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SARS-CoV-2: T cell vaccine could offer protection against new variants of and SARS-like coronaviruses

Gaurav Gaiha, MD, DPhil, a member of the Ragon Institute of MGH, MIT and Harvard, studies HIV, one of the fastest-mutating viruses known to humankind. But HIV’s ability to mutate isn’t unique among RNA viruses – most viruses develop mutations, or changes in their genetic code, over time.

If a virus is disease-causing, the right mutation can allow the virus to escape the immune response by changing the viral pieces the immune system uses to recognize the virus as a threat, pieces scientists call epitopes.

To combat HIV’s high rate of mutation, Gaiha and Elizabeth Rossin, MD, Ph.D., a Retina Fellow at Massachusetts Eye and Ear, a member of Mass General Brigham, developed an approach known as structure-based network analysis. With this, they can identify viral pieces that are constrained, or restricted, from mutation.

Changes in mutationally constrained epitopes are rare, as they can cause the virus to lose its ability to infect and replicate, essentially rendering it unable to propagate itself.

When the pandemic began, Gaiha immediately recognized an opportunity to apply the principles of HIV structure-based network analysis to SARS-CoV-2, the virus that causes COVID-19. He and his team reasoned that the virus would likely mutate, potentially in ways that would allow it to escape both natural and vaccine-induced immunity.

Using this approach, the team identified mutationally constrained SARS-CoV-2 epitopes that can be recognized by immune cells known as T cells.

These epitopes could then be used in a vaccine to train T cells, providing protective immunity. Recently published in Cell, this work highlights the possibility of a T cell vaccine which could offer broad protection against new and emerging variants of SARS-CoV-2 and other SARS-like coronaviruses.

From the earliest stages of the COVID-19 pandemic, the team knew it was imperative to prepare against potential future mutations. Other labs already had published the protein structures (blueprints) of roughly 40% of the SARS-CoV-2 virus, and studies indicated that patients with a robust T cell response, specifically a CD8+ T cell response, were more likely to survive COVID-19 infection.

Gaiha’s team knew these insights could be combined with their unique approach: the network analysis platform to identify mutationally constrained epitopes and an assay they had just developed, a report on which is currently in press at Cell Reports, to identify epitopes that were successfully targeted by CD8+ T cells in HIV-infected individuals.

Applying these advances to the SARS-CoV-2 virus, they identified 311 highly networked epitopes in SARS-CoV-2 likely to be both mutationally constrained and recognized by CD8+ T cells.

“These highly networked viral epitopes are connected to many other viral parts, which likely provides a form of stability to the virus,” says Anusha Nathan, a medical student in the Harvard-MIT Health Sciences and Technology program and co-first author of the study. “Therefore, the virus is unlikely to tolerate any structural changes in these highly networked areas, making them resistant to mutations.”

You can think of a virus’s structure like the design of a house, explains Nathan. The stability of a house depends on a few vital elements, like support beams and a foundation, which connect to and support the rest of the house’s structure. It is therefore possible to change the shape or size of features like doors and windows without endangering the house itself.

Changes to structural elements, like support beams, however, are far riskier. In biological terms, these support beams would be mutationally constrained – any significant changes to size or shape would risk the structural integrity of the house and could easily lead to its collapse.

Highly networked epitopes in a virus function as support beams, connecting to many other parts of the virus. Mutations in such epitopes can risk the virus’s ability to infect, replicate, and ultimately survive. These highly networked epitopes, therefore, are often identical, or nearly identical, across different viral variants and even across closely related viruses in the same family, making them an ideal vaccine target.

The team studied the identified 311 epitopes to find which were both present in large amounts and likely to be recognized by the vast majority of human immune systems. They ended up with 53 epitopes, each of which represents a potential target for a broadly protective T cell vaccine.

Since patients who have recovered from COVID-19 infection have a T cell response, the team was able to verify their work by seeing if their epitopes were the same as ones that had provoked a T cell response in patients who had recovered from COVID-19. Half of the recovered COVID-19 patients studied had T cell responses to highly networked epitopes identified by the research team.

This confirmed that the epitopes identified were capable of inducing an immune reaction, making them promising candidates for use in vaccines.

