To understand immune evasion of emerging variants and vaccine responses, researchers need to go beyond the antibody response and study the T-cell immune response to SARS-CoV-2.
T cells generate immune responses to various regions of the SARS-CoV-2 virus, providing a more comprehensive understanding of the immune response in COVID-19. (1) Because T cells generate a robust and diverse response to multiple regions of the SARS-CoV-2 virus, T-cell-based detection methods may be able to detect immune responses to conserved regions in emerging variants (Figure 1). (2,3)
Figure 1. T-cell and antibody responses to SARS-CoV-2 proteins. CD4+ and CD8+ T cells can respond to SARS-CoV-2 antigens across the proteome, while antibody responses are limited to structural proteins. Adapted from Jarjour et al. (1)
The immunoSEQ® T-MAP™ COVID offering can help researchers identify and study the T-cell immune responses elicited by variants, the T-cell response to vaccines (and to which SARS-CoV-2 epitopes), as well as assess past T-cell immune response to SARS-CoV-2 with a simple positive/negative output.
In a previous article, we explained how to use immunoSEQ T-MAP COVID to monitor the T-cell response in COVID-19. With immunoSEQ T-MAP COVID, researchers can access the underlying technology that powers the first and only T-cell-based clinical test for COVID-19 to receive emergency use authorization (EUA). Such powerful, quantitative, and sequence-level insights cannot be determined using antibody-based methods or ELISpot.
T-cell responses play a critical role in clearing SARS-CoV-2 infection
The adaptive immune response, and in particular the T-cell response, plays a crucial role in clearing viral infections, including influenza viruses and SARS-CoV. (4–6) T-cell responses are an essential component of the coordinated immune response to SARS-CoV-2. (7–13) In one study, 85% of patients with severe COVID-19 had lymphopenia. (14)
Differences in the severity of disease among people with COVID-19 may be due to differences in the T-cell response. Around 20–50% of unexposed donors display significant reactivity to SARS-CoV-2 antigens. (11,15) One study found that 81% of unexposed individuals had pre-existing T-cell responses to SARS-CoV-2 antigens. (16) Pre-existing memory CD4+ T cells are cross-reactive against SARS-CoV-2 and other coronaviruses that cause the common cold. (17) This cross-reactive memory T-cell response may help explain differences in the severity of the disease among people with COVID-19 and provides the basis for heterologous immunity to SARS-CoV-2. (1,16,17)
In the coordinated immune response to SARS-CoV-2, pro-inflammatory cytokines attract T cells to sites of viral infection and the adaptive immune system mounts a robust and diverse response against viral antigens. (7–12) Natural killer cells and cytotoxic CD8+ T cells can kill virus-infected cells. (2,14) Follicular helper T cells and CD4+ T cells help establish the B-cell and antibody responses. (2,14)
Antibodies are produced by specialized B cells called plasma cells. They function by binding to an epitope on a pathogen and either neutralize the pathogen by blocking its function or tag the pathogen for destruction by the immune system. One goal of SARS-CoV-2 vaccines is to elicit neutralizing antibodies (nAbs) against the virus. (3)
In studies comparing the T-cell response with nAb titers, the breadth and depth of T-cell clonality, particularly helper CD4+ T cells to viral antigens from the spike protein, strongly correlated with nAb titer. (18,19) This relationship indicates that detecting the T-cell response is an effective surrogate for protective immunity. (18,19) However, 68% of samples with no detectable nAb titers and 37% of samples with no detectable antibodies had detectable T-cell signatures. (18)
SARS-CoV-2 variants of concern
The emergence of SARS-CoV-2 variants of concern has made it even more important to understand the SARS-CoV-2 interactions with the adaptive immune system. The major SARS-CoV-2 variants that are associated with increased transmission all contain one or more mutations in the spike (S) gene (Figure 2).
