Homologous recombination shapes the genetic diversity and drives the evolution of African swine fever viruses

Recent outbreaks of African swine fever virus (ASFV) in China severely disrupted the swine industry of the country. No vaccine or treatment against ASFV is available in the current. How to effectively control the virus is challenging. Here, by analyzing all ASFV genomes publicly available, we found large genetic diversity among ASFV genomes. Interestingly, they were mainly caused by extensive genomic insertions and deletions (indels) instead of genomic mutations. Genomic diversity resulted in proteome diversity, with one-third to half of proteins variable among ASFV proteomes. Besides, nearly 20% of proteins had replications in adjacent positions. Further analysis identified extensive homologous recombination in the ASFV genomes, which is consistent with the occurrence of indels. Repeated elements of 15~50 bp were widely distributed in ASFV genomes, which may facilitate the occurrence of homologous recombination. Moreover, two homologous recombination-related enzymes, the recombinase and DNA topoisomerase, were found to keep conserved in all ASFVs analyzed here. This work highlights the importance of homologous recombination in evolution of the virus, and thus facilitates the prevention and control of it.