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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.
PLoS One. 2020; 15(9):e0238344.Plos

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.

Authors+Show Affiliations

Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia. Research Center for Advanced Materials Science, King Khalid University, Abha, Saudi Arabia.Department of Biotechnology, Faculty of Science, Taif University, Taif, Saudi Arabia.Department of Infectious Diseases, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea.Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32881907

Citation

Khan, Mohd Imran, et al. "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." PloS One, vol. 15, no. 9, 2020, pp. e0238344.
Khan MI, Khan ZA, Baig MH, et al. 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. PLoS One. 2020;15(9):e0238344.
Khan, M. I., Khan, Z. A., Baig, M. H., Ahmad, I., Farouk, A. E., Song, Y. G., & Dong, J. J. (2020). 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. PloS One, 15(9), e0238344. https://doi.org/10.1371/journal.pone.0238344
Khan MI, et al. 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. PLoS One. 2020;15(9):e0238344. PubMed PMID: 32881907.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Khan,Mohd Imran, AU - Khan,Zainul A, AU - Baig,Mohammad Hassan, AU - Ahmad,Irfan, AU - Farouk,Abd-ElAziem, AU - Song,Young Goo, AU - Dong,Jae-Jun, Y1 - 2020/09/03/ PY - 2020/04/30/received PY - 2020/08/14/accepted PY - 2020/9/4/entrez PY - 2020/9/4/pubmed PY - 2020/9/18/medline SP - e0238344 EP - e0238344 JF - PloS one JO - PLoS One VL - 15 IS - 9 N2 - 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. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/32881907/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_ L2 - https://dx.plos.org/10.1371/journal.pone.0238344 DB - PRIME DP - Unbound Medicine ER -