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Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach.
Infect Genet Evol. 2020 Oct; 84:104389.IG

Abstract

The newly identified SARS-CoV-2 has now been reported from around 185 countries with more than a million confirmed human cases including more than 120,000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins need to be explored to understand the biology of the virus. Spike glycoprotein is one of the major targets to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment. In this study, 483 unique variations have been identified among the genomes of SARS-CoV-2 including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Among the 26 variations detected in S, 12 variations were located at the N-terminal domain (NTD) and 6 variations at the receptor-binding domain (RBD) which might alter the interaction of S protein with the host receptor angiotensin-converting enzyme 2 (ACE2). Besides, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering these variations and their impact on protein structure.

Authors+Show Affiliations

Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.Department of Pathology and Parasitology, Chittagong Veterinary and Animal Sciences University, Chattogram 4202, Bangladesh.Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh. Electronic address: adnan.mannan@cu.ac.bd.Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh; Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32502733

Citation

Lokman, Syed Mohammad, et al. "Exploring the Genomic and Proteomic Variations of SARS-CoV-2 Spike Glycoprotein: a Computational Biology Approach." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 84, 2020, p. 104389.
Lokman SM, Rasheduzzaman M, Salauddin A, et al. Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach. Infect Genet Evol. 2020;84:104389.
Lokman, S. M., Rasheduzzaman, M., Salauddin, A., Barua, R., Tanzina, A. Y., Rumi, M. H., Hossain, M. I., Siddiki, A. M. A. M. Z., Mannan, A., & Hasan, M. M. (2020). Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 84, 104389. https://doi.org/10.1016/j.meegid.2020.104389
Lokman SM, et al. Exploring the Genomic and Proteomic Variations of SARS-CoV-2 Spike Glycoprotein: a Computational Biology Approach. Infect Genet Evol. 2020;84:104389. PubMed PMID: 32502733.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach. AU - Lokman,Syed Mohammad, AU - Rasheduzzaman,Md, AU - Salauddin,Asma, AU - Barua,Rocktim, AU - Tanzina,Afsana Yeasmin, AU - Rumi,Meheadi Hasan, AU - Hossain,Md Imran, AU - Siddiki,A M A M Zonaed, AU - Mannan,Adnan, AU - Hasan,Md Mahbub, Y1 - 2020/06/02/ PY - 2020/04/15/received PY - 2020/05/12/revised PY - 2020/05/31/accepted PY - 2020/6/6/pubmed PY - 2020/10/3/medline PY - 2020/6/6/entrez KW - COVID-19 KW - Genomic variants KW - SARS-CoV-2 KW - Sequence analysis KW - Spike protein SP - 104389 EP - 104389 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect Genet Evol VL - 84 N2 - The newly identified SARS-CoV-2 has now been reported from around 185 countries with more than a million confirmed human cases including more than 120,000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins need to be explored to understand the biology of the virus. Spike glycoprotein is one of the major targets to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment. In this study, 483 unique variations have been identified among the genomes of SARS-CoV-2 including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Among the 26 variations detected in S, 12 variations were located at the N-terminal domain (NTD) and 6 variations at the receptor-binding domain (RBD) which might alter the interaction of S protein with the host receptor angiotensin-converting enzyme 2 (ACE2). Besides, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering these variations and their impact on protein structure. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/32502733/Exploring_the_genomic_and_proteomic_variations_of_SARS_CoV_2_spike_glycoprotein:_A_computational_biology_approach_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1567-1348(20)30220-3 DB - PRIME DP - Unbound Medicine ER -