tetano
Editor, Senior Moderator
Brief Bioinform
. 2020 Dec 30;bbaa383.
doi: 10.1093/bib/bbaa383. Online ahead of print.
Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2
Yashpal Singh Malik[SUP] 1 [/SUP], Mohd Ikram Ansari[SUP] 2 [/SUP], Jobin Jose Kattoor[SUP] 3 [/SUP], Rahul Kaushik[SUP] 4 [/SUP], Shubhankar Sircar[SUP] 5 [/SUP], Anbazhagan Subbaiyan[SUP] 6 [/SUP], Ruchi Tiwari[SUP] 7 [/SUP], Kuldeep Dhama[SUP] 8 [/SUP], Souvik Ghosh[SUP] 9 [/SUP], Shailly Tomar[SUP] 10 [/SUP], Kam Y J Zhang[SUP] 11 [/SUP]
Affiliations
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.
Keywords: ACE2 receptor; COVID-19; S-protein; SARS-CoV-2; codon usage analysis; recombination.
. 2020 Dec 30;bbaa383.
doi: 10.1093/bib/bbaa383. Online ahead of print.
Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2
Yashpal Singh Malik[SUP] 1 [/SUP], Mohd Ikram Ansari[SUP] 2 [/SUP], Jobin Jose Kattoor[SUP] 3 [/SUP], Rahul Kaushik[SUP] 4 [/SUP], Shubhankar Sircar[SUP] 5 [/SUP], Anbazhagan Subbaiyan[SUP] 6 [/SUP], Ruchi Tiwari[SUP] 7 [/SUP], Kuldeep Dhama[SUP] 8 [/SUP], Souvik Ghosh[SUP] 9 [/SUP], Shailly Tomar[SUP] 10 [/SUP], Kam Y J Zhang[SUP] 11 [/SUP]
Affiliations
- PMID: 33377145
- DOI: 10.1093/bib/bbaa383
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.
Keywords: ACE2 receptor; COVID-19; S-protein; SARS-CoV-2; codon usage analysis; recombination.