A comprehensive analysis of the SARS-CoV-2 omicron variant in Tocantins State, Brazil, and tracing the spread of the XBB.1.18.1 lineage

Abstract

This study presents a genomic and epidemiological exploration of the omicron variant sublineages in Tocantins, Brazil. A total of 556 positive samples, obtained from individuals testing positive for SARS-CoV-2 between December 21, 2021, and June 30, 2023, underwent genome sequencing. Following RNA extraction, cDNA synthesis was executed, and a multiplexed PCR assay was employed for sequencing using the Oxford Nanopore MinION platform. The dispersal patterns of the XBB.1.18.1 lineage were analyzed as a case study, employing maximum likelihood phylogenetic tree construction and a discrete phylogeographical model. Subsequent analyses unveiled 39 sublineages, with BQ.1.1, BA.5.2.1, and BA.1.14.1 emerging as the most prevalent over the studied period. Notably, the emergence of the BQ.1.1 and BQ.1 lineages in Tocantins was observed in November and December 2022, respectively. The XBB.1.18.1 lineage, dominant from January to June 2023, exhibited noteworthy local and international circulation. Through mapping the migration patterns of this lineage, Tocantins was identified as a pivotal node for virus dispersal, with minimal importation cases. The study estimated the global emergence of the XBB.1.18.1 lineage in mid- to late-October 2022. This investigation contributes to comprehending SARS-CoV-2 dynamics in Tocantins and underscores the significance of transportation routes in virus propagation.

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