{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T02:10:53Z","timestamp":1777601453427,"version":"3.51.4"},"reference-count":41,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T00:00:00Z","timestamp":1740009600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Public Health"],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>The coronavirus disease 2019 (COVID-19) pandemic has caused significant public health and socioeconomic crises across Africa; however, the prevalent patterns of COVID-19 and the circulating characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the continent remain insufficiently documented.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>In this study, national data on case numbers, infection incidences, mortality rates, the circulation of SARS-CoV-2 variants, and key health indexes were collected from various official and professional sources between January 2020 and December 2023 were analyzed with SaTScan and geographically weighted regression (GWR).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The prevalent profiles and circulating features of SARS-CoV-2 across the African continent, including its five regions and all African countries, were analyzed. Four major waves of the epidemic were observed. The first wave was closely associated with the introduction of the early SARS-CoV-2 strain while the subsequent waves were linked to the emergence of specific variants, including variants of concern (VOCs) Alpha, Beta, variants of interest (VOIs) Eta (second wave), VOC Delta (third wave), and VOC Omicron (fourth wave). SaTScan analysis identified four large spatiotemporal clusters that affected various countries. A significant number of countries (50 out of 56) reported their first cases during February 2020 and March 2020, predominantly involving individuals with confirmed cross-continental travel histories, mainly from Europe. In total, 12 distinct SARS-CoV-2 VOCs and VOIs were identified, with the most prevalent being VOCs Omicron, Delta, Beta, Alpha, and VOI Eta. Unlike the dominance of VOC Delta during the third wave and Omicron during the fourth wave, VOC Alpha was relatively rare in the Southern regions but more common in the other four regions. At the same time, Beta predominated in the Southern region and Eta in the Western region during the second wave. Additionally, relatively higher COVID-19 case incidences and mortalities were reported in the Southern and Northern African regions. Spearman rank correlation and geographically weighted regression (GWR) analyses of COVID-19 incidences against health indexes in 52 African countries indicate that countries with higher national health expenditures and better personnel indexes tended to report higher case incidences.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>This study offers a detailed overview of the COVID-19 pandemic in Africa. Strengthening the capacity of health institutions across African countries is essential for the timely detection of new SARS-CoV-2 variants and, consequently, for preparedness against future COVID-19 pandemics and other potentially infectious disease outbreaks.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fpubh.2025.1526727","type":"journal-article","created":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T06:41:25Z","timestamp":1740033685000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Spatiotemporal prevalence of COVID-19 and SARS-CoV-2 variants in Africa"],"prefix":"10.3389","volume":"13","author":[{"given":"Li-Ping","family":"Gao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Can-Jun","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting-Ting","family":"Tian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alie","family":"Brima Tia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael K.","family":"Abdulai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kang","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dong-Lin","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Shi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhi-Guo","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao-Ping","family":"Dong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,2,20]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"157","DOI":"10.23750\/abm.v91i1.9397","article-title":"WHO declares COVID-19 a pandemic","volume":"91","author":"Cucinotta","year":"2020","journal-title":"Acta Biomed"},{"key":"ref2","volume-title":"WHO director-General\u2019s opening remarks at the media briefing on COVID-19-11 march 2020","year":"2020"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"76","DOI":"10.3390\/tropicalmed8020076","article-title":"Mpox, caused by the MPXV of the clade IIb lineage, Goes global","volume":"8","author":"Gao","year":"2023","journal-title":"Tropic Med Infec Dis"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"67","DOI":"10.3390\/tropicalmed8010067","article-title":"Impact of the COVID-19 pandemic on malaria control in Africa: a preliminary analysis","volume":"8","author":"Gao","year":"2023","journal-title":"Trop Med Infect Dis"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"453","DOI":"10.4269\/ajtmh.20-1488","article-title":"COVID-19 