Bayesian Phylodynamic Analysis Reveals the Dispersal Patterns of African Swine Fever Virus
Zhao-Ji Shen,
Hong Jia,
Chun-Di Xie,
Jurmt Shagainar,
Zheng Feng,
Xiaodong Zhang,
Kui Li,
Rong Zhou
Affiliations
Zhao-Ji Shen
State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Hong Jia
State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Chun-Di Xie
State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Jurmt Shagainar
State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Zheng Feng
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan 528231, China
Xiaodong Zhang
College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
Kui Li
Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
Rong Zhou
State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
The evolutionary and demographic history of African swine fever virus (ASFV) is potentially quite valuable for developing efficient and sustainable management strategies. In this study, we performed phylogenetic, phylodynamic, and phylogeographic analyses of worldwide ASFV based on complete ASFV genomes, B646L gene, and E183L gene sequences obtained from NCBI to understand the epidemiology of ASFV. Bayesian phylodynamic analysis and phylogenetic analysis showed highly similar results of group clustering between E183L and the complete genome. The evidence of migration and the demographic history of ASFV were also revealed by the Bayesian phylodynamic analysis. The evolutionary rate was estimated to be 1.14 × 10−5 substitution/site/year. The large out-migration from the viral population in South Africa played a crucial role in spreading the virus worldwide. Our study not only provides resources for the better utilization of genomic data but also reveals the comprehensive worldwide evolutionary history of ASFV with a broad sampling window across ~70 years. The characteristics of the virus spatiotemporal transmission are also elucidated, which could be of great importance for devising strategies to control the virus.
