Whole genome comparison of Pakistani Corona virus with Chinese and US Strains along with its predictive severity of COVID-19

Abstract

Initially submitted 784 SARS-nCoV2 whole genome sequences on NCBI Virus database were selected for phylogenetic analysis to look into their similarities with two of Pakistani sequenced coronavirus strains having accessions of MT240479 and MT262993. The MT240479 named (Gilgit1-Pak) was found in close proximity to MT184913 named (CruiseA-USA), while MT262993 named (Manga-Pak) was in neighboring to MT039887 named (WI-USA) strain, which were further chosen for variant calling analysis along with reference genome NC_045512 as out-group to construct concluding cladogram and looked for evolutionary distance with PAUP software in this article. Aforementioned Pakistani strains each of having 29,836 bases were compared with MT263429 (WI-USA) of 29,889 bases and MT259229 (Wuhan-P.R. China) of 29,864 bases. Whole genome variant calling pipeline revealed 31 variants in both Pakistani strains collectively (Manga-Pak vs USA having 2del & 7SNPs, while different from Chinese strain with 2del & 2SNPs, similarly Gilgit1-Pak vs USA having 10SNPs, while different from Chinese strains having 8SNPs). These variants harbour ORF1ab , ORF1a and N genes having their role is viral replication/translation, host innate immunity and viral capsid formation respectively. These novel variants may be one of the reasons for low mortality rate in Pakistan with 385 deaths as compared to USA with 63,871 and P.R. China with 4633 by May 01, 2020. However functional characterization of these variants and their integrations with other viral proteins including variability of human receptors (ACE2 & NRP1) may be the other reasons for unlikely COVID-19 statistics in Pakistan which need further confirmatory studies. Moreover, mutated N and ORF1a proteins in Pakistani strains were also analyzed by 3D structure modeling, which give another dimension of comparing these alterations at amino acid level. In a nutshell, these novel variants are correlated with reduced mortality of COVID-19 severity in Pakistan while more robust results can be obtained by wet lab experimentation. This also gives insight of genomic landscape of these indigenous strains to develop diagnostics kits, vaccines and therapeutic interventions.

Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing

“…International travel has been considered as one of the potential risk factors for the transmission and circulation of different variants of SARS-CoV2 in Pakistan [31][32][33][34]. The initial-sequenced local SARS-CoV2 genomes (accession numbers: MT240479 and MT262993) are closely related to the Chinese SARS-CoV2 isolates [9], while the currently sequenced SARS-CoV2 isolate differs from that of the Chinese isolates (Fig. 1).…”

“…Pakistan submitted its first coronavirus whole-genome sequence (SARS-CoV2/ Gilgit1/human/2020/PAK; accession number: MT240479) to the GenBank on March 25, 2020. Following the first WGS of SARS-CoV2 from Pakistan, several WGS-based attempts were made and the sequencing data were submitted to the GenBank (SARS-CoV2/Manga1/human/2020/PAK; accession number: MT262993) [9]. The initial two sequenced strains of Pakistani coronavirus (accession numbers: MT240479 and MT262993) exhibited 99.98% and 100% sequence similarity to the Chinese SARS-CoV2 isolate [9].…”

“…Following the first WGS of SARS-CoV2 from Pakistan, several WGS-based attempts were made and the sequencing data were submitted to the GenBank (SARS-CoV2/Manga1/human/2020/PAK; accession number: MT262993) [9]. The initial two sequenced strains of Pakistani coronavirus (accession numbers: MT240479 and MT262993) exhibited 99.98% and 100% sequence similarity to the Chinese SARS-CoV2 isolate [9]. During the COVID19 pandemic, the mortality pattern of SARS-CoV2 in Pakistan was found to be considerably different from the rest of the world.…”

Response of vaccination on community transmission of COVID-19: a dynamical approach

“…The transmission of the COVID-19 infections is normally increased by the high infection rate, recombination rate and mutation rate. According to various studies, mutation of the virus is also happening which a cause of alarm [ 12 , 13 ]. Due to the onset of various strains/waves of the virus, such as Alpha, beta, Gamma, Delta, and the most alarming, Omicron [ 14 ], affect on human lives in terms of employment, economic stability, loss of lives has been dire.…”