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Whole Genome Comparison of Pakistani Corona Virus with Chinese and US Strains along with its Predictive Severity of COVID-19

Rashid Saif, Tania Mahmood, Aniqa Ejaz, Saeeda Zia, Abdul Rasheed Qureshi
doi: https://doi.org/10.1101/2020.05.01.072942
Rashid Saif
1Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
2Decode Genomics, 323-D, Punjab University Employees Housing Scheme (II), Lahore, Pakistan
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  • For correspondence: rashid.saif37@gmail.com
Tania Mahmood
1Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
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Aniqa Ejaz
1Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
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Saeeda Zia
3Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Lahore, Pakistan
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Abdul Rasheed Qureshi
4Out-Patient Department-Pulmonology, Gulab Devi Chest Hospital, Ferozepur Road, Lahore, Pakistan
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Abstract

Recently submitted 784 SARS-nCoV2 whole genome sequences from NCBI Virus database were taken for constructing phylogenetic tree to look into their similarities. Pakistani strain MT240479 (Gilgit1-Pak) was found in close proximity to MT184913 (CruiseA-USA), while the second Pakistani strain MT262993 (Manga-Pak) was neighboring to MT039887 (WI-USA) strain in the constructed cladogram in this article. Afterward, four whole genome SARS-nCoV2 strain sequences were taken for variant calling analysis, those who appeared nearest relative in the earlier cladogram constructed a week time ago. Among those two Pakistani strains each of 29,836 bases were compared against MT263429 from (WI-USA) of 29,889 bases and MT259229 (Wuhan-China) of 29,864 bases. We identified 31 variants in both Pakistani strains, (Manga-Pak vs USA=2del+7SNPs, Manga-Pak vs Chinese=2del+2SNPs, Gilgit1-Pak vs USA=10SNPs, Gilgit1-Pak vs Chinese=8SNPs), which caused alteration in ORF1ab, ORF1a and N genes with having functions of viral replication and translation, host innate immunity and viral capsid formation respectively. These novel variants are assumed to be liable for low mortality rate in Pakistan with 385 as compared to USA with 63,871 and China with 4,633 deaths by May 01, 2020. However functional effects of these variants need further confirmatory studies. Moreover, mutated N & ORF1a proteins in Pakistani strains were also analyzed by 3D structure modelling, which give another dimension of comparing these alterations at amino acid level. In a nutshell, these novel variants are assumed to be linked with reduced mortality of COVID-19 in Pakistan along with other influencing factors, these novel variants would also be useful to understand the virulence of this virus and to develop indigenous vaccines and therapeutics.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted June 30, 2020.
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Whole Genome Comparison of Pakistani Corona Virus with Chinese and US Strains along with its Predictive Severity of COVID-19
Rashid Saif, Tania Mahmood, Aniqa Ejaz, Saeeda Zia, Abdul Rasheed Qureshi
bioRxiv 2020.05.01.072942; doi: https://doi.org/10.1101/2020.05.01.072942
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Whole Genome Comparison of Pakistani Corona Virus with Chinese and US Strains along with its Predictive Severity of COVID-19
Rashid Saif, Tania Mahmood, Aniqa Ejaz, Saeeda Zia, Abdul Rasheed Qureshi
bioRxiv 2020.05.01.072942; doi: https://doi.org/10.1101/2020.05.01.072942

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