|DIMITROV, KIRIL - Consultant|
Submitted to: Infection, Genetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2017
Publication Date: 2/9/2017
Citation: Taylor, T.L., Dimitrov, K.M., Afonso, C.L. 2017. Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1. Infection, Genetics and Evolution. 50(2017):28-37. doi:10.1016/jmeegid.2017.02.004.
Interpretive Summary: Newcastle disease virus (NDV) is synonymous with avian paramyxovirus 1 (APMV-1), with the virulent forms of the virus causing Newcastle disease, which is endemic in poultry in specific countries and has been identified in wild birds worldwide. The virus replicates in chickens and in wild birds. Because it replicates in multiple hosts, it is important to identify viral adaptation features that contributes to it endemicity. Understanding the adaptations on the viral genetic code that determine the insertion of specific amino acids (codon usage) will contribute to future studies that could evaluate the potential of viruses to cause outbreaks in poultry. To characterize adaptation to different hosts, we have analyzed genome wide and gene specific codon usage, focusing mainly on viruses of low virulence of class I that are known to be maintained in waterfowl and viruses of class II, the majority of which are virulent. Our data indicates there are significant differences in codon usage between class I and class II viruses not only at the full genome level, but also within individual genomic regions and in the fusion gene.
Technical Abstract: In order to characterize the evolutionary adaptations of avian paramyxovirus 1 (APMV-1) genomes, we have compared codon usage and codon adaptation indexes among groups of Newcastle disease viruses that differ in biological, ecological, and genetic characteristics. We have used available GenBank complete genome sequences, and compared viruses from class I (CI-29 sequences containing 132,675 codons) and class II (CII-259 sequences containing 1,184,925 codons). We also compared available complete fusion protein gene sequences (CI-175 sequences containing 96,775 codons; CII-1166 sequences containing 644,798 codons). The codon usage and codon adaptation indexes of complete genomic and selected coding regions of class II viruses were compared. Adaptation to chicken and duck hosts was compared among different groups of viruses, among different genomic regions based on transcriptional levels, or on the fusion gene. Interestingly, distinctive codon usage determined by differences in relative synonymous codon usage and by codon adaptation indexes, was observed for the two APMV-1 classes and for different transcriptional regions within classes. Furthermore, differential use of the third codon position and preferential use of codon pairs were seen for the two different classes and for selected genotypes of class II. However, nucleotide composition was not found to have a significant effect on codon usage. Interestingly, no significant differences in codon usage were found between virulent and non-virulent viruses of the same genotype, nor were clear differences found among viruses of class II of the same genotype based on geographic distribution or time of isolation. The data suggest that codon usage has changed significantly since the two APMV-1 classes diverged, however, these changes are not significantly pronounced among genotypes, suggesting that codon adaptation is likely to occur through a slow, evolutionarily adaptation process.