Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria

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, João I. Mamede, Babafemi O. Taiwo, Judd F. Hultquist*, Ramon Lorenzo-Redondo

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


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.

Original languageEnglish (US)
Article number688
JournalNature communications
Issue number1
StatePublished - Dec 2022

ASJC Scopus subject areas

  • General Physics and Astronomy
  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology


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