SARS-CoV-2 genetic variations associated with COVID-19 severity

Herein, we performed a genome-wide association study on SARS-CoV-2 genomes to identify genetic variations that might be associated with the COVID-19 severity. 152 full-length genomes of SARS-CoV-2 that were generated from original clinical samples and whose patient status could be determined conclusively as either “asymptomatic” or “symptomatic” were retrieved from the GISAID database. We found that nucleotide variations at the genomic position 11,083, locating in the coding region of non-structural protein 6, were associated with the COVID-19 severity. While the 11083G variant (i.e. having G at the position 11,083) was more commonly found in symptomatic patients, the 11083T variant appeared to associate more often with asymptomatic infections. We also identified three microRNAs that differentially target the two variants, namely miR-485-3p, miR-539-3p, and miR-3149. This may in part contribute to the differential association of the two SARS-CoV-2 variants with the disease severity.