Analysis of natural recombination and host?related evolutionarydynamics of avian avulavirus 1 isolates based on positive and negativeselection from 1948 to 2017

AbstractAdaptation and evolution of avian avulavirus 1, or Newcastle disease virus (NDV), has led to tremendous economic lossesworldwide. The occurrence of natural recombination and selection pressure has been traced for NDV based on a few recentreports, but a dominant pattern based on genomic characteristics is lacking. Here, we used bioinformatics tools to searchfor evidence of recombination in all of the available complete genome sequence of NDV (462 sequences) using RDP4software. Geographical linkage and host cell relationships of recombinant viruses were also investigated, and a study ofthe adaptive evolution of avian avulavirus 1 was performed. The results revealed that recombination events could occur inany gene fragment of the NDV genome. Moreover, class I NDV isolates from wild birds could associate to generate a putativerecombinant virus with a class II genome backbone. In addition, not only avirulent-virulent hybrid genotypes but alsovirulent-virulent natural recombinant NDV viruses were generated. Investigation of geographic relationships of recombinantisolates indicated that the highest rate of recombination occurs in Asia and the Middle East, which can be influenced byvaccination failure, evasion of the immune response, live-bird markets, and the bird trade. The M and NP genes were foundto have higher negative selection rates than the other genes, which might lead to the deletion of inadaptable sequences andresult in more conserved sequences. Based on our analysis, the highest rate of positive selection was observed in the L, Fand HN genes, which we suggest could lead to the occurrence of evolved viruses with high pathogenicity and a better chanceof survival under extreme conditions