A Genetic Structure Map of SARS-CoV-2 from 62 Geographic Regions

Successive transmission of SARS-CoV-2 has caused a devastating influence on human health and the global economy. Previous studies have reported the origin, genetic mutation, phylogenetic network, etc., of SARS-CoV-2, since the first report of its outbreak in Wuhan. We presented the spatial genetic structure map of SARS-CoV-2, and further, revealed the genomic regions that were responsible for local adaptation. Spatial genetic variations of SARS-CoV-2 uncovered nuanced geographic clines across adjacent countries and also closely genetic relations between isolates from America, Canada, and Australia. Generally, SARS-CoV-2 isolates exhibited a significant genetic structure with several clusters showing strong genetic differentiation. Notably, one of the clusters was shared only among America, Canada, and Australia isolates, however, it was not found in the isolates of other geographic regions. Whole-genome scan showed that genomic regions of S, E, and M genes were strongly associated with adaptation. This study mirrors a snapshot of SARS-CoV-2 recent transmission and continual evolution on a local and global scale.