Recently submitted whole genome sequences of the South African variant (501Y.V2) were taken for variant calling analysis to see how this strain is related and discriminated from the Pakistani strain (MW447609). After variant calling of 501Y.V2 (South African) vs MW447609 (Karachi Pak) strain, a total of 104 variants were detected in which 77 SNPs, 22 deletions and 5 insertions were included. The functional effect of these variants was spread between all classes of mutations such as missense (69.3%), nonsense (5.3%) and silent (25.3%). The highest number of changes (deletion) were observed in the upstream (51.04%) and downstream (29.143%) regions. These changes may be causing RBD of 501Y.V2 variant to become more functional and critical in binding with a host. As the objective of the study was to identify genomic variations and mutations to predict the severity of disease. We may say that the disease severity, viral load etc. would not be the same in Pakistan as of South African (501Y.V2) variant caused in south Africa. In addition to this, we also hypothesize that vaccines and other therapeutic interventions would be equally affective to MW447609 (Pakistani) strains in contrast to South African (501Y.V2) variant.

Index terms- SARS-COV-2 strain, Whole genome sequence, Variant, Variant calling, South African variant, Genomic variations