Genomic epidemiology of Omicron (BA.1) as a driver of Pakistan's fifth SARS-CoV-2 wave.

The emergence of the SARS-CoV-2 Omicron variant led to Pakistan's Omicron wave from December 2021 to March 2022. This study investigated the molecular epidemiology of the early Omicron wave in Pakistan through genomic surveillance and travel history-informed Bayesian phylogeographic inference. PCR-based genotyping and whole-genome sequencing shows a shift from the BA.1 lineage's early replacement of Delta as Pakistan's dominant lineage in December 2021, until it was replaced by BA.2 predominance by March 2022. We identify rare spike protein mutations and the absence of key mutations in circulating strains. In order to determine the earliest drivers of the BA.1 wave in Pakistan we performed Bayesian phylogeographic analysis which reveals multiple introductions of BA.1 into Pakistan, primarily from Northern Europe. Our findings highlight the importance of continued genomic surveillance, particularly at points of entry, and the need to address global disparities in sequencing capacity to better understand and control the spread of SARS-CoV-2 variants.