Liang Wang ,Yuzi Luo ,Yuhui Zhao ,George F Gao ,Yuhai Bi ,Hua‐Ji Qiu
Transbound Emerg Dis. 2020 Jan 21. doi: 10.1111/tbed.13489. [Epub ahead of print]
The worldwide transmission of African swine fever virus (ASFV) drastically affects the pig industry and global trade. Development of vaccines is hindered by the lack of knowledge of the genomic characteristics of ASFV. In this study, we developed a pipeline for the de novo assembly of the ASFV genome without virus isolation and purification. We then used a comparative genomics approach to systematically study 46 genomes of ASFVs to reveal the genomic characteristics. The analyses revealed that ASFV has an "open" pan-genome based on both protein-coding genes and intergenic regions. Of the 151 - 174 genes found in the ASFV strains, only 86 were identified as core genes; the remainder were flexible accessory genes. Notably, 44 of the 86 core genes and 155 of the 324 accessory genes have been functionally annotated according to the known proteins. Interestingly, a dynamic number of taxis-related genes were identified in the accessory genes, and two potential virulence genes were identified in all ASFV isolates. The "open" pan-genome of ASFV based on gene and intergenic regions reveal its pronounced natural diversity concerning genomic composition and regulation.
© 2020 Blackwell Verlag GmbH.
African swine fever virus; accessory genes; core genes; evolution; open; pan-genome; taxis-related genes