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Literature detail

Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2.

Yashpal Singh Malik1 Mohd Ikram Ansari2 Jobin Jose Kattoor3 Rahul Kaushik4 Shubhankar Sircar5 Anbazhagan Subbaiyan6 Ruchi Tiwari7 Kuldeep Dhama8 Souvik Ghosh9 Shailly Tomar10 Kam Y J Zhang11
Affiliations 11 institutions
  1. College of Animal Biotechnology, GADVASU, Ludhiana.
  2. Aligarh Muslim University India.
  3. ICAR-Indian Veterinary Research Institute, India.
  4. Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, Japan.
  5. Integral University, India.
  6. ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
  7. Department of Vet erinary Microbiology, DUVASU, Mathura, India.
  8. Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
  9. Health Center for Zoonoses and Tropical Veterinary Medicine, Basseterre, St. Kitts, West Indies.
  10. Department of Biotechnology, IIT, Roorkee, India.
  11. Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Japan.
PMID 33377145 2021 Brief Bioinform eng ppublish
PubMed DOI Browse context

Article

Publication summary

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.

ACE2 receptor codon usage analysis COVID-19 recombination S-protein SARS-CoV-2 Biological Evolution Codon Usage Angiotensin-Converting Enzyme 2 Animals Humans Models, Animal Mutation RNA, Transfer SARS-CoV-2 Spike Glycoprotein, Coronavirus spike protein, SARS-CoV-2

Structured evidence records

Evidence records

5 total
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.85
Key finding

Phylogenetic and recombination analyses indicated frequent genetic exchange among SARS-CoV-2, SARS-CoV, and bat-SARS-like-CoV, supporting their shared evolutionary origin.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

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.

Genes or proteins
spike glycoprotein
Analysis methods
recombination analysis; phylogenetic comparison
Genomic Evolution Extraction confidence 0.85
Key finding

Codon usage bias analysis of SARS-CoV-2 spike genes demonstrated evolutionary pressures from natural selection and mutation shaping adaptation among beta-coronaviruses.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

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.

Genes or proteins
S-gene; spike glycoprotein
Analysis methods
codon usage bias analysis; comparative genomic analysis
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.90
Key finding

The N501T mutation in the SARS-CoV-2 spike glycoprotein enhances binding affinity to the mammalian ACE2 receptor, suggesting molecular adaptation for improved receptor binding.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

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.

Genes or proteins
spike glycoprotein
Receptors
ACE2
Mutations
N501T
Mechanism types
receptor_binding
Receptor Usage 1 records
Receptor Usage Extraction confidence 0.80
Key finding

SARS-CoV-2 spike glycoprotein binds to the ACE2 receptor, and the N501T mutation increases its binding affinity to mammalian ACE2 compared to SARS-CoV.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

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.

Receptors
ACE2
Recombination Or Reassortment 1 records
Recombination Or Reassortment Extraction confidence 0.95
Key finding

Recombination among SARS-CoV-2, SARS-CoV, and bat-SARS-like-CoV indicates genetic exchange in animal reservoirs and humans that may underlie the emergence of SARS-CoV-2.

Host
Not specified
Location
Not specified
Supporting text

Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains... 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.

Event type
recombination