Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions.
This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.
Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil. paulo7926@usp.br
Paulo E
PE
Brandão
D000595:Amino Acid Sequence; D000818:Animals; D002645:Chickens / Q000821:virology*; D003062:Codon; D017934:Coronavirus / Q000235:genetics*; D040961:Genetic Drift; D008562:Membrane Glycoproteins / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D012641:Selection, Genetic; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins / Q000235:genetics*
D003062:Codon; D008562:Membrane Glycoproteins; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins; C578557:spike glycoprotein, SARS-CoV; C578553:spike protein, mouse hepatitis virus