Computational Biology of COVID-19, Comparative analysis of codon usage, and phylogenetic relations
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Farzaneh Kargar,1 Mohammad Rahmati,2,* Mojtaba Mortazavi,3 Marzieh Jamalidoust,4 Abbas Karimi,5
1. Department of Clinical Biotechnology, Faculty of Medical School, Tabriz University of Medical Sciences, Tabriz, Iran.
2. Department of Clinical Biotechnology, Faculty of Medical School, Tabriz University of Medical Sciences, Tabriz, Iran.
3. Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
4. Clinical Microbiology Research Center, Shiraz University of Medical Center, Shiraz, Iran
5. Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Introduction: Coronaviruses are enveloped single-stranded RNA genome viruses causing respiratory distress syndromes. Open reading fram1a (ORF1a) encodes the enzymes of the RNA-synthesizing for replication of viral genome and synthesis of subgenomic mRNA. The aim of the present in-silico study was to compare codon usage, rare codon clusters and phylogenetic relations in COVID-19 coronaviruses.
- Methods: The nucleotide sequences and their features of the Coronaviridae family were obtained from NCBI and frequency, number and fraction of 61 codons for each amino acid was evaluated in the structure of viral protein and the preferred codons were assessed using Gene Infinity website. The variation in codon usage bias were quantified by the ENC and CBI in the ACUA software.
- Results: Finally, evolutionary relationship and phylogenetic analysis of Coronaviridae were studied using the MEGA 7 software. The GC3% of the cds was in the range from 15.668 to 16.534 and GC3 Skewness from 0.299 to 0.34. Analysis of codon usage for all of amino acid in COVID-19 showed considerable differences between the viruses. The findings of the present study revealed that the patterns of base compositions in COVID-19 are most likely the result of mutation pressure rather than that of natural selection, since at all codon positions its effects are present.
- Conclusion: In addition, analysis of base composition it was found that the cds of COVID-19 are rich in AT, which should be considered in designing new drugs.
- Keywords: Computational Biology, Coronaviruses, codon, Coronaviridae
