Multiple Expansions of Globally Uncommon SARS-CoV-2 Lineages in Nigeria

Overview

Journal Nat Commun

Specialty Biology

Date 2022 Feb 4

PMID 35115515

Authors

Egon A Ozer

Lacy M Simons

Olubusuyi M Adewumi

Adeola A Fowotade

Ewean C Omoruyi

Johnson A Adeniji

Oluseyi A Olayinka

Taylor J Dean

Janet Zayas

Pavan P Bhimalli

Michelle K Ash

Almoustapha I Maiga

Anou M Somboro

Mamoudou Maiga

Adam Godzik

Jeffrey R Schneider

Joao I Mamede

Babafemi O Taiwo

Judd F Hultquist

Ramon Lorenzo-Redondo

Affiliations

Soon will be listed here.

Abstract

Disparities in SARS-CoV-2 genomic surveillance have limited our understanding of the viral population dynamics and may delay identification of globally important variants. Despite being the most populated country in Africa, Nigeria has remained critically under sampled. Here, we report sequences from 378 SARS-CoV-2 isolates collected in Oyo State, Nigeria between July 2020 and August 2021. In early 2021, most isolates belonged to the Alpha "variant of concern" (VOC) or the Eta lineage. Eta outcompeted Alpha in Nigeria and across West Africa, persisting in the region even after expansion of an otherwise rare Delta sub-lineage. Spike protein from the Eta variant conferred increased infectivity and decreased neutralization by convalescent sera in vitro. Phylodynamic reconstructions suggest that Eta originated in West Africa before spreading globally and represented a VOC in early 2021. These results demonstrate a distinct distribution of SARS-CoV-2 lineages in Nigeria, and emphasize the need for improved genomic surveillance worldwide.

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