Peptide-based vaccine fails to protect mice against SARS-CoV-2 despite T cell response

A recent study posted to the bioRxiv* preprint server observed that peptide-based vaccination against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) failed to protect mice against coronavirus disease 2019 (COVID-19), albeit eliciting T cell responses.

Background

T cell immunity plays a critical role in virus clearance in COVID-19 patients, as supported by various studies on convalescent patients. CD4+ T lymphocytes are implicated in mediating antibody responses; nonetheless, the role of T cells independent of B lymphocytes remains poorly understood.

Synthetic peptides (antigens) are often used as vaccines for pathogens like dengue virus (DENV), human immunodeficiency virus (HIV), and foot-and-mouth disease virus (FMDV). However, these vaccines cannot induce significant neutralizing antibodies unless the target is highly conserved.

Moreover, peptide-based vaccines require additional modifications or conjugation with carriers to improve their conformational stability and valency. However, the elicitation of T cell responses with peptide vaccines is simple, and therefore, peptide vaccines are being explored for cancer vaccination.

Despite its therapeutic potential, T cell-directed peptide vaccines are infrequently used, and the knowledge of and experience with these vaccines are limited than those designed for inducing antibody responses.

The study

In the present study, researchers tested the ability of a peptide-based vaccine in mice to protect against COVID-19 infection or disease upon following challenge with a mouse-adapted virus (SARS-CoV-2-MA10). The vaccine comprised select peptides for T cell immunogenicity, which is alternatively compared with a different group of peptides to induce antibody responses against linear epitopes.

Sixteen synthetic peptides were selected and conjugated with either of two adjuvants – polyinosinic: polycytidylic acid [poly (I:C) and stimulator of interferon genes (STING) agonist BI-1387466 - known to induce potent T cell responses.

The authors analyzed protein sequences of the ancestral strain of SARS-CoV-2 (Wuhan-1 isolate) for T cell epitopes and linear B cell epitopes coinciding with murine major histocompatibility complex (MHC) ligands. Linear epitope mapping of sera from convalescent patients and subsequent computational filtering (for predicted surface accessibility, spatial localization near annotated functional domains of SARS-CoV-2 spike (S) protein, sequence conversion) identified B cell epitopes.

Computational analysis alone helped to derive T cell epitopes. Initially, MHC binding was predicted among different high-frequency human leucocyte antigen (HLA) alleles. These MHC ligands were further screened for predicted immunogenicity, source protein abundance, and sequence conservation. The selection criteria adopted by the researchers identified 22 candidate peptides, of which 16 were finalized through manual curation.

BALB/c mice (aged eight weeks) were immunized subcutaneously with the peptide vaccine on days 1 and 8. Adjuvant vaccination (Poly (I:C) or BI-1387446) without any of the peptides was used as a control. Cheek bleeds were collected on days 8 and 15, and cardiac bleeds on day 22. Mice were intranasally inoculated with 104 plaque-forming units (PFU) of SARS-CoV-2-MA10.

Antibody responses of sera obtained from cardiac bleeds against peptides used for vaccination were tested with peptide enzyme-linked immunosorbent assays (ELISA) and those against SARS-CoV-2 S protein with protein ELISA. T cell response was determined with ELISpot assay.

Findings

Mice immunized with STING agonist- or poly (I:C)-conjugated vaccine had similar T cell response patterns. Still, T cell activity was significantly higher for mice receiving the vaccine with STING agonist adjuvant. These responses were mainly directed at peptides selected for T cell immunogenicity.

Interestingly, one of the peptides selected for B cell responses also elicited T cell responses. Sera from immunized mice did not show sufficient levels of antibody binding with the SARS-CoV-2 S protein, indicating that the B cell responses were lacking or the selected linear epitopes were not a match for S protein conformation.

The antibody neutralization was not determined, assuming no neutralization could occur without antibodies binding to S protein. Moreover, vaccinated mice challenged with the live virus were not immune to SARS-CoV-2 infection despite eliciting T cell responses, suggesting that the vaccine could not confer sufficient protection.

Conclusions

In conclusion, the authors posit three distinct possibilities for the observed findings. First, T cell responses in vaccinated BALB/c mice were not clearing the viral load independent of B lymphocytes. Second, the SARS-CoV-2 T cell epitopes might have been a mismatch with those of BALB/c mice inoculated with mouse-adapted isolate (SARS-CoV-2-MA10). Finally, it has been speculated that, in general, T cell responses in the absence of antibody responses do not protect against SARS-CoV-2.

• Preliminary scientific report. Baxter, V. et al. (2022) "SARS-CoV-2 peptide vaccine elicits T-cell responses in mice but does not protect against infection or disease". bioRxiv. doi: 10.1101/2022.02.22.481499. https://www.biorxiv.org/content/10.1101/2022.02.22.481499v1