Heterotypic immunity from prior SARS-CoV-2 infection but not COVID-19 vaccination associates with lower endemic coronavirus incidence

Abstract

Immune responses from prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and COVID-19 vaccination mitigate disease severity, but they do not fully prevent subsequent infections, especially from genetically divergent strains. We examined the incidence of and immune differences against human endemic coronaviruses (eCoVs) as a proxy for response against future genetically heterologous coronaviruses (CoVs). We assessed differences in symptomatic eCoV and non-CoV respiratory disease incidence among those with known prior SARS-CoV-2 infection or previous COVID-19 vaccination but no documented SARS-CoV-2 infection or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not previous COVID-19 vaccination alone, associates with a lower incidence of subsequent symptomatic eCoV infection. There was no difference in non-CoV incidence, implying that the observed difference was eCoV specific. In a second cohort where both cellular and humoral immunity were measured, those with prior SARS-CoV-2 spike protein exposure had lower eCoV-directed neutralizing antibodies, suggesting that neutralization is not responsible for the observed decreased eCoV disease. The three groups had similar cellular responses against the eCoV spike protein and nucleocapsid antigens. However, CD8⁺ T cell responses to the nonstructural eCoV proteins nsp12 and nsp13 were higher in individuals with previous SARS-CoV-2 infection as compared with the other groups. This association between prior SARS-CoV-2 infection and decreased incidence of eCoV disease may therefore be due to a boost in CD8⁺ T cell responses against eCoV nsp12 and nsp13, suggesting that incorporation of nonstructural viral antigens in a future pan-CoV vaccine may improve vaccine efficacy.

Fig. 1.. Overall study design used in the investigation.

(A) Black arrows detail the grouping and analysis for the incidence of respiratory infections at BMC. (B) Red arrows detail the recruitment and grouping of individuals for the ex vivo assessment of CoV-specific immunity.

Fig. 2.. Previous SARS-CoV-2 infection is associated with lower incidence of symptomatic eCoV infections.

(A and B) Shown are Kaplan Meier plots for eCoV (A) and non-CoV (B) in those with no prior documented SARS-CoV-2 antigen exposure (teal), prior COVID-19 vaccination but no known SARS-CoV-2 infection (pink), and prior SARS-CoV-2 infection (black). Plots show unadjusted analyses with number of individuals at risk in each group at the bottom. Time to event analysis was performed using a log-rank test. (C and D) Shown are HRs of eCoV (C) and non-CoV (D) incidence in time-varying adjusted models. The figures show the covariates that had a P value ≤0.1 in the multivariable Cox-proportional hazard model. No prior documented SARS-CoV-2 antigen exposure group is the reference category. The horizontal lines indicate the HR for each variable along with the 95% confidence interval, and the vertical dotted line indicates an HR of 1.0. **** represent P values <0.0001.

Fig. 3.. Ex vivo immune responses to SARS-CoV-2 antigens differentiate individuals with different SARS-CoV-2 immune histories.

(A to F) Shown are antibody (A and B) and cellular responses (C to F) against SARS-CoV-2 spike protein (A, D, and E) and SARS-CoV-2 nucleocapsid (B, D, and E) in those with no prior SARS-CoV-2 exposure (teal), prior COVID-19 vaccination but no SARS-CoV-2 infection (pink), and prior documented SARS-CoV-2 infection (black). (A and B) SARS-CoV-2 IgG was calculated on the basis of the average enzyme per bead (AEB) against RBD (A) or nucleocapsid (B) measured using Simoa detection system. Statistical analyses were performed using a Kruskal-Wallis test with Dunn multiple comparison test. (C to F) Shown are results of AIM assays with SARS-CoV-2 spike protein (C and D) or SARS-CoV-2 nucleocapsid (E and F) peptide pools. T cell activation was measured on CD4⁺ (CD134⁺ CD137⁺) (C and E) and CD8⁺ (CD69⁺ CD137⁺) (D and F) T cells by flow cytometry. Data were background subtracted against the negative control (DMSO only). The dark horizontal lines in each scatter dot plot denote the median and interquartile range. Statistical analyses were performed using a Kruskal-Wallis test with Dunn multiple comparison test. (G) The antibody and T cell responses against SARS-CoV-2 (A to F) were log transformed and combined to create a spike protein and nucleocapsid protein index. The dotted lines represent the cutoff values to best differentiate the groups. (H) Accuracy and 95% confidence intervals of clinical classifications based on SARS-CoV-2 spike protein (SP) and nucleocapsid protein (NP) immunity index values from (H). **, ***, and **** represent P values <0.01, <0.001, and <0.0001, respectively.

