Induction of trained immunity by influenza vaccination - impact on COVID-19

Abstract

Non-specific protective effects of certain vaccines have been reported, and long-term boosting of innate immunity, termed trained immunity, has been proposed as one of the mechanisms mediating these effects. Several epidemiological studies suggested cross-protection between influenza vaccination and COVID-19. In a large academic Dutch hospital, we found that SARS-CoV-2 infection was less common among employees who had received a previous influenza vaccination: relative risk reductions of 37% and 49% were observed following influenza vaccination during the first and second COVID-19 waves, respectively. The quadrivalent inactivated influenza vaccine induced a trained immunity program that boosted innate immune responses against various viral stimuli and fine-tuned the anti-SARS-CoV-2 response, which may result in better protection against COVID-19. Influenza vaccination led to transcriptional reprogramming of monocytes and reduced systemic inflammation. These epidemiological and immunological data argue for potential benefits of influenza vaccination against COVID-19, and future randomized trials are warranted to test this possibility.

Fig 1. Summary of the clinical study investigating the effects of an influenza vaccine on trained immunity.

Blood was collected 1 week before and 6 weeks after the influenza vaccination from 28 participants. PBMC stimulation, quantification of plasma proteins, and single-cell RNA sequencing were performed.

Fig 2. Transcriptomic changes induced by influenza vaccination on a single cell level.

A. Volcano plot depicting the upregulated and downregulated genes in CD14+ monocytes 6 weeks after influenza vaccination. Red dots show upregulation, while blue dots show downregulation. B. Violin plots showing the expression levels of MNDA and CTSS before and after vaccination in CD14+ monocytes. C. Volcano plot depicting the upregulated and downregulated genes in CD4+ naïve T cells 6 weeks after influenza vaccination. Significantly changing top 15 genes were labeled on the volcano plots. D. Pathway analysis of genes up-regulated or down-regulated by influenza vaccination.

Fig 3. Influenza vaccination downregulates circulating inflammatory proteins.

A. Principal component analysis (PCA) of circulating proteins belonging to 10 participants before and after vaccination. The mean difference between before and after in PC1 was calculated by Wilcoxon signed-rank test. B. Volcano plot depicting the fold changes after influenza vaccination. Red dots show significantly changing proteins. C. Selected chemokines whose abundances significantly decrease after the vaccination. Differences between protein expressions before and after influenza vaccination were analyzed using the Wilcoxon signed-rank test, n = 10. NPX: Normalized protein expression. *p<0.05, **p<0.01.

Fig 4. Ex vivo cytokine responses of the individuals before and after influenza vaccination.

PBMCs were stimulated with heat-killed Influenza H1N1 (California strain), heat-killed SARS-CoV-2, poly I:C, and R848 for 24 hours. A. TNFα, B. IL-6, C. IL-1β, D. IL-1RA, and E. IL-12 responses were quantified. SARS-CoV-2 and Influenza stimulations did not lead to detectable levels of IL-12. Wilcoxon signed-rank test was performed to compare the differences in cytokine production between before and after influenza vaccination. Light blue dots represent the cytokine values before vaccination, while dark blue dots show after vaccination. n = 28 *p<0.05, **p<0.01, ****p<0,0001.

Fig 5. Correlation of ex vivo anti-SARS-CoV-2 responses with circulating inflammatory mediators that are significantly altered by influenza vaccination.

A. Heatmap depicting the baseline (before vaccination) levels of inflammatory mediators that were downregulated by influenza vaccination and are significantly correlated with the induction of cytokines upon SARS-CoV-2 stimulation before vs. after vaccination. Red indicates positive correlation, and blue indicates negative correlation. B. Selected circulating protein and cytokine pairs that are significantly correlated. C. Correlation of circulating proteins that were upregulated by influenza vaccination with anti-SARS-CoV-2 cytokine responses, and dot plot depicting the association of baseline GALNT3 levels and induction IL-6 against SARS-CoV-2 after vaccination. r: Spearman’s correlation coefficient. *p<0.05, **p<0.01, ***p<0,001.