Homologous recombination shapes the genetic diversity of African swine fever viruses

•The genetic diversity of ASFVs was mainly caused by extensive genomic indels instead of point mutations.•Indels may be attributed much to the ectopic homologous recombination.•Extensive repeated elements in ASFV genomes facilitate the occurrence of homologous recombination. The African swine fever...

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Bibliographic Details
Published in:Veterinary microbiology 2019-09, Vol.236, p.108380-108380, Article 108380
Main Authors: Zhu, Zhaozhong, Xiao, Chao-Ting, Fan, Yunshi, Cai, Zena, Lu, Congyu, Zhang, Gaihua, Jiang, Taijiao, Tan, Yongjun, Peng, Yousong
Format: Article
Language:English
Subjects:
African swine fever
African swine fever virus
African Swine Fever Virus - genetics
Asfarviridae
ASFV
Biological evolution
DNA, Viral - genetics
Evolution
genes
Genetic diversity
Genetic Variation
Genome, Viral
Genomes
genomics
Homologous recombination
Homology
Indel
Livestock
Nucleotides
point mutation
pork industry
Reassortant Viruses - genetics
Repeated element
Swine
Vaccines
Viruses
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Summary:•The genetic diversity of ASFVs was mainly caused by extensive genomic indels instead of point mutations.•Indels may be attributed much to the ectopic homologous recombination.•Extensive repeated elements in ASFV genomes facilitate the occurrence of homologous recombination. The African swine fever virus (ASFV) has severely influenced the swine industry of the world. Currently, there is no effective vaccine or drugs against the ASFV. How to effectively control the virus is challenging. In this study, we have analyzed all the publicly available ASFV genomes and demonstrated that there was a large genetic diversity of ASFV genomes. Interestingly, the genetic diversity was mainly caused by extensive genomic insertions and/or deletions (indels) instead of the point mutations. Further analyses showed that the indels may be attributed much to the homologous recombination, as supported by significant associations between the occurrence of extensive recombination events and the indels in the ASFV genomes. Besides, the homologous recombination also led to changes of gene content of ASFVs. Finally, repeated elements of dozens of nucleotides in length were observed to widely distribute and cluster in the adjacent positions of ASFV genomes, which may facilitate the occurrence of homologous recombination. This work highlighted the importance of homologous recombination in shaping the genetic diversity of the ASFVs, and could help understand the evolution of the virus.
ISSN:0378-1135
1873-2542
DOI:10.1016/j.vetmic.2019.08.003