tetano
Editor, Senior Moderator
Gene Rep
. 2021 Jun;23:101055.
doi: 10.1016/j.genrep.2021.101055. Epub 2021 Feb 17.
A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses
Jayanti Saha[SUP] 1 [/SUP], Sukanya Bhattacharjee[SUP] 1 [/SUP], Monalisha Pal Sarkar[SUP] 2 [/SUP], Barnan Kumar Saha[SUP] 1 [/SUP], Hriday Kumar Basak[SUP] 3 [/SUP], Samarpita Adhikary[SUP] 1 [/SUP], Vivek Roy[SUP] 1 [/SUP], Parimal Mandal[SUP] 2 [/SUP], Abhik Chatterjee[SUP] 3 [/SUP], Ayon Pal[SUP] 1 [/SUP]
Affiliations
- PMID: 33615042
- PMCID: PMC7887452
- DOI: 10.1016/j.genrep.2021.101055
Abstract
The novel corona virus disease or COVID-19 caused by a positive strand RNA virus (PRV) called SARS-CoV-2 is plaguing the entire planet as we conduct this study. In this study a multifaceted analysis was carried out employing dinucleotide signature, codon usage and codon context to compare and unravel the genomic as well as genic characteristics of the SARS-CoV-2 isolates and how they compare to other PRVs which represents some of the most pathogenic human viruses. The main emphasis of this study was to comprehend the codon biology of the SARS-CoV-2 in the backdrop of the other PRVs like Poliovirus, Japanese encephalitis virus, Hepatitis C virus, Norovirus, Rubella virus, Semliki Forest virus, Zika virus, Dengue virus, Human rhinoviruses and the Betacoronaviruses since codon usage pattern along with the nucleotide composition prevalent within the viral genome helps to understand the biology and evolution of viruses. Our results suggest discrete genomic dinucleotide signature within the PRVs. Some of the genes from the different SARS-CoV-2 isolates were also found to demonstrate heterogeneity in terms of their dinucleotide signature. The SARS-CoV-2 isolates also demonstrated a codon context trend characteristically dissimilar to the other PRVs. The findings of this study are expected to contribute to the developing global knowledge base in countering COVID-19.
Keywords: CAI, Codon Adaptation Index; CNS, Central Nervous System; COVID-19; CRS, Congenital Rubella Syndrome; CUB, Codon Usage Bias; Codon context; Codon usage bias; Coronaviruses; Fop, Frequency of optimal codons; GC1, Guanine and Cytosine content on the first position of the codon; GC2, Guanine and Cytosine content on the second position of the codon; GC3, Guanine and Cytosine content on the third position of the codon; HCV, Hepatitis C Virus; MERS, Middle East Respiratory Syndrome; MFE, Minimum Free Energy; Nc, Effective Number of Codons; PCA, Principal Component Analysis; PRV, Positive strand RNA Virus; Positive strand RNA virus; RCDI, Relative Codon De-Optimization Index; RSCU, Relative Synonymous Codon Usage; SARS, Severe Acute Respiratory Syndrome; SARS-CoV-2; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2; SCUO, Synonymous Codon Usage Order; SiD, Similarity Index.