Origin, genomic diversity and evolution of African swine fever virus in East Asia

Figure 1.. Characterization and comparisons of genotype II ASFV genomes identified in this study. (A) mapping of sequencing reads against prototype strain China/HLJ/2018. The confirmation results of major gaps using PCR and Sanger sequencing are show under the genomes GD/JiangM/2019, GD/JiangM/2021, GuangX/2021, and GuangX/3/2021. (B) Characterization of SNPs and indels for genomes identified in this study in comparisons with China/HLJ/2018. Variations that occurred in coding regions are represented with solid circles, whereas those in non-coding regions are represented with sold triangles. The color of circles and triangles represent type of SNPs. The 10-bp insertion shown in the figure represents ‘GTTAAGTCAATAGTTTA’ insertion in comparisons to China/HLJ/2018 strain and 17bp insertion preresent ‘TATATAGGAA’ in comparisons to China/HLJ/2018 strain. (C) Mapping reads from sample GuangX/2021 against China/HLJ/2018 confirms the hypovriable region between site 615 and 700 of 360-21R gene. Variations from the reference sequence are shown in different colors, synonymous changes are represented with black triangles, and non-synonymous changes are represented with red solid stars.

Figure 2.. Phylogenetic analyses of ASFV genomes identified in this study. (A) A phylogeny involves all representative ASFV strains. Different genotypes are marked with different color. Viruses identified in this study are represented by solid red circles. (B) A phylogeny involves only genotype II ASFV genomes. Support of the phylogenetic tree topology is only shown on internal nodes. Viruses from different geographic regions are marked with different color. Two well-supported lineages, namely, Eastern Asia Linage and Central European Lineage, were highlighted with red and yellow background colors.

Figure 3.. Phylogenetic network analyses reveal the geographic origin of genotype II ASFV circulating in Eastern Asia. Echo circle represent a strain and the black circle represents a hypothetical strain. Size of circles represents the numbers of gnomes included, the color in the circle represents different country or regions, and the number of striping on the line between two circles represents the number of SNPs. The sequences reported in this study are annotated in red.

Figure 4.. Reconstruction of ancestral geographic regions for genotype II ASFV. Phylogenetic tree was reconstructed using MrBays and ancestral reconstruction of geographic regions was carried out in Mesquite. A consensus tree is shown here with result from ancestral geographic reconstructions (presented in colored pie chart) marked on each of the ancestral nodes. The proportion of area in pie chart represent the probability support for each geographic region in that node.

Figure 5.. Identification of SNPs and Indel markers in genotype II ASFV genomes, all sequences are on the same order. (A) A phylogeny involves only genotype II ASFV genomes, the numbers on the tree represent import nodes. (B) Indels longer than 3 nt and substitution represented by >2 genomes are showed. (C) SNPs relative to strain Georgia/2007. The colors in the tree, indel plot, and SNP plot represent different geographic regions.