Data from: Correlates of protection against African swine fever virus identified by a systems immunology approach
Data files
Jun 09, 2026 version files 85.89 KB
-
Fig._1B_-_clinical_scores.csv
6.49 KB
-
Fig._1B_-_Temperature.csv
8.08 KB
-
Fig._1C_-_Viral_loads_(blood).csv
1.81 KB
-
Fig._1C_-_Viral_loads_(serum).csv
2 KB
-
Fig._1D_-_Viral_loads_(organs).csv
626 B
-
Fig._1E_-_Seroconversion.csv
1.39 KB
-
Fig._1F_-_Clinical_scores.csv
787 B
-
Fig._1F_-_Temperature.csv
1.44 KB
-
Fig._1G_-_Survival.csv
88 B
-
Fig._1H_-_Viral_loads_(blood).csv
538 B
-
Fig._1I_-_Viral_loads_(organs).csv
921 B
-
Fig._2A_-_Serum_cytokines.csv
5.62 KB
-
Fig._2B_-_Correlation_of_ELISA_(post-immunization)_to_clinical_scores.csv
2.27 KB
-
Fig._2C_-_Serum_cytokines.csv
3.10 KB
-
Fig._2D_-_Correlation_of_ELISA_(post-challenge)_to_clinical_scores.csv
2.25 KB
-
Fig._3A_-_Correlation_of_ELISpot_to_clinical_scores.csv
371 B
-
Fig._3A_-_ELISpot_day_169_post-immunization.csv
296 B
-
Fig._3A_-_ELISpot_day_7_post-challenge.csv
276 B
-
Fig._3B_-_T-cell_responses.csv
2.81 KB
-
Fig._3C_-_Correlation_of_T-cell_responses_(day_169_pi)_with_clinical_scores.csv
1.18 KB
-
Fig._3C_-_Correlation_of_T-cell_responses_(day_18_pc)_with_clinical_scores.csv
1.16 KB
-
Fig._3C_-_Correlation_of_T-cell_responses_(day_26_pc)_with_clinical_scores.csv
1.16 KB
-
Fig._3C_-_Correlation_of_T-cell_responses_(day_7_pc)_with_clinical_scores.csv
1.17 KB
-
Fig._8_-_Average_NES_of_BTM_families_after_immunization.csv
5.40 KB
-
README.md
13.72 KB
-
Sup._Fig._1_-_Erythrocytes.csv
1.35 KB
-
Sup._Fig._1_-_Leukocytes.csv
1.51 KB
-
Sup._Fig._1_-_Lymphocytes.csv
1.45 KB
-
Sup._Fig._1_-_Monocytes.csv
1.36 KB
-
Sup._Fig._1_-_Neutrophils.csv
1.36 KB
-
Sup._Fig._1_-_Platelets.csv
1.16 KB
-
Sup._Fig._11_-_SLA_haplotyping.csv
3 KB
-
Sup._Fig._12A_-_Serum_dilution_(anti-p72).csv
397 B
-
Sup._Fig._12B_-_Anti-p72_antibody_levels.csv
407 B
-
Sup._Fig._13_-_Hemadsorption-inhibiting_antibody_titers.csv
369 B
-
Sup._Fig._2_-_Viral_loads_(serum).csv
543 B
-
Sup._Fig._28_-_Average_NES_of_BTM_families_after_challenge.csv
2.70 KB
-
Sup._Fig._3_-_Erythrocytes.csv
439 B
-
Sup._Fig._3_-_Leukocytes.csv
469 B
-
Sup._Fig._3_-_Lymphocytes.csv
450 B
-
Sup._Fig._3_-_Monocytes.csv
438 B
-
Sup._Fig._3_-_Neutrophils.csv
435 B
-
Sup._Fig._3_-_Platelets.csv
387 B
-
Sup._Fig._4_-_Area_under_curve.csv
801 B
-
Sup._Fig._8_-_Cellular_responses.csv
1.91 KB
Abstract
African swine fever virus (ASFV) causes a fatal hemorrhagic disease in domestic pigs and wild boars, which poses a severe threat to the global pork industry. Despite the promise of live attenuated vaccines (LAVs), their narrow margin between efficacy and residual virulence presents major safety challenges. This study bridges a critical knowledge gap in ASF vaccinology by identifying innate and adaptive correlates of protection. This was achieved by using an established model with two groups of pigs differing in baseline immunological status (farm and specific pathogen-free [SPF]). The animals were immunized with an attenuated ASFV strain and subsequently challenged with a related, highly virulent genotype II strain. By applying a systems immunology approach, we correlated kinetic data, including serum cytokines, blood transcription modules (BTMs), T-cell responses, and antibody levels, with clinical outcomes to track protective and detrimental immune responses to the virus over time. Key innate correlates of protection included early and sustained IFN-α response, activation of antigen presentation BTMs, and controlled IL-8 levels during immunization. Lower baseline immune activation observed in SPF pigs in steady state was linked to increased protection. Adaptive correlates encompassed cell cycle, plasma cell, and T-cell BTM responses lasting until day 15 post-immunization. Consequently, an effective response from ASFV-specific Th cells before challenge indicated protection. After the challenge, an early IFN-α response, along with low levels of pro-inflammatory cytokines and a strong induction of memory Th and Tc cells, correlated with improved clinical outcomes. The model highlights the critical role of host-specific factors in vaccine efficacy and provides a valuable framework for optimizing ASFV vaccine design while distinguishing between protective and detrimental immune responses.
