{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T15:49:22Z","timestamp":1791992962084,"version":"4.4.0"},"reference-count":38,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T00:00:00Z","timestamp":1709596800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Education and Research (BMBF)","award":["66.3010.7-002.07"],"award-info":[{"award-number":["66.3010.7-002.07"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Severe acute respiratory tract infections (SARIs) has been well described in South Africa with seasonal patterns described for influenza and respiratory syncytial virus (RSV), while others occur year-round (rhinovirus and adenovirus). This prospective syndromic hospital-based surveillance study describes the prevalence and impact of public interventions on the seasonality of other respiratory pathogens during the coronavirus disease-19 (COVID-19) pandemic. This occurred from August 2018 to April 2022, with 2595 patients who met the SARS case definition and 442 controls, from three sentinel urban and rural hospital sites in South Africa. Naso\/oro-pharyngeal (NP\/OP) swabs were tested using the FastTrack Diagnostics\u00ae Respiratory pathogens 33 (RUO) kit. Descriptive statistics, odds ratios, and univariate\/multivariate analyses were used. Rhinovirus (14.80%, 228\/1540) and Streptococcus pneumoniae (28.50%, 439\/1540) were most frequently detected in NP\/OP swabs and in children &lt;1 years old (35%, 648\/1876). Among others, pathogens associated with SARI cases causing disease were influenza A&amp;B, HRV, RSV, hCoV 229e, Haemophilus influenzae, Staphylococcus aureus, and Streptococcus pneumoniae. Pre-COVID-19, seasonal trends of these pathogens correlated with previous years, with RSV and influenza A seasons only resuming after the national lockdown (2021). It is evident that stringent lockdown conditions have severe impacts on the prevalence of respiratory tract infections.<\/jats:p>","DOI":"10.3390\/v16030404","type":"journal-article","created":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T11:26:59Z","timestamp":1709638019000},"page":"404","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Changes in Prevalence and Seasonality of Pathogens Identified in Acute Respiratory Tract Infections in Hospitalised Individuals in Rural and Urban Settings in South Africa; 2018\u20132022"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8752-8657","authenticated-orcid":false,"given":"Michaela","family":"Davids","sequence":"first","affiliation":[{"name":"Centre for Emerging Respiratory and Arbovirus Research, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siobhan","family":"Johnstone","sequence":"additional","affiliation":[{"name":"Centre for Enteric Diseases, Virology, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriano","family":"Mendes","sequence":"additional","affiliation":[{"name":"Centre for Emerging Respiratory and Arbovirus Research, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gadean","family":"Brecht","sequence":"additional","affiliation":[{"name":"Centre for Emerging Respiratory and Arbovirus Research, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2367-6479","authenticated-orcid":false,"given":"Theunis","family":"Avenant","sequence":"additional","affiliation":[{"name":"Department of Paediatrics, Kalafong Provincial Tertiary Hospital, University of Pretoria, Pretoria 0084, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolette","family":"du Plessis","sequence":"additional","affiliation":[{"name":"Department of Paediatrics, Kalafong Provincial Tertiary Hospital, University of Pretoria, Pretoria 0084, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8766-4296","authenticated-orcid":false,"given":"Maryke","family":"de Villiers","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Kalafong Provincial Tertiary Hospital, University of Pretoria, Pretoria 0084, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5845-4417","authenticated-orcid":false,"given":"Nicola","family":"Page","sequence":"additional","affiliation":[{"name":"Centre for Enteric Diseases, Virology, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa"},{"name":"Centre of Enteric Diseases, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2696-824X","authenticated-orcid":false,"given":"Marietjie","family":"Venter","sequence":"additional","affiliation":[{"name":"Centre for Emerging Respiratory and Arbovirus Research, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,3,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1016\/S1473-3099(18)30310-4","article-title":"Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory infections in 195 countries, 1990\u20132016: A systematic analysis for the Global Burden of Disease Study 2016","volume":"18","author":"Troeger","year":"2018","journal-title":"Lancet Infect. 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