Molecular Variation in Porcine Circovirus Type 2 in Jalisco, Mexico, and Its Potential Impact on Vaccine Efficacy

Figures

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  Figure 1. Neighbor-Joining tree constructed from PCV2 ORF2 nucleotide sequences from Jalisco, Mexico. The analysis included the 70 sequences generated in this study and 764 reference sequences used as anchors for the recognized PCV2 genotypes. Genetic distances were calculated with the Tamura–Nei model, applying a gamma distribution (shape parameter = 0.58) to account for among-site rate variation. After removing positions with gaps or missing data by complete deletion, the final dataset contained 705 nucleotide sites. Sequences from this study are indicated with black circles. The tree was annotated and displayed using the Interactive Tree Of Life (iTOL) platform.

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  Figure 2. Neighbor-Joining tree showing the phylogenetic placement of the 19 PCV2a sequences generated in this study together with 63 PCV2a reference sequences. Two supported groups, Subclade 1 and Subclade 2, are indicated in the tree. Sequence names include the country and year of isolation. Black dots denote sequences from this study, and stars denote sequences with recombination signals. The mean divergence between both subclades was 11.3%, estimated in R from cophenetic distances obtained from the tree topology using the ape and phytools packages. The tree was visualized with iTOL v6.

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  Figure 3. Amino acid alignment of PCV2 ORF2 sequences generated in this study, using JX535296.1 (PCV2d) as the reference strain. Conserved and variable amino acid positions are displayed across the 70 sequences, and predicted antigenic epitopes are shaded in purple. PV235525, which showed greater amino acid divergence within the PCV2d group, is highlighted with a box. The alignment was visualized in Jalview version 2.11.5.1. The asterisk (*) denotes the stop codon at the end of the translated ORF2 sequence. Letters indicate amino acid residues at variable positions using the standard one-letter amino acid code, whereas dots indicate positions identical to the reference sequence.

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  Figure 4. Heatmap depicting the variability of predicted B-cell epitopes across 70 PCV2 ORF2 sequences from Jalisco, Mexico, in comparison with one highly pathogenic reference sequence (GenBank JX535296.1, PCV2d, USA). Epitope-specific amino acid divergence (%) was calculated relative to this reference. Lighter shades represent higher conservation, while darker tones indicate greater variability. Sequences are hierarchically clustered based on epitope-specific amino acid divergence relative to the reference, and the dendrogram above the heatmap indicates groups of sequences with higher similarity. Some sequences from other genotypes (e.g., PCV2a) may appear interspersed if their epitope regions show relatively high similarity to the reference.

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  Figure 5. Geographic distribution of recombinant PCV2 sequences and their putative parental strains identified in Jalisco, Mexico. Each panel corresponds to one recombinant event (Recombinants 1–7). Red triangles indicate recombinant sequences, green diamonds indicate major parental sequences, and yellow diamonds indicate minor parental sequences. Gray lines represent the main transportation corridors for animals, supplies, and technical personnel connecting the regions with the highest swine density, including the Guadalajara metropolitan area, Altos Norte, and Altos Sur (B1, B2, and B3 regions). The inset map shows the location of the study area within Jalisco, Mexico.