SARS-CoV-2 BW.1, a fast-growing Omicron variant from southeast Mexico bearing relevant escape mutations

Purpose The swift growth of the BW.1 SARS-CoV-2 variant coincides with a new rapid increase of COVID-19 cases occurring in Southeast Mexico in October, 2022, putting an end to a period of low transmission after Mexico’s fifth epidemiological wave. Up to 75% of weekly sequenced genomes in the region have been identified as BW.1. In the current study, a comprehensive genomic comparison was carried out to characterize BW.1’s evolutionary history, identifying its origins and its most important mutations. Methods An alignment of all the genomes of BW.1 and its parental BA.5.6.2 variant was carried out to identify their mutations. A phylogenetic reconstruction and a longitudinal analysis of point mutations were performed to trace back their origin and contrast them with key RBD mutations in variant BQ.1, one of the fastest growing lineages to date. Results The BW.1’s genome derives from Mexican sequences of BA.5.6.2. Two traceable synonymous substitutions support its Mexican origin whereas other two are specific to BW.1: S:N460K and ORF1a:V627I. Mutations found in the receptor binding domain, S:K444T, S:L452R, S:N460K and S:F486V, in BW.1 have been reported to be relevant for immune escape and are key mutations in the BQ.1 lineage. Conclusions BW.1 appears to have arisen in the Yucatan Peninsula in Mexico sometime around July 2022 during the fifth COVID-19 wave. Its explosive growth may be in part explained by relevant escape mutations also found in BQ.1.