Genomic characterization and phylogenomic relationship of the beta-variant of SARS- CoV-2 in Pakistan

Abstract In this research, we performed genomic characterization and phylogenomic relationship of beta-variant circulated in Pakistan, compared to the viral population of the world. A set of 105 full-genome sequence samples of beta-VOC from Pakistan, retrieved from GISAID, and aligned through the online tool MAFFT and subjected to mutations identification through Coronapp web-application. Phylogenetic tree was created by using 800 full-genome sequences of beta-variant from ten countries having the highest Pakistani diaspora resides. We found 389 mutations, out of which 227 were missense mutations, however, NSP3 and spike were found to be the most mutable proteins. Interestingly, some characteristic mutations like T265I, K1655N, K3353R in ORF1a, S84L(ORF8) and del241/243(S) which had 92–99% prevalence globally, were not present in beta-variant of Pakistan. Moreover, N501Y(S), E484K(S), L242(S), and S106(NSP6) mutations which had 86%, 85%, 84%, and 91% prevalence globally were only 52%, 50%, 49%, and 73.3% prevalent in Pakistan. Likewise, S794L (NSP3), G30R (N) and W29L (ORF7b) had a global prevalence of just 12%, 0.4%, and 0.3%, but in Pakistan they were 67%, 67%, and 49%, respectively. The phylogeny results showed that majority of the Pakistani samples were clustered together with samples from South Africa, England, and Saudi Arabia. Our results showed that beta-variant of Pakistani population was substantially different from its global population in terms of its genomic variability. However, phylogeny relationship suggested transmission of this variant to Pakistan from South Africa, England, and Saudi Arabia.