High prevalence of SARS-CoV-2 B.1.1.7 (UK variant) and the novel B.1.5.2.5 lineage in Oyo State, Nigeria

Ozer, Egon A.; Simons, Lacy M.; Adewumi, Olubusuyi M.; Fowotade, Adeola A.; Omoruyi, Ewean C.; Adeniji, Johnson A.; Dean, Taylor J.; Taiwo, Babafemi O.; Hultquist, Judd F.; Lorenzo-Redondo, Ramon

The spread of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), has resulted in a global pandemic that has claimed the lives of millions of people. Genomic surveillance of the virus has proven to be a critical tool for tracking the emergence and spread of variants with increased transmission or immune evasion potential. Despite the global distribution of infection, differences in viral genomic surveillance capabilities between countries and regions have resulted in gaps in our understanding of the viral population dynamics underlying the pandemic. Nigeria, despite having the largest population of any country in Africa, has had relatively little SARS-CoV-2 sequence data made publicly available. In this study, we report the whole-genome sequences of 74 SARS-CoV-2 isolates collected from individuals in Oyo State, Nigeria over the first two weeks of January 2021. Forty-six of the isolates belong to the B.1.1.7 “UK variant” lineage. Comparison to available regional and global sequences suggest that the B.1.1.7 isolates in Nigeria are primarily monophyletic, possibly representing a singular successful introduction into the country. The majority of the remaining isolates (17 of 74) belong to the B.1.525 lineage, which contains multiple spike protein mutations, including the E484K mutation associated with potential immune escape. Indeed, Nigeria has the highest reported frequency of this lineage despite its relative rarity worldwide. Phylogenetic analysis of the B.1.525 isolates in this study relative to other local and global isolates suggested a recent origin and rapid expansion of this lineage in Nigeria, with the country serving as a potential source for this lineage in other outbreaks. These results demonstrate the importance of genomic surveillance for identifying SARS-CoV-2 variants of concern in Nigeria and in other undersampled regions across the globe.