Figure 2. Sex-specific response differences to influenza vaccination in COVID-19-recovered individuals and matching controls.

a, Schematic of the sex-specific comparisons of vaccine induced changes from baseline at timepoints post vaccination (D1, D7, and D28) between COVR and HC subjects. Analyses applied to subjects under 65 years of age (see Methods).

b, Box plots of the D1 Interferon Gamma (IFNγ) transcriptional response score (D1 – D0, computed using genes from the Hallmark “Interferon Gamma Response” gene set) for COVR-F (n=15), COVR-M (n=14), HC-F (n=16), and HC-M (n=14).

c, Box plots of the D1 response (D1 – D0) of serum IFNγ protein level for the subjects shown in (b).

d, Surface protein expression-based UMAP (as in Fig. 1e) with cells colored by the D1 IFNγ transcriptional response score (D1 – D0; see (b) for the gene set used) within each cell subset for HC-F (n=8), COVR-F (n=12), and HC-M (n=8), COVR-M (n=12). Darker color indicates a greater difference between D1 and D0 for the indicated cell subset.

e, Similar to (b), but for the indicated cell subsets (computed using the CITE-seq pseudobulk mRNA expression data for the cell subset) in HC-F (n=8), COVR-F (n=12), HC-M (n=8) and COVR-M (n=12). cDC = conventional/myeloid dendritic cells.

f, (left) Box plot showing the D1 transcriptional response score (D1 – D0) of the antigen presentation related genes in classical monocytes for the same subjects in (e) (see Methods). (right) Bubble plot showing the averaged expression of individual leading-edge genes (LEGs) from the antigen presentation genes (see Methods) in classical monocytes.

g, Influenza-specific plasmablast (PB; All HA+ CD27+CD38+CD20^lowCD21^low; see Methods and Supplementary Fig. 3) frequencies at D7 and D0, plotted separately for COVR-F (n=14), HC-F (n=15), COVR-M (n=11), and HC-M (n=9). Lines connect data points from the same subject at D0 and D7.

h, Analysis of the D28/D0 microneutralization titer fold-change (FC) for each of the four strains in the seasonal influenza vaccine (columns) in COVR-F and HC-F. Each dot represents one individual. The orange and grey lines indicate the average fold change for the HC-F and COVR-F, respectively. Unadjusted p values are derived from generalized linear models accounting for age, race, influenza vaccination history and baseline influenza titers (see Methods).

i, Similar to (h), but for COVR-M and HC-M.

All box plots show the median, first and third quantiles (lower and upper hinges) and smallest (lower hinge – 1.5× interquartile range (IQR)) and largest (upper hinge + 1.5× IQR) values (lower and upper whiskers). Unadjusted p values are shown. Unless otherwise noted, statistical significance of difference between groups is determined by two-tailed Wilcoxon test.