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 () and Ramon Lorenzo-Redondo ()
Additional contact information
Egon A. Ozer: Northwestern University Feinberg School of Medicine
Lacy M. Simons: Northwestern University Feinberg School of Medicine
Olubusuyi M. Adewumi: College of Medicine, University of Ibadan
Adeola A. Fowotade: College of Medicine, University of Ibadan
Ewean C. Omoruyi: College of Medicine, University College Hospital, University of Ibadan
Johnson A. Adeniji: College of Medicine, University of Ibadan
Oluseyi A. Olayinka: College of Medicine, University of Ibadan
Taylor J. Dean: Northwestern University Feinberg School of Medicine
Janet Zayas: Rush University Medical Center
Pavan P. Bhimalli: Rush University Medical Center
Michelle K. Ash: Rush University Medical Center
Almoustapha I. Maiga: University Clinical Research Center (UCRC), University of Sciences, Techniques et Technologies of Bamako (USTTB)
Anou M. Somboro: University Clinical Research Center (UCRC), University of Sciences, Techniques et Technologies of Bamako (USTTB)
Mamoudou Maiga: University Clinical Research Center (UCRC), University of Sciences, Techniques et Technologies of Bamako (USTTB)
Adam Godzik: University of California Riverside School of Medicine
Jeffrey R. Schneider: Rush University Medical Center
João I. Mamede: Rush University Medical Center
Babafemi O. Taiwo: Northwestern University Feinberg School of Medicine
Judd F. Hultquist: Northwestern University Feinberg School of Medicine
Ramon Lorenzo-Redondo: Northwestern University Feinberg School of Medicine

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-28317-5

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