Population genomic insights into the evolution of the SARS-CoV-2 Omicron variant

ABSTRACT A thorough understanding of the patterns of population subdivision of a pathogen can prevent disease spread. For SARS-CoV-2, the availability of millions of genomes makes this task analytically challenging. Our study used population genomic methods and identified subtle subdivisions within the Omicron variant, in addition to that captured by the Pango lineage. Further, some of the identified clusters of the Omicron variant revealed statistically significant signatures of selection or expansion revealing the role of microevolutionary processes in the spread of the virus. These are crucial information for policy makers as preventive measures can be designed to mitigate further spread based on a holistic understanding of the variability of the virus and evolutionary processes aiding its spread.