Analysis of codon usage pattern in the viral proteins of chicken anaemia virus and its possible biological relevance

Abstract

Chicken anaemia virus (CAV) is an important poultry pathogen. CAV infection can lead to severe immunosuppression and mortality in birds. The viral proteins (VP1, VP2 and VP3) are major protective immunogens that determine the pathotype of CAV strains. The factors influencing the synonymous codon usage bias and the nucleotide composition of the viral protein genes of CAV have not been studied. In the present study, we have analysed the synonymous codon usage pattern in VP1, VP2 and VP3 genes of CAV. Our results showed that all the genes have a low codon usage bias; however, this bias was slightly higher in the VP2 gene as compared to VP1 and VP3. The major contributing factor for this pattern of codon usage bias in CAV is mutational pressure followed by the host factors. The conclusion was drawn based on codon usage, correspondence analysis, ENC-GC3 plot and correlation analyses among different indices. The study will help us to understand the codon usage bias of CAV and related single-stranded DNA viruses which could further be used to explore their biology.