TY - JOUR
T1 - Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria
AU - Ozer, Egon A.
AU - Simons, Lacy M.
AU - Adewumi, Olubusuyi M.
AU - Fowotade, Adeola A.
AU - Omoruyi, Ewean C.
AU - Adeniji, Johnson A.
AU - Olayinka, Oluseyi A.
AU - Dean, Taylor J.
AU - Zayas, Janet
AU - Bhimalli, Pavan P.
AU - Ash, Michelle K.
AU - Maiga, Almoustapha I.
AU - Somboro, Anou M.
AU - Maiga, Mamoudou
AU - Godzik, Adam
AU - Schneider, Jeffrey R.
AU - Mamede, João I.
AU - Taiwo, Babafemi O.
AU - Hultquist, Judd F.
AU - Lorenzo-Redondo, Ramon
N1 - Funding Information:
This research was supported in part through the computational resources and staff contributions provided for the Quest high-performance computing facility at Northwestern University, which is jointly supported by the Office of the Provost, the Office for Research, and Northwestern University Information Technology. Genome sequencing and analysis were supported by resources and staff at the Center for Pathogen Genomics and Microbial Evolution in the Northwestern University Havey Institute for Global Health. Funding for this work was provided by: a Northwestern Havey Institute for Global Health Catalyzer Research Fund award (R.L.R. and O.M.A.); a Dixon Translational Research Grant made possible by the generous support of the Dixon Family Foundation (E.A.O. and J.F.H.); a COVID-19 Supplemental Research award from the Northwestern University Center for Advanced Technologies (NUCATS - J.F.H.); a COVID-19 Collaborative Innovation Award from the NUCATS (R.L.R); a CTSA supplement to NCATS UL1 TR002389 (J.F.H., E.A.O., and R.L.R.); a supplement to the Northwestern University Cancer Center P30 CA060553 (J.F.H.); the Gilead Sciences Research Scholars Program in HIV (J.F.H.); the NIH-supported Third Coast CFAR P30 AI117943 (R.L.R., J.F.H.); NIH grant R21 AI163912 (J.F.H.); NIH grant U19 AI135964 (E.A.O.); NIH grant D43 TW009608 (B.O.T. and O.M.A.); NIH Fogarty International Center award D43TW009608 (B.O.T.); NIH grant R35 GM118187 (A.G.) and NIH-NIAID Center for Structural Genomics of Infectious Diseases award HHSN272201700060C (A.G.); USAID Bureau for Resilience and Food Security/Center for Agriculture-led Growth, Cooperative Agreement 720-OAA-18-LA-00003 as part of Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification (R.L.R.); and through a generous contribution from the Walder Foundation Foundation’s Chicago Coronavirus Assessment Network (Chicago CAN) Initiative (J.F.H., E.A.O., and R.L.R.) and Walder Foundation grant numbers SCI16 (J.R.S.) and 21-00147(J.R.S.). The authors also acknowledge the Nigeria Center for Disease Control (NCDC) for providing leadership and infrastructure that facilitated the collection of samples included in this study.
Funding Information:
This research was supported in part through the computational resources and staff contributions provided for the Quest high-performance computing facility at Northwestern University, which is jointly supported by the Office of the Provost, the Office for Research, and Northwestern University Information Technology. Genome sequencing and analysis were supported by resources and staff at the Center for Pathogen Genomics and Microbial Evolution in the Northwestern University Havey?Institute for Global Health. Funding for this work was provided by: a Northwestern Havey?Institute for Global Health Catalyzer Research Fund award (R.L.R. and O.M.A.); a Dixon Translational Research Grant made possible by the generous support of the Dixon Family Foundation (E.A.O. and J.F.H.); a COVID-19 Supplemental Research award from the Northwestern University Center for Advanced Technologies (NUCATS - J.F.H.); a COVID-19 Collaborative Innovation Award from the NUCATS (R.L.R); a CTSA supplement to NCATS UL1 TR002389 (J.F.H., E.A.O., and R.L.R.); a supplement to the Northwestern University Cancer Center P30 CA060553 (J.F.H.); the Gilead Sciences Research Scholars Program in HIV (J.F.H.); the NIH-supported Third Coast CFAR P30 AI117943 (R.L.R., J.F.H.); NIH grant R21 AI163912 (J.F.H.); NIH grant U19 AI135964 (E.A.O.); NIH grant D43 TW009608 (B.O.T. and O.M.A.); NIH Fogarty International Center award D43TW009608 (B.O.T.); NIH grant R35 GM118187 (A.G.) and NIH-NIAID Center for Structural Genomics of Infectious Diseases award HHSN272201700060C (A.G.); USAID Bureau for Resilience and Food Security/Center for Agriculture-led Growth, Cooperative Agreement 720-OAA-18-LA-00003 as part of Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification (R.L.R.); and through a generous contribution from the Walder Foundation Foundation?s Chicago Coronavirus Assessment Network (Chicago CAN) Initiative (J.F.H., E.A.O., and R.L.R.) and Walder Foundation grant numbers SCI16 (J.R.S.) and 21-00147(J.R.S.). The authors also acknowledge the Nigeria Center for Disease Control (NCDC) for providing leadership and infrastructure that facilitated the collection of samples included in this study.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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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U2 - 10.1038/s41467-022-28317-5
DO - 10.1038/s41467-022-28317-5
M3 - Article
C2 - 35115515
AN - SCOPUS:85123973964
VL - 13
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
M1 - 688
ER -