{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T07:54:32Z","timestamp":1774079672581,"version":"3.50.1"},"reference-count":40,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T00:00:00Z","timestamp":1724025600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of the Witwatersrand","award":["RINC 001-167-8461201-5121505-4547"],"award-info":[{"award-number":["RINC 001-167-8461201-5121505-4547"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 pandemic resulted in widespread morbidity and mortality, but generally, the diagnosis of other respiratory viruses was limited. This study aimed to assess the prevalence of other respiratory viruses during the 2020\/2021 pandemic among patients of all ages who accessed care at public healthcare facilities in Gauteng Province, South Africa. Laboratory diagnosis for respiratory viruses, with or without SARS-CoV-2, was conducted via multiplex real-time polymerase chain reactions using respiratory specimens. A total of 1776 patients were included from 1 April 2020 to 31 March 2021, of which 766 (43.1%) were positive for respiratory viruses other than SARS-CoV-2. RV (368\/1776; 20.7%) was the most prevalent, followed by RSV (304\/1776; 17.1%), AdV (112\/1776; 6.3%) and EV (105\/1776; 5.9%). hCoV-OC43 (39\/1776; 2.2%) was the most prevalent common coronavirus. SARS-CoV-2 co-infections were detected in 4.8% (24\/500) of patients. Only 27.1% (482\/1776) of patients were admitted to high-care or intensive care units. A decrease in respiratory virus detections was observed, except for RSV, EV and hCoV-OC43. RSV prevalence increased in 2021, while influenza A\/B viruses remained undetected.<\/jats:p>","DOI":"10.3390\/v16081325","type":"journal-article","created":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T10:11:28Z","timestamp":1724062288000},"page":"1325","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Prevalence and Seasonal Patterns of 16 Common Viral Respiratory Pathogens during the COVID-19 Pandemic in Gauteng Province, South Africa, 2020\u20132021"],"prefix":"10.3390","volume":"16","author":[{"given":"Bhaveshan","family":"Reddy","sequence":"first","affiliation":[{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa"},{"name":"National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andiswa","family":"Simane","sequence":"additional","affiliation":[{"name":"National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hloniphile","family":"Mthiyane","sequence":"additional","affiliation":[{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bonolo","family":"Mashishi","sequence":"additional","affiliation":[{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa"},{"name":"National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nonhlanhla","family":"Mbenenge","sequence":"additional","affiliation":[{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa"},{"name":"National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florette K.","family":"Treurnicht","sequence":"additional","affiliation":[{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa"},{"name":"National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,8,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s41256-020-00135-6","article-title":"The Novel Coronavirus Outbreak in Wuhan, China","volume":"5","author":"Zhu","year":"2020","journal-title":"Glob. Health Res. Policy"},{"key":"ref_2","unstructured":"(2024, June 26). WHO COVID-19 Cases | WHO COVID-19 Dashboard. Available online: https:\/\/data.who.int\/dashboards\/covid19\/cases."},{"key":"ref_3","unstructured":"Mkhize, Z. (2024, March 16). First Case of COVID-19 Coronavirus Reported in SA. Available online: https:\/\/www.nicd.ac.za\/first-case-of-covid-19-coronavirus-reported-in-sa\/."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1037\/tra0000812","article-title":"The COVID-19 pandemic in South Africa","volume":"12","author":"Naidu","year":"2020","journal-title":"Psychol. Trauma Theory Res. Pract. Policy"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"105924","DOI":"10.1016\/j.ijantimicag.2020.105924","article-title":"Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Corona Virus disease-2019 (COVID-19): The Epidemic and the Challenges","volume":"55","author":"Lai","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_6","first-page":"104","article-title":"Epidemiology of respiratory virus before and during COVID-19 pandemic","volume":"30","author":"Avolio","year":"2022","journal-title":"Infez. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1097\/INF.0000000000003951","article-title":"Clinical Presentation and Outcome of Acute Respiratory Illnesses in South African Children During the COVID-19 Pandemic","volume":"42","author":"Redfern","year":"2023","journal-title":"\u0152pediatric Infect. Dis. J."