Fig. 4.. Prior SARS-CoV-2 spike protein exposure associates with more HCoV-OC43 nonneutralizing antibodies.

AUC (A to F) and spike protein–binding (G and H) antibody responses to various CoV spike proteins in those with no prior SARS-CoV-2 exposure (teal), prior COVID-19 vaccination but no SARS-CoV-2 infection (pink), and prior documented SARS-CoV-2 infection but no COVID-19 vaccination (black). (A and B) Neutralization responses against pseudoviruses expressing SARS-CoV-2 spike protein are shown for groups categorized by type of exposure (infection versus vaccination) (A) or with any exposure combined (B). (C and D) Neutralization responses against pseudoviruses expressing HCoV-OC43 spike protein are shown for groups categorized by type of exposure (infection versus vaccination) (C) or with any exposure combined (D). (E and F) Neutralization responses against pseudoviruses expressing HCoV-229E spike protein are shown for groups categorized by type of exposure (infection versus vaccination) (E) or with any exposure combined (F). (G and H) HCoV-OC43 (G) and HCoV-229E (H) spike protein–binding IgG antibody titers were measured by ELISA. (I and J) Ratios of HCoV-OC43 spike protein neutralization to binding antibodies are shown for groups categorized by type of exposure (infection versus vaccination) (I) or with any exposure combined (J). Black borders represent the eight individuals identified as potentially having prior asymptomatic SARS-CoV-2 infection. The dark horizontal lines denote the median and interquartile range. Statistical analyses were performed using either Kruskal-Wallis test with Dunn multiple comparison test (A, C, E, G, H, and I) or Mann-Whitney U test (B, D, F, and J). * represents P values <0.05.

Fig. 5.. Prior SARS-CoV-2 infection associates with elevated CD8⁺ T cell responses to HCoV-OC43 nonstructural proteins.

(A to G) The percentage of activated CD4⁺ and CD8⁺ T cells was measured by flow cytometry in response to various HCoV-OC43 proteins in those with no prior SARS-CoV-2 exposure (teal), prior COVID-19 vaccination but no SARS-CoV-2 infection (pink), and prior documented SARS-CoV-2 infection (black). (A and B) PBMCs were stimulated with peptides from HCoV-OC43 spike protein, and CD4⁺ (A) or CD8⁺ (B) T cell responses were measured. (C and D) PBMCs were stimulated with peptides from HCoV-OC43 nucleocapsid protein, and CD4⁺ (C) or CD8⁺ (D) T cell responses were measured. (E and F) PBMCs were stimulated with peptides from HCoV-OC43 nsp12 and nsp13 proteins, and CD4⁺ (E) or CD8⁺ (F) T cell responses were measured. (G) As in (F), but groups are categorized according to those with and without documented SARS-CoV-2 infection. Black borders represent the eight individuals identified as potentially having prior undocumented or asymptomatic SARS-CoV-2 infection. Data were background subtracted against the negative control (DMSO only). The dark horizontal lines in each scatter dot plot denote the median and interquartile range. Note, the y axis varies among the different panels. Statistical analyses were performed using either Kruskal-Wallis test with Dunn multiple comparison test (A to F) or Mann-Whitney U test (G). *** represents P values <0.001.