Early antiviral CD4+ and CD8+ T cells are associated with upper airway clearance of SARS-CoV-2

Abstract

T cells are involved in protective immunity against numerous viral infections. Data regarding functional roles of human T cells in SARS-CoV-2 (SARS2) viral clearance in primary COVID-19 are limited. To address this knowledge gap, we assessed samples for associations between SARS2 upper respiratory tract viral RNA levels and early virus-specific adaptive immune responses for 95 unvaccinated clinical trial participants with acute primary COVID-19 aged 18-86 years old, approximately half of whom were considered at high risk for progression to severe COVID-19. Functionality and magnitude of acute SARS2-specific CD4+ and CD8+ T cell responses were evaluated, in addition to antibody responses. Most individuals with acute COVID-19 developed SARS2-specific T cell responses within 6 days of COVID-19 symptom onset. Early CD4+ T cell and CD8+ T cell responses were polyfunctional, and both strongly associated with reduced upper respiratory tract SARS2 viral RNA, independent of neutralizing antibody titers. Overall, these findings provide evidence for protective roles for circulating SARS2-specific CD4+ and CD8+ T cells during acute COVID-19.

Keywords: Adaptive immunity; Cellular immune response; Immunology; Infectious disease; T cells.

Figure 1. SARS2 NP RNA levels during acute COVID-19 and longitudinally.

(A) Median days post-symptom onset (PSO) from start of COVID-19 symptoms to study entry (study day 0) for all participants. (B) SARS-CoV-2 NP RNA by quantitative reverse transcription polymerase chain reaction for all participants prior to treatment on study day 0. Dotted black line shows limit of detection (LOD). Dotted red line shows limit of quantification (LOQ). Values > LOQ were considered positive. Bar = median. (C) Longitudinal SARS-CoV-2 NP RNA data for the placebo group (n = 49) for study days 0, 7, 14, and 28. Median for each time point in red.

Figure 2. Antigen-specific CD4⁺ T cell responses to primary SARS2 infection and acute COVID-19.

(A and B) Representative flow cytometry plots and frequency of SARS2-specific CD4⁺ T cells to DMSO (negative control), S, and CD4-RE MP stimulation conditions (Combined = sum of S + CD4-RE responses; see Methods for additional details) by (A) AIM using surface OX40 and 41BB coexpression and (B) IFN-γ ICS among surface CD40L⁺ cells. (C–E) Study day 0 SARS2-specific CD4⁺ T cell intracellular cytokine production of (C) GzmB, (D) TNF, or (E) IL-2 among surface CD40L⁺ cells. (F) Parts of a whole donut plot summary of intracellular cytokine (IFN-γ, GzmB, TNF, IL-2) production by SARS2-specific CD4⁺ T cells expressing 0 to 4 cytokines. (G and H) As in A and Supplemental Figure 2B but for SARS2-specific circulating Tfh cells (cTfh). Flow cytometry gates display frequency (%). Bars = geometric mean. Dotted lines = LOQ.

Figure 3. Antigen-specific CD8⁺ T cell responses to primary SARS2 infection and acute COVID-19.

(A) Representative flow cytometry plots and frequency of SARS2-specific CD8⁺ T cells to DMSO (negative control), S, and CD8-RE MP stimulation conditions (Combined = sum of S + CD8-RE responses; see Methods for additional details) by IFN-γ⁺ ICS among CD69⁺ cells. (B–D) Production of (B) IFN-γ and GzmB, (C) TNF, and (D) IL-2. (E) Parts of a whole donut plot summary of intracellular cytokine (IFN-γ, GzmB, TNF, IL-2) production by SARS2-specific CD8⁺ T cells expressing 0 to 4 cytokines. Flow cytometry gates display frequency (%). Bars = geometric mean. Dotted lines = LOQ.

Figure 4. Longitudinal SARS2-specific T cell responses and Ab responses to primary SARS2 infection and acute COVID-19.

(A–C) Longitudinal combined (S plus non-S) (A) CD4⁺ AIM, (B) CD4⁺ AIM+ICS, and (C) CD8⁺ IFN-γ⁺ T cell responses in placebo group (n = 49) participants at study days 0, 7, and 28. Red dots and lines represent median. Dotted line = LOQ. (D) Study day 0 pretreatment nAb titers for all participants. Dotted black line indicates LOD; seropositivity defined by values > LOD. Bar is median. nAb, neutralizing antibody. (E) Study day 0 pretreatment RBD IgG binding titers for all participants. Dotted black line indicates cutoff for seropositivity. Bar is geometric mean titer.

Figure 5. Correlative relationships between SARS2-specific adaptive immunity and upper airway viral RNA in acute COVID-19.

(A–D) Relationships between study day 0 SARS2 NP RNA and combined day 0 SARS2-specific T cell responses by (A) CD4⁺AIM⁺, (B) CD4⁺IFN-γ⁺, (C) CD8⁺IFN-γ⁺, and (D) nAb titers.