Data for Adaptive VP1 Sites 93 and 97 Modulate Antigenic Evolution and Receptor Binding of Senecavirus A: Phylogenetic Analysis and Validation with Recombinant Viruses
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Supporting data for “Adaptive VP1 Sites 93 and 97 Modulate Antigenic Evolution and Receptor Binding of Senecavirus A: Phylogenetic Analysis and Validation with Recombinant Viruses”.
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Figure 1. An ML tree was inferred with IQ-TREE (via PhyloSuite v1.2.3) and saved as raw data Figure 1A.treefile, then formatted in iTOL to generate Figure 1A. Root-to-tip regression (TempEst v1.5.3) produced raw data for Figure 1B_root to tip and Figure 1B. Figure S1. Same pipeline as Figure 1A, using a dataset including the 2012 Taiwan strain (PV002716.1). Figure 2. BEAUti v1.10.5 produced Figure 2A_status.xml; BEAST v1.10.5 (with BEAGLE) generated Figure 2A_log.txt, 2B_location rates log.txt, and 2_MCC tree.tree. Tracer v1.7.2 confirmed convergence (ESS > 200). Posterior trees were summarized with TreeAnnotator v10.5.0 to Figure 2A_MCC tree.nwk and styled in iTOL for Figure 2A; node posteriors are in 2_MCC tree.tree. Discrete diffusion and BSSVS in SpreaD3 v0.9.6 (MCC tree + location-rates log) yielded locations and Bayes factors (Figure 2B.xlsx); the Figure 2B map was drawn in ArcGIS Pro and Adobe Illustrator 2020. A Bayesian SkyGrid plot (Figure 2C) was created in Tracer from Figure 2A_log.txt. Figure 3. Each SVA protein was analyzed on Datamonkey (HyPhy v2.5.68) using FEL and MEME to generate JSON output files, which were processed with Python scripts to produce Figures 3A and 3B and assembled into Figure 3C. Figure 4. Structures 6CX1 and 6ADR (RCSB PDB) were visualized with PyMOL and Adobe Illustrator 2020 (Figure 4A). Annual allele frequencies at VP1 positions 62/63/93/97 across 263 sequences are in Figure 4B_VP1_pos62/63/93/97_per_year_counts.xlsx; the logo (Figure 4B) was generated by Figure 4B_logo.py. Figure 5. The reverse-genetics scheme (5A) and mutation diagrams (5B) were created in Adobe Illustrator 2020. Figure 6. Raw IFA and plaque images for 6A/6C are in Figure 6A_IFA Figures and Figure 6A_Plaque Figures. Growth curves (6B) were generated in GraphPad Prism v10 from TCID50 data (MOI = 0.1); raw data are in raw data for Figure 6B and shown as mean ± SD. Plaque diameters (6D) were measured in ImageJ with a fixed pixel-to-mm scale; raw values are in raw data for Figure 6D, and scatter plots with mean ± SD were made in Prism (30 and 36 hpi; WT, V93A, D97G, V93A+D97G). Figure 7. NT50 values from neutralization assays were computed in GraphPad Prism v10, reported as log2 serum dilutions; raw data are in raw data for Figure 7, displayed as points with mean ± SD. Figure 8. BLI binding/dissociation traces and KD values were exported from the instrument software and plotted in GraphPad Prism v10. Figure S2. All raw IFA images for S2A are in Figure S2A_IFA Figures. S2B growth curves follow the Figure 6B workflow (MOI = 0.1) with raw data in raw data for Figure 6B. Supplementary Table S1. Lists all sequences (accession, isolate name, collection date, and location). Supplementary Materials. Contain Figures S1 and S2 as referenced above.
Institutions
- Northeast Agricultural University