Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach.
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.
['Lokman|Syed Mohammad|SM|', 'Rasheduzzaman|Md|M|', 'Salauddin|Asma|A|', 'Barua|Rocktim|R|', 'Tanzina|Afsana Yeasmin|AY|', 'Rumi|Meheadi Hasan|MH|', 'Hossain|Md Imran|MI|', 'Siddiki|A M A M Zonaed|AMAMZ|', 'Mannan|Adnan|A|', 'Hasan|Md Mahbub|MM|']
D000073638:Alphacoronavirus D000085962:Angiotensin-Converting Enzyme 2 D000818:Animals D001483:Base Sequence D000073640:Betacoronavirus D001665:Binding Sites D002685:Chiroptera D015870:Gene Expression D016679:Genome, Viral D006801:Humans D008958:Models, Molecular D009154:Mutation D007703:Peptidyl-Dipeptidase A D011485:Protein Binding D000072756:Protein Conformation, alpha-Helical D000072757:Protein Conformation, beta-Strand D054730:Protein Interaction Domains and Motifs D045473:SARS Virus D000086402:SARS-CoV-2 D016415:Sequence Alignment D064370:Spike Glycoprotein, Coronavirus D040681:Structural Homology, Protein D053585:Virus Attachment
SARS-CoV-2 Spike protein COVID-19 Genomic variants Sequence analysis