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
Mateus Silva Santos, Ueric José Borges de Souza, Franciano Dias Pereira Cardoso, Jucimária Dantas Galvão, Fernando Rosado Spilki, Célia Maria de Almeida Soares, Fabrício Souza Campos
TL;DR
This study analyzes the spread of SARS-CoV-2 omicron sublineages in Tocantins, Brazil, identifying key lineages and tracing the global and local movement of the XBB.1.18.1 variant.
Contribution
The study provides new insights into the dispersal patterns of the XBB.1.18.1 lineage and highlights Tocantins as a key node for virus spread.
Findings
39 sublineages were identified, with BQ.1.1, BA.5.2.1, and BA.1.14.1 being the most prevalent.
The XBB.1.18.1 lineage became dominant in Tocantins from January to June 2023.
Tocantins was identified as a pivotal node for virus dispersal with minimal importation cases.
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…
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Taxonomy
TopicsSARS-CoV-2 and COVID-19 Research · SARS-CoV-2 detection and testing · COVID-19 epidemiological studies