An in-silico study on SARS-CoV-2: Its compatibility with human tRNA pool, and the polymorphism arising in a single lineage over a month

SARS-CoV-2 has caused a global pandemic that has costed enormous human lives in the recent past. The present study is an investigation of the viral codon adaptation, ORF9s stability and tRNA co-adaptation with humans. We observed that for the codon usage bias in viral ssRNA, ORFs have near values of folding free energies and codon adaptation index with mRNAs of the human housekeeping CDS. However, the correlation between the stability of the ORFs in ssRNA and CAI is stronger than the mRNA stability and CAI of HKG, suggesting a greater expression capacity of SARS-CoV-2. Mutational analysis reflects polymorphism 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. Viruses in general have high mutation rates. To understand the chances of survival for the mutated SARS-CoV-2 we did simulation for synonymous mutations. It resulted in 50% ORFs with higher stability than their native equivalents. Thus, considering only the synonymous mutations the virus can exhibit a lot of polymorphism. Collectively our data provides new insights for SARS-CoV-2 mutations and the human t-RNA compatibility.