Genomic Epidemiology of African Swine Fever Virus Identified in Domestic Pig Farms in South Korea during 2019–2021

Figures

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  Figure 1. Mutations in whole-genome sequences of African swine fever viruses isolated from South Korea compared with the reference strain Georgia 2007/1. The nucleotide numbers are marked based on reference sequence (Georgia 2007/1). The location of the gaps in the reference sequence generated by nucleotide insertions of South Korea isolates is marked with a slash (/) between two nucleotide numbers. The sequences in open reading frames (ORFs) are highlighted in red in the reference sequence, whereas those located in intergenic regions (IGRs) are represented in black. Nonsynonymous mutations are marked with filled stars. Three nucleotide insertions between 20405 and 20406 are shown in the ASFV/Korea/Pig/Goseong/2021 strain. Mutations clustered in MGF 505-9R assumed to be the result of self-recombination in ASFV/Korea/Pig/Inje2/2021 and the GAATATATAG insertion at I73R-I329L IGR in all Korean isolates are not included in this figure.

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  Figure 2. Diagram illustrating self-recombination in the ASFV/Korea/Pig/Inje2/2021 strain. Thirteen mutations were identified within the 52 bp segment of the MGF 505-9R gene and identical sequences were found in the MGF 505-10R gene. The original sequences (above) were identified in all other Korean isolates. The results indicated possible self-recombination between MGF 505-9R and MGF 505-10R in the ASFV/Korea/Pig/Inje2/2021 strain (below).

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  Figure 3. Maximum-likelihood phylogenetic tree of genotype II African swine fever viruses. Taxa with red font are the ASFV isolates from South Korean domestic pigs and taxa with green font are the ASFV isolates from South Korean wild boars. Phylogenetic trees were constructed using the maximum-likelihood method in RAxML with 500 bootstrap replicates. Bootstrap values are shown in each node. Each node sharing identical nucleotide mutations, insertion, or deletion among Korean isolates is annotated.

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  Figure 4. Time-scaled maximum clade credibility tree of the genotype II African swine fever viruses. Taxa with red font are the ASFV isolates from South Korean domestic pigs and taxa with green font are the ASFV isolates from South Korean wild boars. The size and the color of the node (circle) indicate the posterior, which means the probability associated with forming one clade. Korean ASF was divided into three groups according to the posterior probability.

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  Figure 5. Distribution of ASFVs isolated in South Korea during 2019–2021 based on phylogenetic analysis. The shapes represent the year of isolation and the colors represent the viral groups in South Korea.