misinformation and Infodemic in rural Africa","volume":"104","author":"Okereke","year":"2020","journal-title":"Am J Trop Med Hyg"},{"key":"ref6","volume-title":"World employment and social outlook trend 2022","year":"2022"},{"key":"ref7","article-title":"COVID-19 in Africa: socio-economic impact, policy response and opportunities[J]","volume-title":"SSRN Electronic Journal","author":"Ozili","year":"2020"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e006108","DOI":"10.1136\/bmjgh-2021-006108","article-title":"Building resilient health systems in Africa beyond the COVID-19 pandemic response. BMJ glob","volume":"6","author":"Gebremeskel","year":"2021","journal-title":"Health"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"7","DOI":"10.21141\/PJP.2020.09","article-title":"Cross-contamination in molecular diagnostic Laboratories in low- and Middle-income Countries","volume":"5","author":"Albano","year":"2020","journal-title":"PJP"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"957265","DOI":"10.3389\/fpubh.2022.957265","article-title":"Evolving trend change during the COVID-19 pandemic","volume":"10","author":"Gao","year":"2022","journal-title":"Front Public Health"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1038\/s41586-021-03402-9","article-title":"Detection of a SARS-CoV-2 variant of concern in South Africa","volume":"592","author":"Tegally","year":"2021","journal-title":"Nature"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"e2381","DOI":"10.1002\/rmv.2381","article-title":"Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: implications for immune escape and transmission","volume":"32","author":"Shrestha","year":"2022","journal-title":"Rev Med Virol"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.15212\/ZOONOSES-2021-0024","article-title":"Genome characterization and potential risk assessment of the novel SARS-CoV-2 variant omicron (B.1.1.529)","volume":"1","author":"Si Qin","year":"2021","journal-title":"Zoonoses"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"957277","DOI":"10.3389\/fpubh.2022.957277","article-title":"Multiple introduced lineages and the single native lineage co-driving the four waves of the COVID-19 pandemic in West Africa","volume":"10","author":"Gao","year":"2022","journal-title":"Front Public Health"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1016\/j.dsx.2021.04.025","article-title":"Correlation study to identify the factors affecting COVID-19 case fatality rates in India","volume":"15","author":"Upadhyay","year":"2021","journal-title":"Diabetes Metab Syndr"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"66","DOI":"10.29063\/ajrh2020\/v24i2s.11","article-title":"COVID-19 perception, knowledge, and preventive practice: comparison between South Korea, Ethiopia, and Democratic Republic of Congo","volume":"24","author":"Lee","year":"2020","journal-title":"Afr J Reprod Health"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"306","DOI":"10.3934\/publichealth.2020026","article-title":"Parameter estimation and prediction for coronavirus disease outbreak 2019 (COVID-19) in Algeria","volume":"7","author":"Bentout","year":"2020","journal-title":"AIMS Public Health"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1038\/d41591-020-00004-2","article-title":"Nigeria responds to COVID-19; first case detected in sub-Saharan Africa","volume":"26","author":"Adepoju","year":"2020","journal-title":"Nat Med"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"21108","DOI":"10.1038\/s41598-021-00267-w","article-title":"Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa","volume":"11","author":"Wruck","year":"2021","journal-title":"Sci Rep"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1186\/s13048-021-00820-1","article-title":"COVID-19 in Africa: an ovarian victory?","volume":"14","author":"Dufailu","year":"2021","journal-title":"J Ovarian Res"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"138959","DOI":"10.1016\/j.scitotenv.2020.138959","article-title":"Prediction of the COVID-19 spread in African countries and implications for prevention and control: a case study in South Africa, Egypt, Algeria, Nigeria, Senegal and Kenya","volume":"729","author":"Zhao","year":"2020","journal-title":"Sci Total Environ"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1126\/science.abj4336","article-title":"A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa","volume":"374","author":"Wilkinson","year":"2021","journal-title":"Science"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"3115","DOI":"10.1007\/s10653-021-00920-3","article-title":"The effectiveness of travel restriction measures in alleviating the COVID-19 epidemic: evidence from Shenzhen","volume":"44","author":"Ji","year":"2022","journal-title":"China Environ Geochem Health"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"102252","DOI":"10.1016\/j.tmaid.2021.102252","article-title":"Tracking and controlling the spatiotemporal spread of SARS-CoV-2 omicron variant in South Africa","volume":"46","author":"Tong","year":"2022","journal-title":"Travel Med Infect Dis"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"105772","DOI":"10.1016\/j.landusepol.2021.105772","article-title":"How COVID-19 reshaped quality