Genome Evolution and Early Introductions of the SARS-CoV-2 Omicron Variant in Mexico

A new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), named Omicron (Pango lineage designation B.1.1.529), was first reported to the World Health Organization by South African health authorities on 24 November 2021. The Omicron variant possesses numerous mutations associated with increased transmissibility and immune escape properties. In November 2021, Mexican authorities reported Omicron’s presence in the country. In this study, we infer the first introductory events of Omicron and the impact that human mobility has had on the spread of the virus. We also evaluated the adaptive evolutionary processes in Mexican SARS-CoV-2 genomes during the first month of the circulation of Omicron. We inferred 160 introduction events of Omicron in Mexico since its first detection in South Africa; subsequently, after the first introductions there was an evident increase in the prevalence of SARS-CoV-2 during January. This higher prevalence of the novel variant resulted in a peak of reported cases; on average 6 weeks after, a higher mobility trend was reported. During the peak of cases in the country from January to February 2022, the Omicron BA.1.1 sub-lineage dominated, followed by the BA.1 and BA.15 sub-lineages. Additionally, we identified the presence of diversifying natural selection in the genomes of Omicron and found six non-synonymous mutations in the receptor binding domain of the spike protein, all of them related to evasion of the immune response. In contrast, the other proteins in the genome are highly conserved; however, we identified homoplasic mutations in non-structural proteins, indicating a parallel evolution.