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Open Sci."],"published-print":{"date-parts":[[2024,6]]},"abstract":"<jats:p>The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. A total of 7540 complete nucleotide genomes from 51 African nations were obtained and analysed using the National Center for Biotechnology Information and Global Initiative on Sharing Influenza Data databases to examine the genetic diversity and spread dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Using various clade and lineage nomenclature schemes, we examined their diversity and used maximum parsimony inference methods to reconstruct the evolutionary hypotheses about the spread of the virus in Africa. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa three years after the COVID-19 pandemic, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya and Nigeria as key sources of viral transmission among sub-Saharan African nations. These findings provide insights into the viral strains that circulate in Africa and their evolutionary patterns.<\/jats:p>","DOI":"10.1098\/rsos.231326","type":"journal-article","created":{"date-parts":[[2024,6,5]],"date-time":"2024-06-05T03:39:39Z","timestamp":1717558779000},"update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations"],"prefix":"10.1098","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6861-2391","authenticated-orcid":true,"given":"Desire","family":"Mtetwa","sequence":"first","affiliation":[{"name":"Department of Biotechnology, School of Health Science and Technology, Chinhoyi University of Technology, Private Bag 7724 , Chinhoyi, Zimbabwe"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tafadzwa","family":"Manjengwa","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, School of Health Science and Technology, Chinhoyi University of Technology, Private Bag 7724 , Chinhoyi, Zimbabwe"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zedias","family":"Chikwambi","sequence":"additional","affiliation":[{"name":"African Institute of Biomedical Science and Technology, 911 Chiedza Park, Boronia , Harare, Zimbabwe"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2024,6,5]]},"reference":[{"key":"e_1_3_8_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.03.035"},{"key":"e_1_3_8_3_2","unstructured":"Zukurov JP do Nascimento-Brito S Volpini AC Oliveira GC Mario Janini LR Antoneli F . Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage. See http:\/\/tanden.url.ph\/."},{"key":"e_1_3_8_4_2","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2020.1775132"},{"key":"e_1_3_8_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2020.11.190"},{"key":"e_1_3_8_7_2","unstructured":"World Health Organization . WHO coronavirus (COVID-19) dashboard. See https:\/\/covid19.who.int (accessed 28 February 2023)."},{"key":"e_1_3_8_8_2","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045"},{"key":"e_1_3_8_9_2","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens9050331"},{"key":"e_1_3_8_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-018-0118-9"},{"key":"e_1_3_8_11_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-981-15-4814-7_3"},{"key":"e_1_3_8_12_2","unstructured":"National Center for Biotechnology Information (NCBI) National Library of Medicine (US) . 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(doi:10.1093\/ve\/veab064)","journal-title":"Virus Evol."},{"key":"e_1_3_8_19_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msz131"},{"key":"e_1_3_8_20_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj4336"},{"key":"e_1_3_8_21_2","doi-asserted-by":"publisher","DOI":"10.7189\/jogh.12.03085"},{"key":"e_1_3_8_22_2","unstructured":"Katella K . 2023 Omicron Delta Alpha and more: what to know about the coronavirus variants. Yale Medicine. See https:\/\/www.yalemedicine.org\/news\/covid-19-variants-of-concern-omicron (accessed 3 February 2023)."},{"key":"e_1_3_8_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04411-y"},{"key":"e_1_3_8_24_2","unstructured":"Cella E . 2021 Chemotherapy. SARS-COV-2 lineages and sub-lineages circulating worldwide: a dynamic overview. See https:\/\/www.karger.com\/Article\/FullText\/515340 (accessed 28 February 2023)."},{"key":"e_1_3_8_25_2","unstructured":"Haseltine WA . 2021 A second east African variant: A.23.1. Forbes. 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