Abstract
SARS-CoV-2, the virus causing the COVID-19 pandemic emerged in December 2019 in China and raised fears it could overwhelm healthcare systems worldwide. Mutations of the virus are monitored by the GISAID database from which we downloaded sequences from four West African countries Ghana, Gambia, Senegal and Nigeria from February 2020 to April 2020. We subjected the sequences to phylogenetic analysis employing the nextstrain pipeline. We found country-specific patterns of viral variants and supplemented that with data on novel variants from June 2021. Until April 2020, variants carrying the crucial Europe-associated D614G amino acid change were predominantly found in Senegal and Gambia, and combinations of late variants with and early variants without D614G in Ghana and Nigeria. In June 2021 all variants carried the D614G amino acid substitution. Senegal and Gambia exhibited again variants transmitted from Europe (alpha or delta), Ghana a combination of several variants and in Nigeria the original Eta variant. Detailed analysis of distinct samples revealed that some might have circulated latently and some reflect migration routes. The distinct patterns of variants within the West African countries point at their global transmission via air traffic predominantly from Europe and only limited transmission between the West African countries.
Highlights
The COVID-19 pandemic resulting from the SARS-CoV-2 coronavirus infection which emerged in December 2019 in Wuhan, China, spread all over the world and after a delay of a few months appeared on the African continent
For France it could be deduced by the distinction between clade G and the earlier phylogenetic branches that the first SARS-CoV-2 did not lead to local transmission while the clade G was circulating for a considerable time before the first recorded case which was of clade G and had no travel events or traveler contact[6]
Campbell et al calculated that the Eta and Alpha variant relative to non-variants had about a 25% higher effective reproducibility while the Delta variant had nearly a 100% higher effective reproducibility[19]. In this phylogenetic analysis of SARS-CoV-2 sequences from the West African countries Gambia, Ghana, Nigeria and Senegal, we identified country-specific patterns of earlier (L, S, V) and later Europe-associated (G, GR, GH) clades
Summary
The COVID-19 pandemic resulting from the SARS-CoV-2 coronavirus infection which emerged in December 2019 in Wuhan, China, spread all over the world and after a delay of a few months appeared on the African continent. Starting with the first sequenced human sample of SARS-CoV-2, several mutations of the virus sequence arose which could be grouped into clades allowing associations with regional prevalence. Previous studies reported the potential impact of the D614G amino acid substitution which is a result of the A23403G single nucleotide polymorphism (SNP)[1] and associated with the branch of the phylogenetic tree referred to as clade G. Korber et al hypothesized that the D614 amino acid on the surface of the subunit S1 of the spike protein of the virus might have a hydrogen bond to the T859 amino acid in the subunit S2 residing on the m embrane[1] They showed that clade G rapidly starts to replace other clades associated with the D614 amino acid in each country entered[1]. Cabore et al proposed a model estimating risk of exposure for African countries based on a Hidden Markov model which accounts for factors such as gathering, weather, distribution and hygiene with the conclusion that with respect to the high calculated infection rates effective containment is indispensable[11]
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