Phylogenetic and genome-wide mutational analysis of SARS-CoV-2 strains circulating in Nigeria: no implications for attenuated COVID-19 outcomes

OBJECTIVES: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The COVID-19 incidence and mortality rates are low in Nigeria compared to global trends. This research mapped the evolution of SARS-CoV-2 circulating in Nigeria and globally to determine whether the Nigerian isolates are genetically distinct from strains circulating in regions of the world with a high disease burden. METHODS: Bayesian phylogenetics using BEAST 2.0, genetic similarity analyses, and genome-wide mutational analyses were used to characterize the strains of SARS-CoV-2 isolated in Nigeria. RESULTS: SARS-CoV-2 strains isolated in Nigeria showed multiple lineages and possible introductions from Europe and Asia. Phylogenetic clustering and sequence similarity analyses demonstrated that Nigerian isolates were not genetically distinct from strains isolated in other parts of the globe. Mutational analysis demonstrated that the D614G mutation in the spike protein, the P323L mutation in open reading frame 1b (and more specifically in NSP12), and the R203K/G204R mutation pair in the nucleocapsid protein were most prevalent in the Nigerian isolates. CONCLUSION: The SARS-CoV-2 strains in Nigeria were neither phylogenetically nor genetically distinct from virus strains circulating in other countries of the world. Thus, differences in SARS-CoV-2 genomes are not a plausible explanation for the attenuated COVID-19 outcomes in Nigeria.