of life in cities: a synthesis and implications for urban planning","volume":"111","author":"Mouratidis","year":"2021","journal-title":"Land Use Policy"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1093\/cid\/ciaa934","article-title":"Spatiotemporal characteristics of the COVID-19 epidemic in the United States","volume":"72","author":"Wang","year":"2021","journal-title":"Clin Infect Dis"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1021\/acschemneuro.0c00788","article-title":"Chemosensory systems in COVID-19: evolution of scientific research","volume":"12","author":"Veronese","year":"2021","journal-title":"ACS Chem Neurosci"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1080\/21505594.2021.1877066","article-title":"COVID-19 evolution during the pandemic - implications of new SARS-CoV-2 variants on disease control and public health policies","volume":"12","author":"van Oosterhout","year":"2021","journal-title":"Virulence"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.1002\/jmv.27526","article-title":"Omicron and Delta variant of SARS-CoV-2: a comparative computational study of spike protein","volume":"94","author":"Kumar","year":"2022","journal-title":"J Med Virol"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1080\/22221751.2021.2023329","article-title":"SARS-CoV-2 omicron variant shows less efficient replication and fusion activity when compared with Delta variant in TMPRSS2-expressed cells","volume":"11","author":"Zhao","year":"2022","journal-title":"Emerg Microbes Infect"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1126\/science.abe1916","article-title":"Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors","volume":"371","author":"Uyoga","year":"2021","journal-title":"Science"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"n334","DOI":"10.1136\/bmj.n334","article-title":"Covid-19 deaths in Africa: prospective systematic postmortem surveillance study","volume":"372","author":"Mwananyanda","year":"2021","journal-title":"BMJ"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1186\/s12889-024-18457-2","article-title":"Correlation of pre-existing comorbidities with disease severity in individuals infected with SARS-COV-2 virus","volume":"24","author":"Maru\u0161i\u0107","year":"2024","journal-title":"BMC Public Health"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"747","DOI":"10.7196\/SAMJ.2022.v112i9.16417","article-title":"Undiagnosed comorbidities among individuals hospitalised with COVID-19 in south African public hospitals","volume":"112","author":"Jassat","year":"2022","journal-title":"S Afr Med J"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"100841","DOI":"10.1016\/j.cegh.2021.100841","article-title":"Impact of poor disease surveillance system on COVID-19 response in africa: time to rethink and rebuilt","volume":"12","author":"Aborode","year":"2021","journal-title":"Clin Epidemiol Glob Health"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"2370","DOI":"10.3390\/ijerph15112370","article-title":"Stress testing the capacity of health systems to manage climate change-related shocks and stresses","volume":"15","author":"Ebi","year":"2018","journal-title":"Int J Environ Res Public Health"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e213","DOI":"10.1017\/S0950268820002149","article-title":"Spreading of SARS-CoV-2 in West Africa and assessment of risk factors","volume":"148","author":"Tinto","year":"2020","journal-title":"Epidemiol Infect"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"2465","DOI":"10.1002\/jmv.26159","article-title":"COVID-19: a perspective on Africa's capacity and response","volume":"92","author":"Dzinamarira","year":"2020","journal-title":"J Med Virol"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.15212\/ZOONOSES-2023-0003","article-title":"Next-generation vaccines against COVID-19 variants: beyond the spike protein","volume":"3","author":"Bonam","year":"2023","journal-title":"Zoonoses (Burlingt)"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"114224","DOI":"10.1016\/j.ijheh.2023.114224","article-title":"The dominance of co-circulating SARS-CoV-2 variants in wastewater","volume":"253","author":"Pilapil","year":"2023","journal-title":"Int J Hyg Environ Health"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"e28241","DOI":"10.1002\/jmv.28241","article-title":"In silico evaluation of the impact of omicron variant of concern sublineage BA.4 and BA.5 on the sensitivity of RT-qPCR assays for SARS-CoV-2 detection using whole genome sequencing","volume":"95","author":"Sharma","year":"2023","journal-title":"J Med Virol"}],"container-title":["Frontiers in Public Health"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpubh.2025.1526727\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T06:41:30Z","timestamp":1740033690000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpubh.2025.1526727\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,20]]},"references-count":41,"alternative-id":["10.3389\/fpubh.2025.1526727"],"URL":"https:\/\/doi.org\/10.3389\/fpubh.2025.1526727","relation":{},"ISSN":["2296-2565"],"issn-type":[{"value":"2296-2565","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,20]]},"article-number":"1526727"}}