“A T cell vaccine that effectively targets these highly networked epitopes,” says Rossin, who is also a co-first author of the study, “would potentially be able to provide long-lasting protection against multiple variants of SARS-CoV-2, including future variants.”

By this time, it was February 2021, more than a year into the pandemic, and new variants of concern were showing up across the globe. If the team’s predictions about SARS-CoV-2 were correct, these variants of concerns should have had little to no mutations in the highly networked epitopes they had identified.

The team obtained sequences from the newly circulating B.1.1.7 Alpha, B.1.351 Beta, P1 Gamma, and B.1.617.2 Delta SARS-CoV-2 variants of concern. They compared these sequences with the original SARS-CoV-2 genome, cross-checking the genetic changes against their highly networked epitopes. Remarkably, of all the mutations they identified, only three mutations were found to affect highly networked epitopes sequences, and none of the changes affected the ability of these epitopes to interact with the immune system.

“Initially, it was all prediction,” says Gaiha, an investigator in the MGH Division of Gastroenterology and senior author of the study. “But when we compared our network scores with sequences from the variants of concern and the composite of circulating variants, it was like nature was confirming our predictions.”

In the same time period, mRNA vaccines were being deployed and immune responses to those vaccines were being studied. While the vaccines induce a strong and effective antibody response, Gaiha’s group determined they had a much smaller T cell response against highly networked epitopes compared to patients who had recovered from COVID-19 infections.

While the current vaccines provide strong protection against COVID-19, Gaiha explains, it’s unclear if they will continue to provide equally strong protection as more and more variants of concern begin to circulate. This study, however, shows that it may be possible to develop a broadly protective T cell vaccine that can protect against the variants of concern, such as the Delta variant, and potentially even extend protection to future SARS-CoV-2 variants and similar coronaviruses that may emerge.


SARS-CoV-2 vaccines have largely focused on generation of B cell responses to trigger production of neutralizing antibodies [1,2,3]. SARS-CoV-2 enters cells through interaction of the viral receptor binding domain (RBD) with angiotensin-converting enzyme 2 (ACE2) receptors, found on the surface of human nasopharyngeal, lung, and gut mucosa [4].

Neutralizing antibodies targeting the RBD and other functional domains of the SARS-CoV-2 spike protein are a major route for achieving immunity and vaccine efficacy [5,6,7,8,9,10]. When work on this study began in March 2020, little was known about the relative contribution of different adaptive immune compartments to immunity against SARS-CoV-2.

Broadly, it was understood that CD4+ and CD8+ T cells have roles in the antiviral immune response, including against SARS-CoV-1 [11,12,13]. Prior studies in SARS-CoV-1 have demonstrated T cell responses against viral epitopes, with strong T cell responses correlated with generation of higher neutralizing antibody titers [13]. Unlike antibody epitopes, T cell epitopes need not be limited to accessible regions of surface proteins.

In SARS-CoV-1, concurrent CD4+ and CD8+ activation and central memory T cell generation were induced in exposed patients, with increased Th2 cytokine polarization observed in patients with fatal disease [13]; conversely, Th1 response has been associated with less severe disease in SARS-CoV-2 [14]. Additionally, Type 1 and Type 2 immunity are not strictly synonymous with cell-mediated and humoral immunity, respectively, with Th1 polarization capable of inducing moderate antibody production [15].

Because of these considerations, most groups developing vaccines for SARS-CoV-2 have focused on promoting Th1 response due to safety concerns and demonstrated efficacy of Th1 response [16]. To this end, we deduced that vaccines targeting humoral (B cells) and cytotoxic arms (CD8+ T cells) with concurrent helper signalling (CD4+ T cells), delivered with adjuvants promoting Th1 polarization, may provide optimal immunity against SARS-CoV-2.

In the intervening year, many vaccine strategies for SARS-CoV-2 have demonstrated efficacy in clinical trials, including mRNA encoding of the spike glycoprotein, recombinant spike protein, adenovirus vector expressing the surface glycoprotein, as well as delivery of whole inactivated virus [2, 3, 17,18,19,20,21,22,23,24,25].

