Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach.
Infect Genet Evol
; 84: 104389, 2020 Oct.
Article
in English
| MEDLINE | ID: covidwho-459162
Preprint
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This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
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.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Genome, Viral
/
Peptidyl-Dipeptidase A
/
Severe acute respiratory syndrome-related coronavirus
/
Spike Glycoprotein, Coronavirus
/
Alphacoronavirus
/
Betacoronavirus
Topics:
Variants
Limits:
Animals
/
Humans
Language:
English
Journal:
Infect Genet Evol
Journal subject:
Biology
/
Communicable Diseases
/
Genetics
Year:
2020
Document Type:
Article
Affiliation country:
J.meegid.2020.104389
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