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

Author

Listed:
  • Egon A. Ozer

    (Northwestern University Feinberg School of Medicine
    Northwestern University Havey Institute for Global Health)

  • Lacy M. Simons

    (Northwestern University Feinberg School of Medicine
    Northwestern University Havey Institute for Global Health)

  • Olubusuyi M. Adewumi

    (College of Medicine, University of Ibadan
    College of Medicine, University of Ibadan)

  • Adeola A. Fowotade

    (College of Medicine, University of Ibadan
    College of Medicine, University College Hospital, University of Ibadan)

  • Ewean C. Omoruyi

    (College of Medicine, University College Hospital, University of Ibadan)

  • Johnson A. Adeniji

    (College of Medicine, University of Ibadan
    College of Medicine, University of Ibadan)

  • Oluseyi A. Olayinka

    (College of Medicine, University of Ibadan
    College of Medicine, University of Ibadan)

  • Taylor J. Dean

    (Northwestern University Feinberg School of Medicine
    Northwestern University Havey Institute for Global Health)

  • 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)
    University of KwaZulu-Natal)

  • Mamoudou Maiga

    (University Clinical Research Center (UCRC), University of Sciences, Techniques et Technologies of Bamako (USTTB)
    Northwestern University)

  • 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
    Northwestern University Havey Institute for Global Health)

  • Ramon Lorenzo-Redondo

    (Northwestern University Feinberg School of Medicine
    Northwestern University Havey Institute for Global Health)

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.

Suggested Citation

  • 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., 2022. "Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28317-5
    DOI: 10.1038/s41467-022-28317-5
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