Dataset DOI: 10.5061/dryad.cnp5hqcm5
Description of the data and file structure
- Fig.1B-_clinical_scores.csv - Cumulative clinical scores for 9 parameters recorded in farm and SPF pigs after immunization with the Estonia 2014 strain, assessed on a scale from 0 (normal) to 3 (severe abnormality)
Variables: time (day), animal group/number, clinical score
- Fig.1B-_Temperature.csv – Rectal temperatures in degrees Celsius recorded for farm and SPF pigs after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, temperature (degrees Celsius)
- Fig.1C-Viral_loads(blood).csv – Viral loads (gEq/mL) measured in blood samples from farm and SPF pigs after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, viral load (genome equivalents per milliliter)
- Fig.1C-Viral_loads(serum).csv– Viral loads (gEq/mL) measured in serum samples from farm and SPF pigs after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, viral load (genome equivalents per milliliter)
- Fig.1D-Viral_loads(organs).csv – Viral loads (gEq/mg) measured in organs from farm and SPF pigs collected on day 17 after immunization with the Estonia 2014 strain
Variables: organ name, animal group/number, viral load (genome equivalents per milligram)
- Fig.1E-_Seroconversion.csv – Seroconversion expressed as % inhibition (anti-p72 antibody levels) and measured by competitive ELISA
Variables: time (day), animal group/number, % inhibition
- Fig.1F-_Clinical_scores.csv– Cumulative clinical scores for 9 parameters recorded in farm and SPF pigs after challenge with the Armenia 2008 strain, assessed on a scale from 0 (normal) to 3 (severe abnormality)
Variables: time (day), animal group/number, clinical score
- Fig.1F-_Temperature.csv – Rectal temperatures in h Celsius recorded for farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, temperature (degrees Celsius)
- Fig.1G-_Survival.csv – Survival after challenge with the Armenia 2008 strain
Variables: time (day), 1 - death event, 0 - survived until the end of the experiment
- Fig.1H-Viral_loads(blood).csv – Viral loads (gEq/mL) measured in blood samples from farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, viral load (genome equivalents per milliliter)
- Fig.1I-Viral_loads(organs).csv – Viral loads (gEq/mg) measured in organs from farm and SPF pigs collected after challenge with the Armenia 2008 strain
Variables: organ name, animal group/number, viral load (genome equivalents per milligram)
- Fig.2A-_Serum_cytokines.csv – Serum cytokine levels in pigs after immunization with the Estonia 2014 strain measured by conventional ELISA
Variables: time (day), animal group/number, cytokine name (IFN-a – interferon alpha, IL-1a – interleukin-1 alpha, IL-1b – interleukin-1 beta, IL-1RA - interleukin-1 receptor antagonist, IL-2 – interleukin-2, IL-8 – interleukin-8, IFN-g – interferon gamma, TNF – tumor necrosis factor), cytokine concentration (U/mL for IFN-a and ng/mL for all other cytokines)
- Fig.2B-Correlation_of_ELISA(post-immunization)_to_clinical_scores.csv - Correlation of serum cytokine levels (post-immunization) with clinical scores after Armenia 2008 challenge
Variables: Pearson correlation coefficient (r), 95% confidence interval, R-squared, p-value, p value summary (ns – not significant; * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001), significance, AUC - area under curve as a summary measure of clinical scores
- Fig.2C-_Serum_cytokines.csv – Serum cytokine levels in pigs after challenge with the Armenia 2008 strain measured by conventional ELISA (U/mL for IFN-α and ng/mL for all other cytokines)
Variables: time (day), animal group/number, cytokine name (IFN-a – interferon alpha, IL-1a – interleukin-1 alpha, IL-1b – interleukin-1 beta, IL-1RA - interleukin-1 receptor antagonist, IL-2 – interleukin-2, IL-8 – interleukin-8, IFN-g – interferon gamma, TNF – tumor necrosis factor), cytokine concentration (U/mL for IFN-a and ng/mL for all other cytokines)
- Fig.2D-Correlation_of_ELISA(post-challenge)_to_clinical_scores.csv - Correlation of serum cytokine levels (post-challenge) with clinical scores (AUC - area under curve) after Armenia 2008 challenge
