Genomic and epidemiological characteristics of SARS-CoV-2 in Africa
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Date
2021
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PLOS ONE
Abstract
ince late 2019, the coronavirus disease 2019 (COVID-19) outbreak, caused by SARS CoV-2,
has rapidly evolved to become a global pandemic. Each country was affected but with a
varying number of infected cases and mortality rates. Africa was hit late by the pan demic
but the number of cases rose sharply. In this study, we investigated 224 SARS-CoV 2 genome
sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) in the early part
of the outbreak, of which 69 were from Africa. We analyzed a total of 550 muta tions by
comparing them with the reference SARS-CoV-2 sequence from Wuhan. We clas sified the
mutations observed based on country and region, and afterwards analyzed common and
unique mutations on the African continent as a whole. Correlation analyses showed that the
duo variants ORF1ab/RdRp 4715L and S protein 614G variants, which are strongly linked to
fatality rate, were not significantly and positively correlated with fatality rates (r = -0.03757, P
= 0.5331 and r = -0.2876, P = 0.6389, respectively), although increased number of cases
correlated with number of deaths (r = 0.997, P = 0.0002). Fur thermore, most cases in Africa
were mainly imported from American and European coun tries, except one isolate with no
mutation and was similar to the original isolate from Wuhan. Moreover, unique mutations
specific to countries were identified in the early phase of the outbreak but these mutations
were not regional-specific. There were common mutations in all isolates across the continent
as well as similar isolate-specific mutations in different regions. Our findings suggest that
mutation is rapid in SARS-CoV-2 in Africa and although
Description
This article is published by Plos One and is also available at https://doi.org/10.1371/journal.pntd.0009335
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Citation
Lamptey J, Oyelami FO, Owusu M, Nkrumah B, Idowu PO, Adu-Gyamfi EA, et al. (2021) Genomic and epidemiological characteristics of SARS-CoV-2 in Africa. PLoS Negl Trop Dis 15(4): e0009335