},{"key":"ref_8","first-page":"94","article-title":"Prevalence of respiratory viruses by Multiplex PCR: A four-and-a-half-year retrospective study in an Italian general hospital","volume":"29","author":"Leli","year":"2021","journal-title":"Le Infez. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41579-021-00535-6","article-title":"Transmissibility and transmission of respiratory viruses","volume":"19","author":"Leung","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s40249-023-01066-3","article-title":"Non-pharmaceutical interventions for COVID-19 reduced the incidence of infectious diseases: A controlled interrupted time-series study","volume":"12","author":"Zhang","year":"2023","journal-title":"Infect. Dis. Poverty"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"van Doorn, H.R., and Yu, H. (2020). Viral Respiratory Infections. Hunter\u2019s Tropical Medicine and Emerging Infectious Diseases, Elsevier.","DOI":"10.1016\/B978-0-323-55512-8.00033-8"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Prasad, S., Lownik, E., and Ricco, J.A. (2016). Viral Infections of the Respiratory Tract, Springer eBooks.","DOI":"10.1007\/978-3-319-04414-9_41"},{"key":"ref_13","first-page":"195","article-title":"The effects of the COVID-19 pandemic on community respiratory virus activity","volume":"21","author":"Chow","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Subramoney, K., Mtileni, N., Davis, A., Giandhari, J., Tegally, H., Wilkinson, E., Naidoo, Y., Ramphal, Y., Pillay, S., and Ramphal, U. (2023). SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0286373"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"(2023). Comparison of fifteen SARS-CoV-2 nucleic acid amplification test assays used during the Canadian Laboratory Response Network\u2019s National SARS-CoV-2 Proficiency Program, May 2020 to June 2021. Can. Commun. Dis. Rep., 49, 180\u2013189.","DOI":"10.14745\/ccdr.v49i05a03"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1111\/irv.12650","article-title":"Health and economic burden of influenza-associated illness in South Africa, 2013\u20132015","volume":"13","author":"Tempia","year":"2019","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Audi, A., AlIbrahim, M., Kaddoura, M., Hijazi, G., Yassine, H.M., and Zaraket, H. (2020). Seasonality of Respiratory Viral Infections: Will COVID-19 Follow Suit?. Front. Public Health, 8.","DOI":"10.3389\/fpubh.2020.567184"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Principi, N., Autore, G., Ramundo, G., and Esposito, S. (2023). Epidemiology of Respiratory Infections during the COVID-19 Pandemic. Viruses, 15.","DOI":"10.3390\/v15051160"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.15585\/mmwr.mm7029a1","article-title":"Changes in influenza and other respiratory virus activity during the COVID-19 pandemic\u2014United States, 2020\u20132021","volume":"70","author":"Olsen","year":"2021","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2001600","DOI":"10.2807\/1560-7917.ES.2021.26.29.2001600","article-title":"Decline of influenza and respiratory syncytial virus detection in facility-based surveillance during the COVID-19 pandemic, South Africa, January to October 2020","volume":"26","author":"Tempia","year":"2021","journal-title":"Eurosurveillance"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Razanajatovo, N.H., Randriambolamanantsoa, T.H., Rabarison, J.H., Ankasitrahana, R.M.F., Ratsimbazafy, A., Raherinandrasana, A.H., Razafimanjato, H., Raharinosy, V., Andriamandimby, S.F., and Heraud, J.-M. (2022). Epidemiological Patterns of Seasonal Respiratory Viruses during the COVID-19 Pandemic in Madagascar, March 2020\u2013May 2022. Viruses, 15.","DOI":"10.3390\/v15010012"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Davids, M., Johnstone, S., Mendes, A., Brecht, G., Avenant, T., du Plessis, N., de Villiers, M., Page, N., and Venter, M. (2024). 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. Viruses, 16.","DOI":"10.3390\/v16030404"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"858","DOI":"10.7196\/SAMJ.2020.v110i9.14934","article-title":"Comparative strategic approaches to COVID-19 in Africa: Balancing public interest with civil liberties","volume":"110","author":"Obasa","year":"2020","journal-title":"S. Afr. Med. J."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e13065","DOI":"10.1111\/irv.13065","article-title":"Seasonal respiratory virus circulation was diminished during the COVID-19 pandemic","volume":"17","author":"Heiskanen","year":"2022","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1007\/s00430-021-00720-7","article-title":"Influenza and RSV incidence during COVID-19 pandemic\u2014An observational study from in-hospital point-of-care testing","volume":"210","author":"Stamm","year":"2021","journal-title":"Med. Microbiol. Immunol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"661","DOI":"10.2147\/IDR.S396434","article-title":"The Impact of the COVID-19 Pandemic on Respiratory Syncytial Virus Infection: A Narrative Review","volume":"16","author":"Chuang","year":"2023","journal-title":"Infect. Drug Resist."