Variables: Pearson correlation coefficient (r), 95% confidence interval, R-squared, p-value, p-value summary (ns – not significant; * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001), significance, AUC - area under the curve as a summary measure of clinical scores
- Fig.3A-_Correlation_of_ELISpot_to_clinical_scores.csv – Correlation of IFN-γ responses measured by ELISpot with clinical scores (AUC - area under curve) after Armenia 2008 challenge
Variables: Pearson correlation coefficient (r), 95% confidence interval, R-squared, p-value, p-value summary (ns – not significant; * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001), significance, AUC - area under the curve as a summary measure of clinical scores
- Fig.3A-_ELISpot_day_7_post-challenge.csv – IFN-γ responses measured by ELISpot (performed in triplicate) after whole-virus restimulation using PBMCs collected on day 7 post-challenge
Variables: animal group/number, SFC - spot-forming cells
- Fig.3A-_ELISpot_day_169_post-immunization.csv – IFN-γ responses measured by ELISpot (performed in triplicate; SFC, spot-forming cells) after whole-virus restimulation using PBMCs collected on day 169 post-immunization
Variables: animal group/number, SFC - spot-forming cells
- Fig.3B-_T-cell_responses.csv – T-cell responses following whole-virus restimulation expressed as % cytokine-positive cells within each subset and measured by intracellular cytokine staining of PBMCs collected before and after challenge
Variables: time (day), animal group/number, cell subset name (Th – T helper, DP Th – double-positive T helper, Tc – cytotoxic T cell), cytokine name (IFN-g – interferon gamma, TNF – tumor necrosis factor), percentage of positive cells (mock-stimulated values were subtracted from virus-restimulated values)
- Fig.3C-Correlation_of_T-cell_responses(day_7_pc)_with_clinical_scores.csv - Correlation of T-cell responses (day 7 post-challenge) with clinical scores (AUC - area under curve) after Armenia 2008 challenge
Variables: Pearson correlation coefficient (r), 95% confidence interval, R-squared, p-value, p-value summary (ns – not significant; * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001), significance, AUC - area under the curve as a summary measure of clinical scores
- Fig.3C-Correlation_of_T-cell_responses(day_18_pc)_with_clinical_scores.csv- Correlation of T-cell responses (day 18 post-challenge) with clinical scores (AUC - area under curve) after Armenia 2008 challenge
Variables: Pearson correlation coefficient (r), 95% confidence interval, R-squared, p-value, p-value summary (ns – not significant; * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001), significance, AUC - area under the curve as a summary measure of clinical scores
- Fig.3C-Correlation_of_T-cell_responses(day_26_pc)_with_clinical_scores.csv - Correlation of T-cell responses (day 26 post-challenge) with clinical scores (AUC - area under curve) after Armenia 2008 challenge
Variables: Pearson correlation coefficient (r), 95% confidence interval, R-squared, p-value, p-value summary (ns – not significant; * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001), significance, AUC - area under the curve as a summary measure of clinical scores
- Fig.3C-Correlation_of_T-cell_responses(day_169_pi)_with_clinical_scores.csv - Correlation of T-cell responses (day 169 post-immunization) with clinical scores (AUC - area under curve) after Armenia 2008 challenge
Variables: Pearson correlation coefficient (r), 95% confidence interval, R-squared, p-value, p-value summary (ns – not significant; * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001), significance, AUC - area under the curve as a summary measure of clinical scores
- Fig.8-_Average_NES_of_BTM_families_after_immunization.csv - Average normalized enrichment scores (NES) of BTM families after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, BTM family name, NES – normalized enrichment score
- Sup._Fig.1-_Erythrocytes.csv– Erythrocyte counts analyzed by VetScan in farm and SPF pigs after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, erythrocyte counts (×10¹²/L blood)
