Genomic Diversity and Geographic Distribution of SARS-CoV-2 in Mexico: Insights From 4 Years of Genomic Surveillance.

Background: As of September 2024, Mexico had reported over 7.6 million confirmed cases of COVID-19 and 334,785 deaths. Genomic surveillance has been essential, with 94,799 SARS-CoV-2 genomes sequenced nationwide, 38.5% by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex).

Aims: Analyze the genomic diversity and geographic distribution of SARS-CoV-2 across Mexico's nine pandemic waves, with an emphasis on the seventh to ninth waves.

Methods: Data from 94,799 SARS-CoV-2 genomes spanning from February 2020 to September 2024 were analyzed. Sublineages with a prevalence of at least 5% were tracked, and their temporal and regional trends were evaluated using diversity indices and statistical models.

Results: Of the 996 sublineages identified, 72 had a prevalence greater than 5%, and 33 exceeded 10%. Each wave featured dominant sublineages, some of which emerged locally and prevailed during one or more waves, but were later displaced by new ones. Regional differences were identified in all waves, driven by population density, mobility, and variant introductions.

Conclusions: Our findings highlight the dynamic evolution of SARS-CoV-2 in Mexico, the emergence of locally relevant variants, and the critical need for sustained genomic surveillance to guide public health strategies during the transition to an endemic state.