In this study, we investigated the genomic variability of alpha-VOC of SARS-CoV-2 in Pakistan, in context of the global population of this variant. A set of 461 whole-genome sequences of Pakistani samples of alpha-variant, retrieved from GISAID, were aligned in MAFFT and used as an input to the Coronapp web-application. Phylogenetic tree was constructed through maximum-likelihood method by downloading the 100 whole-genome sequences of alpha-variant for each of the 12 countries having the largest number of Pakistani diasporas. We detected 1725 mutations, which were further categorized into 899 missense mutations, 654 silent mutations, 52 mutations in non-coding regions, 25 in-frame deletions, 01 in-frame insertion, 51 frameshift deletions, 21 frameshift insertions, 21 stop-gained variants, and 1 stop-gained deletion. We found NSP3 and Spike as the most variable proteins with 355 and 233 mutations respectively. However, some characteristic mutations like Δ144(S), G204R(N), and T1001I, I2230T, del3675–3677(ORF1ab) were missing in the Pakistani population of alpha-variant. Likewise, R1518K(NSP3), P83L(NSP9), and A52V, H164Y(NSP13) were found for the first time in this study. Interestingly, Y145 deletion(S) had 99% prevalence in Pakistan but globally it was just 4.2% prevalent. Likewise, R68S substitution (ORF3a), F120 frameshift deletion, L120 insertion, L118V substitution (ORF8), and N280Y(NSP2) had 20.4%, 14.3%, 14.8%, 9.1%, 13.9% prevalence locally but globally they were just 0.1%, 0.2%, 0.04%, 1.5%, and 2.4% prevalent respectively. The phylogeny analysis revealed that majority of Pakistani samples were grouped together in the same clusters with Italian, and Spanish samples suggesting the transmission of alpha-variant to Pakistan from these western European countries.

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.