Coincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria
Open accessAbstract
The emergence of new SARS-CoV-2 variants with enhanced transmissibility or decreased susceptibility to immune responses is a major threat to global efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Disparities in viral genomic surveillance capabilities and efforts have resulted in gaps in our understanding of the viral population dynamics across the globe. Nigeria, despite having the largest population of any nation in Africa, has had relatively little SARS-CoV-2 sequence data made publicly available. Here we report the whole-genome sequences of 74 SARS-CoV-2 isolates collected from individuals in Oyo State, Nigeria in January 2021. Most isolates belonged to either the B.1.1.7 Alpha “variant of concern” or the B.1.525 Eta lineage, which is currently considered a “variant of interest” containing multiple spike protein mutations previously associated with enhanced transmissibility and possible immune escape. Nigeria has the highest reported frequency of the B.1.525 lineage globally with phylogenetic characteristics consistent with a recent monophyletic origin and rapid expansion. Spike protein from the B.1.525 lineage displayed both increased infectivity and decreased neutralization by convalescent sera compared to Spike proteins from other clades. These results, along with indications that the virus is outpacing the B.1.1.7 lineage in Nigeria, suggest that the B.1.525 lineage represents another “variant of concern” and further underline the importance of genomic surveillance in undersampled regions across the globe.
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The Eta variant is present at low levels in many countries, with Nigeria having the highest proportion of infections.
“The Eta variant is present at low levels in many countries, with Nigeria having the highest proportion of infections 236 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [236]
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References 75 · Cited by 34
Research works printed but not linked: 1
- Davies, N.G., et al. Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England. medRxiv, 2020.2012.2024.20248822 (2020).
- Authors
- Ozer, E. A., Simons, L. M., Adewumi, O. M., Fowotade, A. A., Omoruyi, E. C., Adeniji, J. A., Dean, T. J., Zayas, J., Bhimalli, P. P., Ash, M. K., Godzik, A., Schneider, J. R., Mamede, J. I., Taiwo, B. O., Hultquist, J. F., & Lorenzo-Redondo, R.
- Affiliations
- Northwestern University (US)
- University of Ibadan (NG)
- Rush University Medical Center (US)
- University of California, Riverside (US)
- Corresponding author
- Hultquist, Judd F.
- ORCID
- Venue
- medRxiv
- Publisher
- openRxiv
- Published
- 2021-04-17
- PMC
- PMC8057251
- OpenAlex
- W3152773214
- Cited by
- 34
- References
- 75
- Citations by year
- 2024: 3 · 2023: 5 · 2022: 10 · 2021: 16
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- medRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- Gilead Sciences (COVID-19)
- Northwestern University (CA060553, P30CA060553)
- Georgia Clinical and Translational Science Alliance (UL1 TR002389)
- National Institutes of Health (COVID-19, HHSN272201700060 C, CA-060553, AI135964, UL1TR002389)
- Quest High Performance Computing
- National Cancer Institute (P30CA060553)
- National Institute of General Medical Sciences (R35GM118187)
- National Institute of Allergy and Infectious Diseases (COVID-19, AI117943, K22AI136691, AI135964, HHSN272201700060C, P30AI117943, U19AI135964)
- Fogarty International Center (D43TW009608)
- National Center for Advancing Translational Sciences
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Keywords
- SARS-CoV-2, B.1.1.7 Alpha variant, variants of concern, variants of interest, spike protein mutations, viral transmissibility, immune evasion, whole genome sequencing, genomic surveillance, Nigeria, Oyo State, monophyletic origin, viral population dynamics
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