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Epidemiology and Genetic Diversity of SARS-CoV-2 Lineages Circulating in Africa

53 Pages Posted: 27 May 2021 Publication Status: Published

See all articles by Olayinka Sunday Okoh

Olayinka Sunday Okoh

Anchor University - Department of Chemical Sciences

Nicholas Israel Nii-Trebi

University of Ghana - Department of Medical Laboratory Sciences

Abdulrokeeb Jakkari

Lagos State University - Department of Microbiology

Tosin Titus Olaniran

Ladoke Akintola University of Technology - Department of Pure and Applied Biology - Department of Pure and Applied Biology (Microbiology Unit)

Tosin Yetunde Senbadejo

Fountain University - Department of Biological Sciences

Anna Aba Kafintu-kwashie

University of Ghana Medical School - Department of Medical Microbiology Clinical Virology Unit

Emmanuel Oluwatobi Dairo

University of Ibadan - Department of Virology

Tajudeen Oladunni Ganiyu

Fountain University - Department of Biological Sciences

Ifiokakaninyene Ekpo Akaninyene

Ladoke Akintola University of Technology - Department of Pure and Applied Biology - Department of Pure and Applied Biology (Microbiology Unit)

Louis Odinakaose Ezediuno

University of Ilorin - Department of Microbiology

Idowu Jesulayomi Adeosun

Adeleke University - Laboratory of Molecular Biology, Immunology and Bioinformatics

Michael Asebake Ockiya

Niger Delta University - Department of Animal Science

Esther Moradeyo Jimah

University of Ilorin - Department of Medical Microbiology and Parasitology

David Spiro

National Institutes of Health - Fogarty International Center

Elijah Kolawole Oladipo

Adeleke University - Laboratory of Molecular Biology, Immunology and Bioinformatics

Nídia Sequeira Trovão

National Institutes of Health - Fogarty International Center

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Abstract

COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent.

To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences.

In this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains.

These results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.

Declaration of Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Keywords: SARS-CoV-2, COVID-19, lineages, motifs, functional patterns, mutations, Africa, genomic diversity, epidemiology

Suggested Citation

Okoh, Olayinka Sunday and Nii-Trebi, Nicholas Israel and Jakkari, Abdulrokeeb and Olaniran, Tosin Titus and Senbadejo, Tosin Yetunde and Kafintu-kwashie, Anna Aba and Dairo, Emmanuel Oluwatobi and Ganiyu, Tajudeen Oladunni and Akaninyene, Ifiokakaninyene Ekpo and Ezediuno, Louis Odinakaose and Adeosun, Idowu Jesulayomi and Ockiya, Michael Asebake and Jimah, Esther Moradeyo and Spiro, David and Oladipo, Elijah Kolawole and Trovão, Nídia Sequeira, Epidemiology and Genetic Diversity of SARS-CoV-2 Lineages Circulating in Africa. Available at SSRN: https://ssrn.com/abstract=3855074 or http://dx.doi.org/10.2139/ssrn.3855074
This version of the paper has not been formally peer reviewed.

Olayinka Sunday Okoh

Anchor University - Department of Chemical Sciences ( email )

Department of Business Administration
Lagos, Ipaja PMB 001
Nigeria

Nicholas Israel Nii-Trebi

University of Ghana - Department of Medical Laboratory Sciences ( email )

PO Box 25
Legon, Accra LG
Ghana

Abdulrokeeb Jakkari

Lagos State University - Department of Microbiology ( email )

Lagos/bagagry express road lagos nigeria.
PMB 0001 LASU OJO Lagos Nigeria
Lagos, LA lagos 234
Nigeria

Tosin Titus Olaniran

Ladoke Akintola University of Technology - Department of Pure and Applied Biology - Department of Pure and Applied Biology (Microbiology Unit) ( email )

Ogbomosho, Oyo State
Nigeria

Tosin Yetunde Senbadejo

Fountain University - Department of Biological Sciences ( email )

Osogbo
Osogbo, 2341
Nigeria

Anna Aba Kafintu-kwashie

University of Ghana Medical School - Department of Medical Microbiology Clinical Virology Unit ( email )

Accra
Ghana

Emmanuel Oluwatobi Dairo

University of Ibadan - Department of Virology ( email )

Ibadan
Nigeria

Tajudeen Oladunni Ganiyu

Fountain University - Department of Biological Sciences ( email )

Osogbo
Osogbo, 2341
Nigeria

Ifiokakaninyene Ekpo Akaninyene

Ladoke Akintola University of Technology - Department of Pure and Applied Biology - Department of Pure and Applied Biology (Microbiology Unit) ( email )

P.M.B 4000
Ogbomoso, Oyo State
Nigeria

Louis Odinakaose Ezediuno

University of Ilorin - Department of Microbiology ( email )

DEPARTMENT OF GEOLOGY UNIVERSITY OF ILORIN
Ilorin, KS Kwara State 0834
Nigeria

Idowu Jesulayomi Adeosun

Adeleke University - Laboratory of Molecular Biology, Immunology and Bioinformatics ( email )

Ede
Nigeria

Michael Asebake Ockiya

Niger Delta University - Department of Animal Science ( email )

Faculty of Law,
Dept of Private & Property Law
Ovom, Yenagoa, 561001
Nigeria

Esther Moradeyo Jimah

University of Ilorin - Department of Medical Microbiology and Parasitology ( email )

DEPARTMENT OF GEOLOGY UNIVERSITY OF ILORIN
Ilorin, KS 0834
Nigeria

David Spiro

National Institutes of Health - Fogarty International Center ( email )

Bethesda, MD
United States

Elijah Kolawole Oladipo

Adeleke University - Laboratory of Molecular Biology, Immunology and Bioinformatics ( email )

Ede
Nigeria

Nídia Sequeira Trovão (Contact Author)

National Institutes of Health - Fogarty International Center ( email )

Bethesda, MD
United States

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