Okoh, Olayinka SundayNii-Trebi, Nicholas IsraelJakkari, AbdulrokeebOlaniran, Tosin TitusSenbadejo, Tosin YetundeKafintu-kwashie, Anna AbaDairo, Emmanuel OluwatobiGaniyu, Tajudeen OladunniAkaninyene, Ifiokakaninyene EkpoEzediuno, Louis OdinakaoseAdeosun, Idowu JesulayomiOckiya, Michael AsebakeJimah, Esther MoradeyoSpiro, David J.Oladipo, Elijah KolawoleTrovao, Nıdia S.2023-11-272023-11-272022-03-18Okoh, O.S., Nii-Trebi, N.I., Jakkari, A. et al. 2022, 'Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa', iScience, vol. 25, art. 103880, pp. 1-20. https://DOI.org/10.1016/j.isci.2022.103880.2589-004210.1016/j.isci.2022.103880http://hdl.handle.net/2263/93458DATA AND CODE AVAILABILITY : The accession numbers of sequences used in the study and respective GISAID acknowledgment table are provided in Data S5. All original code used in the manuscript has been deposited at: https://github.com/Yinkaokoh/ updatedSARCoV2_project. Additional supplemental items are available from Mendeley Data at: https://doi.org/10.17632/bczg8z7yg2.1. d Any additional information required to reanalyze the data reported in this work paper is available from the lead contact upon request.SUPPLEMENTAL INFORMATION : DOCUMENT S1. Figures S1–S7, Table S3, and Data S1 and S2. DATA S4. Pango lineages circulating in Africa, related to STAR Methods section. DATA S5. Accession numbers of sequences used in the study and acknowledgment table, related to STAR Methods section. DATA S3. Continent-specific pairwise distance, related to Figure 9.There is a dearth of information on COVID-19 disease dynamics in Africa. To fill this gap, we investigated the epidemiology and genetic diversity of SARSCoV- 2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We investigated the circulating diversity, reconstructed the viral evolutionary divergence and history, and studied the case and death trends in the continent. Almost a fifth (144/782, 18.4%) of Pango lineages found worldwide circulated in Africa, with five different lineages dominating over time. Phylogenetic analysis revealed that African viruses cluster more closely with those from Europe. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the epidemiological and evolutionary dynamics of the circulating viral diversity in Africa. They also emphasize the need to expand surveillance efforts in Africa to help inform and implement better public health measures.en© 2022. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Disease dynamicsAfricaCOVID-19 pandemicCoronavirus disease 2019 (COVID-19)Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)SDG-03: Good health and well-beingEpidemiologyGenetic diversityArticle