One such variant contains an S protein mutation, D614G, in the carboxy (C)-terminal region of the S1 domain. (20) The 501Y.V1 (B.1.1.7) variant identified in the UK contains three mutations within the S protein: N501Y, which is one of six key contact residues within the receptor-binding domain (RBD), the spike (S) deletion 69-70del, and P681H, which is adjacent to the furin cleavage site. (21) The 501Y.V2 (B.1.351) variant identified in South Africa contains eight mutations in the spike protein, including three at important residues in the RBD (K417N, E484K, and N501Y). (22) The 501Y.V3 (P.1) variant identified in individuals from Brazil contains 12 mutations in the S protein, including K417T, E484K, and N501Y. (23) The B.1.617 variant identified in India contains seven mutations within the S protein, including the key mutations L452R and E484Q. (24)
SARS-CoV-2 variants of concern are associated with higher transmission rates and possibly higher viral loads, but research is still ongoing to determine if they are associated with increased disease severity.
Figure 2. SARS-CoV-2 variants. Emerging variants of concern have mutations located within the spike protein, in addition to other mutations within the viral genome. Adapted from Zhang et al., Rambaut et al., Tegally et al., and Toovey et al., (20–23)
Comparing T-cell responses to neutralizing antibody responses in SARS-CoV-2 variants
Since SARS-CoV-2 variants harbor mutations in the viral spike (S) protein that may alter virus–host cell interactions and confer resistance to inhibitors and antibodies, comparing the nAb response with the T-cell response is important. Multiple studies show that nAb responses are reduced against SARS-CoV-2 variants and that vaccine cross-neutralization is poor, especially towards the B.1.351 (South Africa) variant. (25,26) One study observed that therapeutic antibodies might provide incomplete or no protection against the B.1.351 and P.1 variants. (25)
In one study, individuals were vaccinated with one or two doses of mRNA vaccines and serum samples were analyzed against 10 circulating variants of SARS-CoV-2. (26) Results showed that P.1 and B.1.351 exhibit limited antibody neutralization. Cross-neutralization of B.1.351 variants was comparable to more distantly related coronaviruses, suggesting that only a relatively small number of mutations are required to escape nAb responses. Mutations both within and outside the RBD were able to mediate nAb escape. (26)
However, an analysis of CD4+ and CD8+ T-cell responses against the ancestral strain of SARS-CoV-2, multiple variants, and Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) COVID-19 vaccines showed that SARS-CoV-2 T-cell epitopes were not affected by variants. (27)
In another study, results showed that CD8+ T-cell responses from 30 COVID-19 convalescent individuals could potentially maintain recognition of the major SARS-CoV-2 variants. (28) Out of 45 mapped variant mutations, only one fell within an epitope recognized by CD8+ T cells. (28)
In a study of the ChADOx1 vaccine against the B.1.351 variant, of 13 vaccine recipients with no evidence of previous SARS-CoV-2 infection before or during follow-up, 7 out of 12 (58%) participants with nAb activity against B.1.1 had undetectable nAbs against the B.1.351 variant. (29)
Peripheral blood mononuclear cells (PBMCs) from 17 recipients of the ChADOx1 vaccine in the UK were evaluated with TCRβ sequencing with the immunoSEQ® Assay. Expansion of both CD4+ and CD8+ T-cells was observed. (29) Although the correlation between antibody response and vaccine efficacy is high, suggesting that the nAb response is important, T-cell responses may contribute to protection from COVID-19 even in the presence of lower levels of nAb titers. (29)
Figure 3. The immune response to SARS-CoV-2 and variants of concern. Follicular helper T cells and CD4+ T cells help establish the B-cell and antibody response, including nAbs. Evidence suggests that relatively few mutations allow SARS-CoV-2 variants to escape the nAb response, but the T-cell response to SARS-CoV-2 variants remains consistently high. Adapted from Cox et al., Yadav et al., Hoffmann et al., Garcia-Beltran et al., Tarke, et al., Redd et al., and Madhi, et al., Stephens et al. (2,24–30)
In a study of the Ad26.COV2.S vaccine against variants of concern, it was observed that nAb responses elicited by the Ad26.COV2.S vaccine were 5.0-fold lower against B.1.351 and 3.3-fold lower against the P.1 variant than against the original WA1/2020 strain (Figure 4). (31) The study showed that while nAb responses were reduced, non-nAb responses and CD4+ and CD8+ T-cell responses were largely preserved, indicating the possibility that functional non-nAbs and/or CD8+ T-cell responses may also contribute to protection. (31)
Figure 4. SARS-CoV-2 pseudovirus nAb (psVNA) responses against WA1/2020, D614G, B.1.1.7, CAL.20C, P.1, and B.1.351. The nAb responses to SARS-CoV-2 variants in placebo vs. Ad26.COV2.S-vaccinated samples at Day 57 post-vaccination and Day 71 post-vaccination.
