Resolving the Phylogenetic Placement of the FSfaCV/PCV5‐Related Viruses Within the Genus Macochavirus

Figures

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  Figure 1. Genomic and geographic characterization of novel porcine circular DNA viruses. (A) Geographic distribution of the identified viral genomes. Colored regions indicate provinces where the sequences were detected, and the bar chart represents the number of sequences identified in each province. (B) Schematic diagram of the genomic structure of novel porcine circular DNA viruses.

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  Figure 2. Maximum‐likelihood phylogenetic tree of cressdnaviruses inferred from Rep amino sequences. The tree was constructed using IQ‐TREE2 based on aligned Rep amino acid sequences. Representative sequences from 21 families of cressdnaviruses were included, together with previously reported FSfaCV and putative PCV5 sequences. The 10 new cressdnavirus sequences identified here are highlighted in purple, whereas sequences from other taxa are displayed in distinct colors. Colored blocks delineate different viral families, facilitating visualization of taxonomic classification and evolutionary relationships.

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  Figure 3. Phylogenetic analysis of PMV sequences within the family Pecoviridae. Maximum‐likelihood phylogenetic trees were inferred using IQ‐TREE2 based on (A) complete genome sequences, (B) Rep protein sequences, and (C) Cap protein sequences, respectively. The outer colored ring indicates different genera within the family Pecoviridae, while members of the genus Macochavirus are further distinguished using different colors to highlight intra‐genus variation.

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  Figure 4. Sequence similarity and identity analysis of PMV sequences within the family Pecoviridae. (A) Sequence demarcation tool (SDT) analysis was conducted to evaluate the pairwise nucleotide identity between the 10 porcine‐derived cressdnaviruses (PMV) sequences identified in this study and representative members of different genera within the family Pecoviridae. (B) Sequence similarity analysis further illustrates the genetic relatedness among these viruses. The 10 PMV sequences are indicated by blue circles, and their corresponding genus assignments are labeled on the left.

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  Figure 5. Haplotype network analysis of PMV sequences within the family Pecoviridae. The network was constructed based on aligned sequences using a TCS Network approach implemented in PopART and Launch DnaSP6 software. The 10 PMV sequences identified in this study, together with closely related FSfaCV and PCV5 sequences, are indicated by green circles. Each node represents a unique haplotype, and the connections between nodes indicate mutational steps among sequences. The network illustrates the haplotype structure and genetic relationships among these viruses.

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  Figure 6. Sliding window analysis of nucleotide diversity (π) among PMV sequences and related viruses within the family Pecoviridae. The red line represents nucleotide diversity calculated from a combined dataset comprising the 10 PMV sequences together with closely related FSfaCV and PCV5 sequences. Other colored lines represent nucleotide diversity estimated from this combined dataset supplemented with representative sequences from each genus within Pecoviridae. This analysis highlights patterns of genetic variation across different sequence groupings.