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

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          Abstract

          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.

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          Author and article information

          Journal
          Journal ID (nlm-ta): iScience
          Journal ID (iso-abbrev): iScience
          Title: iScience
          Publisher: Elsevier
          ISSN (Electronic): 2589-0042
          Publication date PMC-release: 5 February 2022
          Publication date (Electronic): 5 February 2022
          Electronic Location Identifier: 103880
          Affiliations
          [1 ]Department of Chemical Sciences, Anchor University, Lagos, Nigeria
          [2 ]Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
          [3 ]Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
          [4 ]Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
          [5 ]Helix Biogen Institute, Ogbomoso, Nigeria
          [6 ]Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
          [7 ]Department of Medical Microbiology, Clinical Virology unit, University of Ghana Medical School, Accra, Ghana
          [8 ]Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
          [9 ]Department of Microbiology, Faculty of life sciences, University of Ilorin, Nigeria
          [10 ]Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
          [11 ]Division of Microbiology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield Pretoria 0028, South Africa
          [12 ]Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria
          [13 ]Department of Medical Microbiology and Parasitology, University of Ilorin, Nigeria
          [14 ]Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
          Author notes
          [+ ]Corresponding author: Nídia S. Trovão E-mail: (nidia.trovao [at] nih.gov ; nidiastrovao [at] gmail.com)
          [#]

          Contributed equally

          [∗]

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          Article
          Publisher Item ID: S2589-0042(22)00150-X Publisher ID: 103880
          DOI: 10.1016/j.isci.2022.103880
          PMC ID: 8817759
          PubMed ID: 35156006
          SO-VID: 11e9583e-9686-486f-bf5b-25e5b2a5bd8c
          Copyright © © 2022.
          License:

          Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

          History
          Date received : 3 August 2021
          Date revision received : 29 November 2021
          Date accepted : 3 February 2022
          Categories
          Subject: Article

          Keywords: sars-cov-2,covid-19,lineages,motifs,functional patterns,mutations,africa,genomic diversity,epidemiology
          Data availability:
          Keywords: sars-cov-2, covid-19, lineages, motifs, functional patterns, mutations, africa, genomic diversity, epidemiology

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