In the Ad26.COV2.S vaccine study, researchers used the immunoSEQ® Assay for CDR3 sequencing of TCRβ chains and the immunoSEQ T-MAP COVID offering to assess the T-cell repertoire and T-cell immune response map to COVID-19. They observed an increase in spike-specific T-cell breadth and depth in vaccinated samples compared with controls. The breadth of non-spike TCRs was comparable in vaccine recipients and controls, which was expected because the Ad26.COV2.S vaccine did not contain any non-spike immunogens (Figure 5).
Figure 5. TCRβ repertoire analysis. Spike and non-Spike T-cell breadth by TCRβ Sequencing (immunoSEQ Assay) on day 63.
This T-cell immune response was further investigated using the immunoSEQ T-MAP COVID tool and the study showed that Ad26.COV2.S elicited a broad CD4+ and CD8+ T-cell immune response to multiple epitopes. When the T-cell immune response elicited by the Ad26.COV2.S vaccine was mapped against regions where mutations occur in variants of concern (Figure 6), there are regions where a CD4+ and CD8+ T-cell immune response is observed to regions of the virus that are not affected in variants, meaning in regions that remain conserved even in emerging variants.
It was observed that most public CD8+ T-cell responses observed are against a.a. 265–277 of spike regions and most public CD4+ T-cell responses observed are against a.a. 160–218 of spike regions – both regions that are not affected in the emerging variants (B.1.1.7, B.1.351*, P.1, and CAL.20C). This indicates that the T-cell responses elicited by the Ad26.COV2.S vaccine may still be able to detect studied variants of concern. Additional studies are needed to confirm this finding and investigate the T-cell immune response against variants of concern, but this study provides insights into the T-cell immune response post-vaccination and indicates that although the nAb response is reduced, vaccination still elicits a strong and broad immune response from CD4+ and CD8+ T-cells, which are the first responders of the adaptive immune system and activate the antibody response.
Figure 6. T-cell immune response elicited by Ad26.COV2.S, as investigated using the immunoSEQ T-MAP COVID offering. The T-cell responses were overlaid with regions of the spike protein that are affected in the B.1.351 (SA) variant and the B.1.1.7 (UK) variant. Red boxes mark the most public CD8+ (a.a. 265–277) and CD4+ T-cell responses (a.a. 160–218) of the spike regions. *Note: CD4+ T-cell response may be affected by the D215G mutation in the B.1.351 variant.
Overall, early T-cell immune response data from the Alter et al. study (31) that looks at the Johnson & Johnson (Ad26.COV2.S) COVID-19 vaccine and the Tarke et al. study (27) that assesses the Moderna (mRNA-1273) and Pfizer/BioNTech (BNT162b2) COVID-19 vaccines indicates that T-cell immune responses are elicited to conserved regions of the SARS-CoV-2 virus and that these responses are broad to multiple epitopes/regions of the virus. Even though the correlation between antibody response and vaccine efficacy is high, which suggests that the nAb response is important, T-cell responses may contribute to protection from COVID-19 even in the presence of lower nAb titers. In a study by Geer et al. (32), researchers stimulated PBMCs from BNT162b2 mRNA-vaccinated healthcare workers with peptide pools spanning the mutated S regions of B.1.1.7 and B.1.351. They observed no differences in CD4+ T-cell activation in response to variant antigens, indicating that the B.1.1.7 and B.1.351 S proteins do not escape T-cell-mediated immunity elicited by the vaccines. It is critical for us to better study and understand the vaccine-elicited T-cell immune response as well as investigate if/how a vaccine-elicited T-cell immune response differs from natural responses against these emerging SARS-CoV-2 variants of concern.
Continuing research is needed to understand vaccine immune responses and study the long-term implications of COVID-19, impact on immunosuppressed patients, neurological impact, as well as role in autoimmune diseases. (33–35) Understanding the differences in transmission of evolving variants, their interaction with the host immune system, and the role of T-cell responses will be crucial to guide global public policy decisions and improve drug development and vaccine research. (36)
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