Genomic surveillance and phylo-evolutionary analysis of SARS-CoV-2 variants in Osun state, Nigeria during the second wave of COVID-19 pandemic

SARS-CoV-2 genome sequencing, genomic characterization, and global data sharing are recommended to facilitate countermeasures against COVID-19. This study involved whole genome sequencing and phylo-evolutionay analysis of SARS-CoV-2 variants circulating in Osun State, Nigeria between January and June, 2021. In the present retrospective, molecular epidemiologic study, a total of 60 nasopharyngeal samples from RT-qPCR-positive COVID-19 patients originating from eight study locations were analyzed. This was done using RNA extraction application of the McKinsey Global Institute’s (MGI) DNBSEQ-G50RS high-throughput genome Sequencing Technology and Bioinformatics Analysis Pipeline. Quantitative data were analyzed with descriptive and inferential statistics. Forty-five SARS-CoV-2 (45/60) whole genome sequences (WGSs) were successfully analyzed with participants being mostly male adults (64.4%) and a median age of 44 years. Five PANGO lineages including: B (35.6%), B.1.525 (31.1%), B.1.1.7 (28.9%), B.1 (2.2%), and L.3 (2.2%) were identified, with Eta VOI (14/45) and Alpha VOC (13/45) as the dominant variants. A total of 29/45 of these genomes exhibited amino acid (aa) substitutions in the viral spike (S) protein, totaling 275 substitutions. Six of these genome sequences carried key mutations, including H69del, V70del, Y144del, D614G, N501Y, A570D, P681H, T716I, and Q677H. These mutations are known to influence SARS-CoV-2 transmissibility, virulence, and potential resistance to neutralization by vaccine-induced antibodies/convalescent sera. Phylo-evolutionary analysis revealed three distinct clusters, 16 sequences from Lineage B clustered closely with the reference Wuhan-Hu-1 strain (NC_045512.2). Notably, 19 of our WGSs showed genomic relatedness to SARS-CoV-2 strains from other regions of Nigeria, as well as, from West/other African countries, including Egypt, Senegal, Morocco and South Africa. The single L.3 lineage reported clustered with strains from Nigeria and Benin. These evidences suggest inbound or outbound transmission of the dominant Eta and Alpha variants. The study highlights the dominance of Eta VOIs and Alpha VOCs during the second COVID-19 wave in Osun State, Nigeria, suggesting potential inbound and outbound spread of the virus between other states in Nigeria and other African countries. The general absence of severe illness (except for four participants with shortness of breath) among study participants may indicate a protective effect of post-exposure immune response; however, underreporting of severe cases cannot be ruled out as a potential contributing factor.