Genomic Epidemiology of SARS-CoV-2 Variant Emergence and Transmission Clusters in Rivers State During the Delta Wave

The Delta variant of SARS-CoV-2 (B.1.617.2) caused a devastating global resurgence in 2021, with its emergence and spread in sub-Saharan Africa driving significant excess mortality. Genomic epidemiology provides the analytical framework to reconstruct variant emergence events, track transmission clusters, and assess the effectiveness of public health interventions. This study investigated the genomic epidemiology of SARS-CoV-2 variant emergence and transmission clustering in Rivers State, South-South Nigeria, during the Delta wave period (May-October 2021). A total of 180 SARS-CoV-2-positive nasopharyngeal samples were sequenced using the ARTIC amplicon-based protocol on an Oxford Nanopore MinION platform. Consensus genomes were assembled with ARTIC bioinformatics pipeline and lineages assigned using Pangolin v4. Phylogenetic analysis and transmission cluster inference were performed using TreeTime and TransPhylo in R. Delta variant (B.1.617.2) represented 73% of sequenced genomes, with AY.46 and AY.39 sub-lineages dominant. Phylogenetic clustering identified five probable transmission clusters of five or more genetically linked cases, with two clusters involving healthcare settings in Port Harcourt. Introduction events were phylogenetically linked to Lagos and international travel origins. Temporal Bayesian analysis estimated a mean SARS-CoV-2 effective reproduction number of 1.42 during the Delta wave peak in Rivers State. These findings demonstrate the value of near-real-time genomic surveillance for public health response coordination. Keywords: SARS-CoV-2, genomic epidemiology, Delta variant, nanopore sequencing, Rivers State.