Analysis of codon usage bias of classical swine fever virus

Abstract

Background and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/ codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.

Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype

“…An ENC value >35 indicates a low CUB in the ASFV complete genome [ 25 ]. This finding aligns with previous studies on other porcine viruses, such as porcine circoviruses (54.71±0.87) [ 43 ], porcine parvoviruses (57.433±0.192) [ 44 ] and classical swine fever virus (52.69±0.47) [ 45 ]. The limited codon preference observed in these viruses may promote effective replication in diverse host cells [ 46 ].…”

Codon usage bias analysis of the gene encoding NAD+-dependent DNA ligase protein of invertebrate iridescent virus 6

“…Earlier studies reported similar results in related plots [40,73,90,91]. While ENC-GC3 plot analysis is widely utilized to measure CUB, it alone is not su cient to discern the speci c contributions of mutation pressure and translational selection [65,92]. In order to delve deeper into the factors shaping codon usage patterns, neutrality plot analysis and PR2 plot analysis were conducted.…”

“…We observed that the frequencies of CG and TA dinucleotides in the IIV6 DNA ligase gene were underrepresented among the 16 dinucleotides. Dinucleotide CG is generally underrepresented in most viruses, including Hepatitis C virus, Hepatitis E virus and classical swine fever virus [92,100,101]. Moreover, the underrepresentation of CG and TA dinucleotides is considered as a strategy employed by viruses to evade reduce nonsense mutations, the host immune system and prevent cleavage by RNase [102,103].…”

The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses

“…In addition, the extent to which the bias in the codon usage pattern affects viral-host adaptiveness influences replication efficiency, virulence, protein synthesis, and virus survival. Several studies have suggested that mutational pressure is the primary driving force behind the formation of a codon use pattern [8,9].…”

“…To estimate selection and evolutionary pressure on protein-coding areas, the proportion of the substitution rate at non-synonymous and synonymous sites is quantified. The dN/dS ratio is the most used method [9].…”