Senecavirus A nonstructural protein 2C and 3A-specific T cell-epitopes promote inactivated vaccine efficacy in pigs via synergistic cellular and humoral immunity

This dataset comprises experimental data generated to investigate T-cell immune responses against Seneca Valley Virus (SVA) in pigs and to evaluate a novel epitope-based vaccine candidate. The data were generated through controlled animal infection and vaccination studies, followed by extensive cellular and molecular immunology assays.Data were generated from two sequential animal experiments. In the first experiment, three specific-pathogen-free pigs were inoculated with the SVA strain CH-HB-2017 via combined intramuscular and intranasal routes, with one pig serving as a PBS-inoculated control. In the second experiment, fifteen pigs were divided into three groups (n=5 per group) receiving either a combination vaccine (recombinant T-cell epitope protein + inactivated SVA), inactivated SVA alone, or PBS, followed by an SVA challenge. Key procedures included: clinical monitoring and scoring; serial blood collection for serum and peripheral blood mononuclear cell (PBMC) isolation; virus titration and RNA quantification by RT-qPCR; high-throughput T-cell response profiling using intracellular cytokine staining (ICS) and flow cytometry; epitope screening using IFN-γ ELISpot; serum neutralizing antibody detection by virus neutralization test (VNT); and swine leukocyte antigen (SLA) genotyping via PCR and sequencing. Data processing involved flow cytometry analysis (FlowJo v10), ELISpot plate reading (AID ELISpot Reader), viral titer calculation (Reed-Muench method), sequence alignment (Geneious Prime), and statistical analysis (GraphPad Prism 8.0).The data were generated from laboratory-based animal studies conducted at the Lanzhou Veterinary Research Institute, China. The temporal scope covers the experimental timelines: for infection studies, samples were collected from 0 to 28 days post-challenge (dpc); for vaccination studies, from day 0 post-vaccination (dpv) through 28 dpv and 0-10 dpc.Data Structure and Content:The dataset is primarily tabular, containing results from multiple assays. Key data tables include:Clinical & Virological Data: Rows represent individual pigs at specific time points. Columns include animal ID, group, time point, clinical score, and SVA RNA copy number in serum (log10 copies/mL).Immunological Assay Data (ICS, ELISpot): Rows represent individual animal samples under specific stimulation conditions. Columns include sample ID, stimulus (e.g., peptide, pool, control), and response metrics (e.g., percentage of IFN-γ+ CD4+/CD8+ T cells, spot-forming units per million cells).Serology Data (VNT): Rows represent serum samples. Columns include animal ID, time point, and neutralizing antibody titer (expressed as the reciprocal of the highest serum dilution that neutralized 50% of the virus).Epitope and Sequence Data: Includes a table listing the 44 synthesized overlapping peptides (rows) covering SVA 2C and 3A proteins, with columns for peptide ID, sequence, and corresponding protein region. Conservation analysis results are presented for the identified epitopes across 237 SVA strains.SLA Genotyping Data: Rows represent individual pigs. Columns list the assigned SLA class I and class II alleles.The total number of data entries varies by table, corresponding to the number of animals, time points, and experimental replicates described in the methods.Missing Data:No systematic missing data is reported. All planned measurements and samples from the described experimental cohorts are accounted for in the results.Data Errors and Uncertainty:Measurement uncertainties are inherent to the techniques used. These include: the limit of detection for RT-qPCR; the error range associated with serial dilution in VNT (typically within one two-fold dilution); and the variability intrinsic to flow cytometry and ELISpot assays, mitigated by the use of replicate wells and standardized gating/analysis protocols. Statistical significance (p-values) and measures of variance (means ± standard deviations) are reported for quantitative comparisons, indicating the precision and reliability of the observed differences.