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

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 11th 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.