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Original Research Article

Revisiting SARS-CoV-2: Evolution, polymorphism and compatibility with human tRNA pool in a lineage over a month

Manish Prakash Victor, Rohit Das, Tapash Chandra Ghosh

1.Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta,
Calcutta, India
2.Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
3.Raiganj University, Raiganj, West Bengal, India

Ind.J.Applied.Microbiol. 2023 .25(2) : 11-36

*Corresponding author


The present study presents a comparative analysis of SARS-CoV-2’s survival capacity in its human host in an area within a month.
Materials and Methods:
Codon usage bias study has been carried using Emboss package and evolutionary study has been carried using pn/ps packages in python and R for statistical analysis.
The virus has overlapping genes exhibiting a high codon usage bias and optimization with human Lung housekeeping genes. Viral ORFs have near values of minimum folding energies and codon adaptation index with mRNAs of the human Lung housekeeping genes. Then too, viruses showed a greater expression capacity. Polymorphism is in the virus for ORF1ab, surface glycoprotein and nucleocapsid phosphoprotein ORFs. Non-synonymous       mutations have            shown  non-polar substitutions. Out of the twelve mutations nine are for a higher t-RNA copy number. Synonymous mutation simulation mimicking evolution revealed fitter newer strains.
Through this study we have explained the inherent codon adaptation of SARS-CoV-2 with        human tRNA pool and how the virus shows polymorphism in-order to keep up with its infectious capacity. Hence, giving an insight into viral rapid adaptability.

Keywords: SARS-CoV-2 mutations, codon adaptation index, minimum folding energy, Homo sapiens tRNA pool, effective number of codons

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