Whole Genome Sequencing Analysis of SARS-CoV-2 Variants Circulating in South South Nigeria During the Delta and Omicron Waves

The emergence and succession of SARS-CoV-2 variants of concern, including Delta and Omicron, significantly reshaped the COVID-19 pandemic trajectory globally. In South South Nigeria, variant-specific genomic data were largely absent during these critical epidemic waves, limiting the capacity to understand local transmission dynamics. This study performs retrospective whole genome sequencing (WGS) analysis of SARS-CoV-2 isolates from confirmed COVID-19 cases in Rivers, Delta, and Bayelsa states during the Delta (July to December 2021) and Omicron (December 2021 to June 2022) waves. Archived nasopharyngeal swab RNA extracts from 200 RT-PCR-positive samples per wave will be subjected to next-generation sequencing using the ARTIC network amplicon protocol on the Illumina MiSeq platform. Bioinformatics pipelines (PANGOLIN, Nextstrain) will be used for lineage assignment, phylogenetic reconstruction, and identification of spike protein mutations. Comparative analysis will assess whether the variant wave timings and lineage distributions in South South Nigeria paralleled or lagged national and continental trends. This study fills a documented gap in Nigeria's SARS-CoV-2 genomic surveillance data, the bulk of which derives from Lagos and Abuja. Findings will characterise South South-specific SARS-CoV-2 evolutionary dynamics and contribute sequences to the GISAID global repository to support international pandemic preparedness planning. Keywords: SARS-CoV-2, whole genome sequencing, Delta variant, Omicron variant, South South Nigeria