Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Issue 2 (30th December 2020)

• Record Type: Journal Article
• Authors: Malik, Yashpal Singh; Ansari, Mohd Ikram; Kattoor, Jobin Jose; Kaushik, Rahul; Sircar, Shubhankar; Subbaiyan, Anbazhagan; Tiwari, Ruchi; Dhama, Kuldeep; Ghosh, Souvik; Tomar, Shailly; Zhang, Kam Y J
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 2(2021)
• Page Start: 1006
• Page End: 1022
• Publication Date: 2020-12-30
• Subjects: COVID-19 -- SARS-CoV-2 -- S-protein -- ACE2 receptor -- recombination -- codon usage analysis; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbaa383
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported to strengthen its binding affinity to mammalian ACE2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains, irrespective of their geographical origin or hosts. Investigation further supports a common origin among SARS-CoV-2 and its predecessors, SARS-CoV and bat-SARS-like-CoV. The recombination events suggest a constant exchange of genetic material among the co-infecting viruses in possible reservoirs and human hosts before SARS-CoV-2 emerged. Furthermore, a comprehensive analysis of codon usage bias (CUB) in SARS-CoV-2 revealed significant CUB among the S-genes of different beta-coronaviruses governed majorly by natural selection and mutation pressure. Various indices of codon usage of S-genes helped in quantifying its adaptability in other animal hosts. These findings might help in identifying potential experimental animal models for investigating pathogenicity for drugs and vaccine development experiments.