Phyloevolutionary analysis of delta variant of SARS-CoV 2 in Nigeria

Abstract

Background & Aims : The evolution of SARS-CoV-2 from its inception created a need for phyloepidemiological approaches to provide unanswered questions regarding the viral emergence and evolvement of various mutated strains. Unfortunately, there is an absolute dearth of information on the evolution of the delta variant strain in Nigeria. This study investigated the phyloepidemiology of the delta variant of SARS-CoV-2 in Nigeria. Materials & Methods : A total of 33 complete genomic sequences of the SARS-CoV-2 delta variant (B.1.617.2) from Nigeria, India, United Arab Emirates (UAE), United States of America (USA), Canada, United Kingdom (UK), China, and the reference sequence were retrieved from the GISAID EpiFlu™ on the 11 th of August 2021 . The sequences were selected based on the most visited tourist destinations of Nigerians (USA, UK, China, UAE, India, and Canada). The evolutionary history was inferred using the maximum likelihood method based on the general time-reversible model. Finally, a phylogenetic tree was constructed to determine the common ancestor of each sequence. Results : The phylogenetic analysis revealed that the delta strain in Nigeria clustered in a monophyletic clade with other Nigeria strains with its root from the reference Wuhan sublineage. Nucleotide alignment also showed a 99% similarity indicating a common origin of evolution. Conclusion : Our findings revealed that the current outbreak of the delta variant of SARS-CoV-2 infection in Nigeria stemmed from a genetic mutation that shared a consensus similarity with the reference SARS-CoV-2 human genome from Wuhan and was not imported from other countries as widely reported.