- Sup._Fig.1-_Leukocytes.csv – Leukocyte counts analyzed by VetScan in farm and SPF pigs after immunization with the Estonia 2014strain
Variables: time (day), animal group/number, leukocyte counts (×109/L blood)
- Sup._Fig.1-_Lymphocytes.csv– Lymphocyte counts analyzed by VetScan in farm and SPF pigs after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, lymphocyte counts (×109/L blood)
- Sup._Fig.1-_Monocytes.csv – Monocyte counts analyzed by VetScan in farm and SPF pigs after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, monocyte counts (×109/L blood)
- Sup._Fig.1-_Neutrophils.csv– Neutrophil counts analyzed by VetScan in farm and SPF pigs after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, neutrophil counts (×109/L blood)
- Sup._Fig.1-_Platelets.csv – Platelet counts analyzed by VetScan in farm and SPF pigs after immunization with the Estonia 2014 strain
Variables: time (day), animal group/number, platelet counts (×109/L blood)
- Sup._Fig.2-Viral_loads(serum).csv – Viral loads (gEq/mL) measured in serum samples from farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, viral load (genome equivalents per milliliter)
- Sup._Fig.3-_Erythrocytes.csv – Erythrocyte counts analyzed by VetScan in farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, erythrocyte counts (×10¹²/L blood)
- Sup._Fig.3-_Leukocytes.csv – Leukocyte counts analyzed by VetScan in farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, leukocyte counts (×109/L blood)
- Sup._Fig.3-_Lymphocytes.csv – Lymphocyte counts analyzed by VetScan in farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, lymphocyte counts (×109/L blood)
- Sup._Fig.3-_Monocytes.csv – Monocyte counts analyzed by VetScan in farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, monocyte counts (×109/L blood)
- Sup._Fig.3-_Neutrophils.csv – Neutrophil counts analyzed by VetScan in farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, neutrophil counts (×109/L blood)
- Sup._Fig.3-_Platelets.csv– Platelet counts analyzed by VetScan in farm and SPF pigs after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, platelet counts (×109/L blood)
- Sup._Fig.4-_Area_under_curve.csv– Clinical scores recorded after Armenia 2008 challenge to calculate areas under the curves (AUCs)
Variables: time (day), animal group/number, clinical score
- Sup._Fig.8-_Cellular_responses.csv– γδ T cell and NK cell responses following whole-virus restimulation expressed as % cytokine-positive cells within each subset and measured by intracellular cytokine staining of PBMCs collected before and after challenge
Variables: time (day), animal group/number, cell subset name (γδ – γδ T cell, NK – NK cell), cytokine name (IFN-g – interferon gamma, TNF – tumor necrosis factor), percentage of positive cells (mock-stimulated values were subtracted from virus-restimulated values)
- Sup._Fig.11-_SLA_haplotyping.csv – SLA alleles in farm and SPF pigs (fragment length in base pairs, bp)
Variables: animal number, template (sequence ID | SLA allele designation | sequence length in base pairs – bp)
- Sup._Fig.12A-Serum_dilution(anti-p72).csv - Two serum samples from a randomly selected protected SPF (#1963) and a non-protected farm pig (#13) were serially diluted to define by competitive ELISA the non-saturating concentration estimated to provide 20–80% inhibition (anti-p72 antibody levels)
Variables: serum sample (animal number, day of collection), serum dilution, % inhibition
- Sup._Fig.12B-_Anti-p72_antibody_levels.csv – Anti-p72 antibody levels expressed as % inhibition and measured in farm and SPF pigs by competitive ELISA using a 1:1250 serum dilution
Variables: animal number, % inhibition
- Sup._Fig.13-_Hemadsorption-inhibiting_antibody_titers.csv - ND50 titers of hemadsorption-inhibiting antibodies calculated with the Spearman-Kärber formula using red blood cell (RBC) rosette counts from ImageJ
Variables: animal number, ND50 titers
- Sup._Fig.28-_Average_NES_of_BTM_families_after_challenge.csv - Average normalized enrichment scores (NES) of BTM families after challenge with the Armenia 2008 strain
Variables: time (day), animal group/number, BTM family name, NES – normalized enrichment score