These strategies have proven successful at eliciting neutralizing antibody responses against conformational epitopes [26] and offer impressive protection from both infection and disease [22, 23, 27, 28]. More recently, however, concern has emerged regarding the rapid evolution [29, 30] of the virus with concomitant decrease or loss of neutralization from some novel variants [31,32,33].

Currently circulating variants, however, do not appear to abrogate T cell reactivity [34] and there is hope that vaccine induced T cell responses provide a second line of defense against viral infection [35, 36]. Whether future variants would also be recognized by T cell evolutionary pressure to escape T cell responses is unclear. Multi-epitope peptide vaccination is an alternative approach which targets smaller antigenic fragments of viral proteins.

Peptide vaccines have historically been most successful at eliciting T cell responses [37,38,39,40] and, in certain pathogens, they have also been able to elicit neutralizing antibodies against linear epitopes [41,42,43,44]. Peptide vaccines may have a complementary role relative to existing SARS-CoV-2 vaccines due to their history of safe administration [45,46,47,48], rapid development [49, 50], and precise selection of antigenic content. A peptide vaccine can easily exclude polymorphic antigenic regions or be updated to include antigenic fragments from newly emerging variants.

We report here a design methodology for selecting SARS-CoV-2 vaccine peptides which combines linear B cell epitopes with both CD4+ and CD8+ T cell epitopes, as well as an evaluation of our strategy based on a murine vaccination study and a comparison with a curated dataset of published SARS-CoV-2 T cell epitopes (Fig. 1).

We start with a survey of the T and B cell epitope space of SARS-CoV-2 (Fig. 2). Predicted T cell epitopes were derived from in silico predictions filtered on binding affinity and immunogenicity models generated from epitopes deposited in the Immune Epitope Database (IEDB) [51], population diversity, and source protein abundance in order to select peptides that bind common HLA alleles and are likely to generate robust CD8+ and CD4+ T cell activity.

B cell epitope candidates were curated from linear epitope mapping studies and further filtered by accessibility, glycosylation, polymorphism, and adjacency to functional domains to identify peptides most likely to generate robust antibody responses. Given the utility of murine-adapted SARS-CoV-2 models for evaluating vaccine candidates [7, 52,53,54], we also identified peptides derived from viral proteins predicted to bind murine MHC coded for by H2-Db/d, H2-Kb/d, and H2-IAb/d haplotypes.

We then selected 22 longer sequence regions for use as vaccine antigens. These vaccine peptides each span multiple predicted CD4+/CD8+ T cell and linear B cell epitopes, along with predicted murine MHC-I/II ligands. We compared this vaccine peptide selection process with a curated dataset of eight studies mapping SARS-CoV-2 T cell epitopes from COVID-19 patients and found that many of the recurrent epitope regions were captured by our vaccine peptides.

We also evaluated 16 of the 22 vaccine peptides in a murine vaccination experiment and found that the same subset of the peptides elicited T cell responses in combination with two different adjuvants.

figure1
Visual summary of T and B cell epitope vaccine prediction and validation. (1) We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining source protein abundance, sequence conservation, coverage of high frequency HLA alleles, and predicted immunogenicity. (2) B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for sequence conservation, surface accessibility, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. (3) Vaccine selection of 27mers peptides was performed by optimizing population HLA coverage of T cell epitopes, evaluating human/murine MHC ligand co-coverage, as well as examining peptides with optimal coverage of B cell, CD4+, and CD8+ epitopes. (4) Lastly, validation was performed through comparison against a curated dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, as well as murine ELISA/ELISpot studies using animals vaccinated with synthetic 27mer peptides with human/murine epitope co-coverage
figure2
Summary of B cell and CD4+/CD8+ epitope prediction workflows. Pathways are colored by B cell (blue), human T cell (black), and murine T cell (red) epitope prediction workflows. Color bars represent proportions of epitopes derived from internal proteins (ORF), nucleocapsid phosphoprotein, and surface-exposed proteins (spike, membrane, envelope)

reference link : https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00910-1


More information: Anusha Nathan et al, Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses, Cell (2021). DOI: 10.1016/j.cell.2021.06.029

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