Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
Olayinka Sunday Okoh,
Nicholas Israel Nii-Trebi,
Abdulrokeeb Jakkari,
Tosin Titus Olaniran,
Tosin Yetunde Senbadejo,
Anna Aba Kafintu-kwashie,
Emmanuel Oluwatobi Dairo,
Tajudeen Oladunni Ganiyu,
Ifiokakaninyene Ekpo Akaninyene,
Louis Odinakaose Ezediuno,
Idowu Jesulayomi Adeosun,
Michael Asebake Ockiya,
Esther Moradeyo Jimah,
David J. Spiro,
Elijah Kolawole Oladipo,
Nídia S. Trovão
Affiliations
Olayinka Sunday Okoh
Department of Chemical Sciences, Anchor University, Lagos, Nigeria
Nicholas Israel Nii-Trebi
Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
Abdulrokeeb Jakkari
Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
Tosin Titus Olaniran
Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria; Helix Biogen Institute, Ogbomoso, Nigeria
Tosin Yetunde Senbadejo
Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
Anna Aba Kafintu-kwashie
Department of Medical Microbiology, Clinical Virology Unit, University of Ghana Medical School, Accra, Ghana
Emmanuel Oluwatobi Dairo
Helix Biogen Institute, Ogbomoso, Nigeria; Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
Tajudeen Oladunni Ganiyu
Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
Ifiokakaninyene Ekpo Akaninyene
Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria; Helix Biogen Institute, Ogbomoso, Nigeria
Louis Odinakaose Ezediuno
Department of Microbiology, Faculty of Life Sciences, University of Ilorin,1515 P.M.B, Ilorin, Nigeria
Idowu Jesulayomi Adeosun
Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria; Division of Microbiology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield Pretoria 0028, South Africa
Michael Asebake Ockiya
Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa, Nigeria
Esther Moradeyo Jimah
Helix Biogen Institute, Ogbomoso, Nigeria; Department of Medical Microbiology and Parasitology, University of Ilorin 1515, P.M.B, Ilorin, Nigeria
David J. Spiro
Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
Elijah Kolawole Oladipo
Helix Biogen Institute, Ogbomoso, Nigeria; Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria
Nídia S. Trovão
Fogarty International Center, National Institutes of Health, Bethesda, MD, USA; Corresponding author
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.
