Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa

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 SARS-CoV-2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We inv...

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Published in:	iScience Vol. 25; no. 3; p. 103880
Main Authors:	Okoh, Olayinka Sunday, Nii-Trebi, Nicholas Israel, Jakkari, Abdulrokeeb, Olaniran, Tosin Titus, Senbadejo, Tosin Yetunde, Kafintu-kwashie, Anna Aba, Dairo, Emmanuel Oluwatobi, Ganiyu, Tajudeen Oladunni, Akaninyene, Ifiokakaninyene Ekpo, Ezediuno, Louis Odinakaose, Adeosun, Idowu Jesulayomi, Ockiya, Michael Asebake, Jimah, Esther Moradeyo, Spiro, David J., Oladipo, Elijah Kolawole, Trovão, Nídia S.
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 18-03-2022 Elsevier
Subjects:	Genomics Phylogenetics Virology Phylogenetics Genomics Virology
Online Access:	Get full text
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Summary:	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 SARS-CoV-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. [Display omitted] •SARS-CoV-2 viruses from Africa cluster predominantly with European strains•Lower viral diversity observed in Africa is likely due to genomic under-surveillance•Number of cases, deaths, and testing show substantial heterogeneity across Africa•Two motifs could function as integrin-binding sites and N-glycosylation domains Genomics; Virology; Phylogenetics
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors are contributed equally Lead contact
ISSN:	2589-0042 2589-0042
DOI:	10.1016/j.isci.2022.103880