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DOI: https://doi.org/10.21203/rs.3.rs-42668/v1
Parapoxvirus (PPV) has been identified in most mammals and poses a great threat to both the livestock production and public health. However, it is still not fully understood the viral prevalence and evolution of PPV coding sequences. Here, we performed a comparative approach integrating viral genetics, molecular selection pressure and genomic structure to investigate the genomic features and evolution of PPVs. We noticed that although there were significant differences of GC contents between ORFV and other three species of PPVs, all PPVs showed almost identical nucleotide bias, that is GC richness. This reflected a common mechanism which determines GC compositions for virus with similar life cycles. The structural analysis of PPV genomes showed the divergence of different PPV species, which may due to the specific adaptation to their natural hosts. Additionally, we estimated the phylogenetic diversity of segmented genome of PPV. Our results suggested that during the 2010 – 2018 outbreak, the orf virus has been the dominant species under the selective pressure of the optimal gene patterns. Furthermore, we found the mean substitution rates were between 3.56×10-5 to 4.21×10-4 in different PPV segments, and the PPV VIR gene was evolved at the highest substitution rate. In these protein-coding regions, purifying selection was the major evolutionary pressure, while the GIF and VIR genes suffered the greatest positive selection pressure. These results may provide useful knowledge on the virus genetic evolution from a new perspective which could help create prevention and control strategies.
This preprint is available for download as a PDF.
Fig. S1. The phylogenetic tree of PPV B2L genes. The tree was generated by the maximum likelihood (ML) method using PAML v4.9. The tree was designed by using the online tool “iTOL”. Here; different colors represent different collection locations. The color of each leaf node represents different virus species.