reaction was used to detect rhinoviruses, respiratory syncytial virus (RSV), influenza virus, human coronaviruses (hCoV), and adenoviruses. Results From 11 sites, 5451 NP\/OP specimens were collected and tested from patients. Of these, 40.2% were positive for at least one of the targeted respiratory viruses. The most frequently detected were rhinoviruses (17.0%) and RSV A\/B (10.5%), followed by influenza A (6.2%), adenovirus (6.0%) and hCoV (4.2%). RSV was most prevalent among infants aged &lt;12 months old (18.9%), adenovirus among children aged 12\u201323 months old (11.0%), influenza A among children aged 24\u201359 months (9.3%), and rhinovirus across all age groups (range, 12.7\u201319.0%). RSV had a higher virus positivity in the inpatient setting (12.5%) compared to outpatient setting (4.8%). The overall percent virus positivity varied by surveillance site, health facility type and case definition used in surveillance. Conclusions We identify rhinoviruses, RSV, and influenza A as the most prevalent respiratory viruses. Higher RSV positivity in inpatients, and in infants, strengthens the case for RSV vaccination. To inform the design and delivery of public health interventions, long-term surveillance is required to establish regional heterogeneities in respiratory virus circulation and seasonality.<\/ns3:p>","DOI":"10.12688\/wellcomeopenres.17908.4","type":"journal-article","created":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T08:54:08Z","timestamp":1765443248000},"page":"234","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Surveillance of respiratory viruses at health facilities from across Kenya, 2014"],"prefix":"10.12688","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5304-2210","authenticated-orcid":false,"given":"Nickson","family":"Murunga","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0069-1473","authenticated-orcid":false,"given":"Bryan","family":"Nyawanda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7215-6539","authenticated-orcid":false,"given":"Joyce U.","family":"Nyiro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3053-1369","authenticated-orcid":false,"given":"Grieven P.","family":"Otieno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Everlyn","family":"Kamau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2160-567X","authenticated-orcid":false,"given":"Charles N.","family":"Agoti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clement","family":"Lewa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Gichuki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Mutunga","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nancy","family":"Otieno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lilian","family":"Mayieka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melvin","family":"Ochieng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2307-2280","authenticated-orcid":false,"given":"Gilbert","family":"Kikwai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4450-621X","authenticated-orcid":false,"given":"Elizabeth","family":"Hunsperger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clayton","family":"Onyango","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gideon","family":"Emukule","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Godfrey","family":"Bigogo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer R.","family":"Verani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9453-7057","authenticated-orcid":false,"given":"Sandra S.","family":"Chaves","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5426-1984","authenticated-orcid":false,"given":"D. 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Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v4\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v4\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v4\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T10:29:08Z","timestamp":1769509748000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,11]]},"references-count":27,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.17908.4","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/wellcomeopenres.17908.3","asserted-by":"subject"},{"id-type":"doi","id":"10.12688\/wellcomeopenres.17908.2","asserted-by":"subject"},{"id-type":"doi","id":"10.12688\/wellcomeopenres.17908.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.28024.r144052","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.28024.r144052","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,11]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v4#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.22125.r66631, David P Moore, Vaccine and Infectious Diseases Analytics (VIDA) Research Unit, University of the Witwatersrand, Johannesburg, 23 Oct 2023, version 3, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v3#referee-response-66631","order":0,"name":"referee-response-66631","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Nickson Murunga<\/b>; \n<i>Posted: 09 Dec 2025<\/i>; Major comments: The fact that RSV was more prevalent in hospitalised participants is not highlighted in the Results and Discussion sections. It would be useful to include a Table with viral detection prevalence stratified by inpatient versus outpatient status.  \n<b>Response: <\/b>We thank the reviewer for this observation. We have updated the Results section to include Table 5, which presents viral detection prevalence stratified by inpatient and outpatient setting, and revised the accompanying text to highlight the higher RSV prevalence among hospitalised participants. This table, together with our earlier supplementary material (Extended data: Supplementary File, Supplementary Figure 1), provides summary of prevalence patterns across the two settings.  Death as an outcome is not described in this study. How many of the participants had an outcome of death? It would be useful to include a Table with viral detection prevalence stratified by survival status.  \n<b>Response: <\/b>We appreciate the reviewer\u2019s comment and agree that such a summary would have been valuable for understanding disease severity. However, due to the retrospective nature of our testing and the lack of standardised data collection across sites, outcome information was incomplete across sites and insufficient for comparing viral detection by survival status. This limitation is acknowledged in the Discussion.  How did viral co-infection impact on hospitalisation and outcome status? It would be useful to include this in the suggested tables mentioned above.  \n<b>Response: <\/b>\n<i>We have now included Table 5, which presents viral co-detection patterns stratified by inpatient and outpatient facilities. However, as noted in the Discussion, outcome data were incomplete across surveillance sites and could not be reliably incorporated into this summary.<\/i>  Minor comments: In the Abstract, mention in the results section that RSV was more prevalent in inpatients compared to outpatients.  \n<b>Response: <\/b>\n<i>Thank you for the suggestion. We have now included this information in the abstract.<\/i>  In the first paragraph of the Introduction, suggest omit the word \u201crecent\u201d in the sentence which highlights the introduction of bacterial conjugate vaccines.  \n<b>Response: <\/b>\n<i>Thank you for the suggestion. The word \u201crecent\u201d has now been omitted from the Introduction as recommended.<\/i>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v4#referee-comment-6351","order":1,"name":"referee-comment-6351","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.22125.r66632, W. Abdullah Brooks, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 02 Nov 2023, version 3, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v3#referee-response-66632","order":2,"name":"referee-response-66632","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.28024.r144052, Rino Rappuoli, Fondazione Biotecnopolo di Siena, Siena, 27 Jan 2026, version 4, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-234\/v4#referee-response-144052","order":3,"name":"referee-response-144052","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [102975, <a href=https:\/\/doi.org\/10.35802\/102975>https:\/\/doi.org\/10.35802\/102975<\/a>], and U.S. Centers for Disease Control and Prevention through Cooperative Agreement [#6U01GH002143].\r\n\r\nThe findings and conclusions in this study are those of the authors and do not necessarily represent the official position of the KEMRI, or U.S. Centers for Disease Control and Prevention and the Center for Global Health. Use of trade names is for identification only and does not imply endorsement by [the Centers for Disease Control and Prevention\/the Agency for Toxic Substances and Disease Registry], the Public Health Service, or the U.S. Department of Health and Human Services. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}