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Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight

Authors
 Mohd Imran Khan  ;  Zainul A Khan  ;  Mohammad Hassan Baig  ;  Irfan Ahmad  ;  Abd-ElAziem Farouk  ;  Young Goo Song Jae-Jun Dong 
Citation
 PLOS ONE, Vol.15(9) : e0238344, 2020-09 
Journal Title
 PLOS ONE 
Issue Date
2020-09
MeSH
Betacoronavirus / classification ; Betacoronavirus / genetics* ; Cysteine Endopeptidases / chemistry ; Cysteine Endopeptidases / genetics* ; Genetic Variation ; Genome, Viral* ; Molecular Dynamics Simulation ; Mutation* ; Nucleocapsid Proteins / chemistry ; Nucleocapsid Proteins / genetics* ; Phylogeny ; Spike Glycoprotein, Coronavirus / chemistry ; Spike Glycoprotein, Coronavirus / genetics* ; Viral Envelope Proteins / chemistry ; Viral Envelope Proteins / genetics* ; Viral Nonstructural Proteins / chemistry ; Viral Nonstructural Proteins / genetics*
Abstract
A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. In this study, we have made an attempt to investigate the SARS-CoV-2 genome reported from 13 different countries, identification of mutations in major coronavirus proteins of these different SARS-CoV-2 genomes and compared with SARS-CoV. These thirteen complete genome sequences of SARS-CoV-2 showed high identity (>99%) to each other, while they shared 82% identity with SARS-CoV. Here, we performed a very systematic mutational analysis of SARS-CoV-2 genomes from different geographical locations, which enabled us to identify numerous unique features of this viral genome. This includes several important country-specific unique mutations in the major proteins of SARS-CoV-2 namely, replicase polyprotein, spike glycoprotein, envelope protein and nucleocapsid protein. Indian strain showed mutation in spike glycoprotein at R408I and in replicase polyprotein at I671T, P2144S and A2798V,. While the spike protein of Spain & South Korea carried F797C and S221W mutation, respectively. Likewise, several important country specific mutations were analyzed. The effect of mutations of these major proteins were also investigated using various in silico approaches. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. It was found that the R60C mutation in Mpro affects the protein dynamics, thereby, affecting the binding of inhibitor within its active site. The implications of mutation on structural characteristics were determined. The information provided in this manuscript holds great potential in further scientific research towards the design of potential vaccine candidates/small molecular inhibitor against COVID19.
Files in This Item:
T202003452.pdf Download
DOI
10.1371/journal.pone.0238344
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Family Medicine (가정의학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
Yonsei Authors
Dong, Jae June(동재준) ORCID logo https://orcid.org/0000-0002-2420-2155
Song, Young Goo(송영구) ORCID logo https://orcid.org/0000-0002-0733-4156
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/179946
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