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"ofv139","DOI":"10.1093\/ofid\/ofv139","article-title":"Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009\u20132014","volume":"2","author":"Cohen","year":"2015","journal-title":"Open Forum Infect. Dis."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Parsons, J., Korsman, S., Smuts, H., Hsiao, N.-Y., Valley-Omar, Z., Gelderbloem, T., and Hardie, D. (2023). Human Parainfluenza Virus (HPIV) Detection in Hospitalized Children with Acute Respiratory Tract Infection in the Western Cape, South Africa during 2014\u20132022 Reveals a Shift in Dominance of HPIV 3 and 4 Infections. Diagnostics, 13.","DOI":"10.3390\/diagnostics13152576"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1002\/hsr2.59","article-title":"Human bocavirus, coronavirus, and polyomavirus detected among patients hospitalised with severe acute respiratory illness in South Africa, 2012 to 2013","volume":"1","author":"Subramoney","year":"2018","journal-title":"Health Sci. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"04001","DOI":"10.7189\/jogh.13.04001","article-title":"Molecular epidemiology of respiratory syncytial virus in children with acute respiratory illnesses in Africa: A systematic review and meta-analysis","volume":"13","author":"Tafa","year":"2023","journal-title":"J. Glob. Health"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/s41467-023-44275-y","article-title":"Incidence and transmission of respiratory syncytial virus in urban and rural South Africa, 2017\u20132018","volume":"15","author":"Cohen","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"ofad400","DOI":"10.1093\/ofid\/ofad400","article-title":"Risk Factors for SARS-CoV-2 Infection and Severe Outcomes Among People With Human Immunodeficiency Virus: Cohort Study","volume":"10","author":"Hanna","year":"2023","journal-title":"Open Forum Infect. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Stobbelaar, K., Mangodt, T.C., Van Delhaise, L., Andries, J., Gille, V., Barbezange, C., Smet, A., Winter De, J., Schepens, T., and Els Cos, P. (2023). Risk Factors Associated with Severe RSV Infection in Infants: What Is the Role of Viral Co-Infections?. Microbiol. Spectr., 11.","DOI":"10.1128\/spectrum.04368-22"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Matera, L., Manti, S., Petrarca, L., Pierangeli, A., Maria Giulia Conti Mancino, E., Leonardi, S., Midulla, F., and Nenna, R. (2023). An overview on viral interference during SARS-CoV-2 pandemic. Front. Pediatr., 11.","DOI":"10.3389\/fped.2023.1308105"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Vafadar, S., Shahdoust, M., Kalirad, A., Zakeri, P., and Sadeghi, M. (2021). Competitive exclusion during co-infection as a strategy to prevent the spread of a virus: A computational perspective. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0247200"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e2365","DOI":"10.1002\/rmv.2365","article-title":"Respiratory viral co-infections in patients with COVID-19 and associated outcomes: A systematic review and meta-analysis","volume":"33","author":"Krumbein","year":"2023","journal-title":"Rev. Med. Virol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1097\/INF.0000000000003981","article-title":"Respiratory Coinfections in Children With SARS-CoV-2","volume":"42","author":"Westbrook","year":"2023","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1991","DOI":"10.1007\/s00431-021-03947-x","article-title":"Viral co-infections among SARS-CoV-2-infected children and infected adult household contacts","volume":"180","author":"Pigny","year":"2021","journal-title":"Eur. J. Pediatr."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e296","DOI":"10.1016\/S1473-3099(20)30982-8","article-title":"Importance of non-pharmaceutical interventions in lowering the viral inoculum to reduce susceptibility to infection by SARS-CoV-2 and potentially disease severity","volume":"21","author":"Spinelli","year":"2021","journal-title":"Lancet Infect. Dis."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"558","DOI":"10.3390\/idr14040059","article-title":"Impact of COVID-19 on the Changing Patterns of Respiratory Syncytial Virus Infections","volume":"14","author":"Garg","year":"2022","journal-title":"Infect. Dis. Rep."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/8\/1325\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:39:06Z","timestamp":1760110746000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/8\/1325"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,19]]},"references-count":40,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2024,8]]}},"alternative-id":["v16081325"],"URL":"https:\/\/doi.org\/10.3390\/v16081325","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,19]]}}}