Vaccine component BNT162b4 enhances T-cell immunity against SARS-CoV-2 variants for reduced COVID-19 disease severity

By Neha MathurApr 17 2023Reviewed by Lily Ramsey, LLM

In a recent article published in the Cell Journal, researchers designed a novel messenger ribonucleic acid (mRNA) vaccine component designated BNT162b4.

This component could be used alongside mRNA-based BNT162b2, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S)-encoding vaccine, to enhance T-cell immunity against all SARS-CoV-2 variants.

Study: The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection. Image Credit: SeventyFour/Shutterstock.com

Background

The vaccine component encoded the most T-cell immunogenic SARS-CoV-2 antigens. These include nucleocapsids (N), membranes (M), and open reading frame 1abs (ORF1ab), which are conserved across all variants and target diverse human leucocyte agent (HLA) alleles.

The researchers demonstrated its efficacy in preventing severe coronavirus disease 2019 (COVID-19) during live virus challenges in hamsters, an animal model most closely resembling COVID-19 manifestations in humans.

They observed that BNT162b4 elicited polyfunctional CD4⁺ and CD8⁺ T-cell-mediated immune responses from diverse epitopes, alone or in combination with BNT162b2 while preserving S-specific immunity. It also protected hamsters from severe illness.

Introduction

CD8+ cytotoxic T lymphocytes (CTLs) recognize pathogen-infected cells via epitopes presented by major histocompatibility complex (MHC) class I molecules on the host cell surface.

Subsequently, they exert cytotoxic functions to eliminate infected cells and limit pathogen spread within the host.

Similarly, CD4+ T cells recognize their cognate epitopes on MHC class II molecules and secrete cytokines and chemokines to promote antibody production by B cells.

While antigen-specific neutralizing antibody (nAb) titers induced by vaccination or prior exposure decay quickly with time, vaccine-induced T cell-mediated immunity persistently provides robust protection from severe disease.

Most importantly, antigen-specific T-cell memory persists in recovered patients for over a decade, highlighting the durability of T-cell immunity against SARS-CoV-2.

These aspects of the cellular arm of immunity make it immensely significant in the control and clearance of beta-coronaviruses (CoVs), including SARS-CoV-2.

So far, SAR-CoV-2 S-encoding mRNA vaccine BNT162b2 has been inducing long-lasting T-cell responses in vaccinees. Even during breakthrough infections post-vaccination, researchers of several studies confirmed a positive correlation between T-cell activation and the rate of SARS-CoV-2 clearance and, as expected, a negative correlation with the viral titers.

However, some recent studies reported reduced S-specific T-cell responses in breakthrough cases following vaccination due to the absence of variant-reactive T cells. The SARS-CoV-2 variant of concern (VOC), Omicron and its sublineages, are highly infectious and evade nAbs.

The role, molecular mechanism, and factors contributing to vaccine-induced T cells against Omicron and its subvariants remain unclear. In addition, there is a lack of data on vaccine-induced SARS-CoV-2 S-specific T-cell responses.

Considering the durable nature of T-cell immunity, it makes perfect sense to explore and harness it in developing next-generation mRNA technology-based vaccines, which would work against multiple antigens conserved across all beta CoVs.

Notably, compared to nAb epitopes, T-cell epitopes get activated faster and are conserved across SARS-CoV-2 VOCs. Their diverse nature due to certain HLA haplotypes could serve as an additional barrier to viral evasion.

About the study

In the present study, researchers designed a novel mRNA vaccine component BNT162b4 which encoded segments of the SARS-CoV-2 M, N, and ORF1ab proteins. It helped them expand T-cell responses of SARS-CoV-2 S-encoding vaccines, such as BNT162b2.

The researchers used mass spectrometry (MS) to demonstrate its efficacy in generating T-cell epitopes on HLA-I complexes in cell lines derived from humans.

Specifically, the team used three SARS-CoV-2 variants, the ancestral strain, and Delta, and Omicron VOCs, in the hamster model based on the findings in a mouse model that BNT162b4 induced robust T-cell response against the N, M, and ORF1ab SARS-CoV-2 proteins of all three variants alone and in combination with BNT162b2.

Accordingly, BNT162b4 is under clinical evaluation in combination with the Omicron-BA.4/BA.5 updated bivalent version of BNT162b2.

Study findings

The study results highlighted the need for enhancing the activity of mRNA vaccines encoding SARS-CoV-2 S protein because they lose efficacy against newly emerging SARS-CoV-2 variants, e.g., Omicron, which increased the rate of breakthrough infections. There is a need for COVID-19 vaccines that offer durable immunity and prevent severe illness.

Using targeted MS, the authors demonstrated that BNT162b4 generated T-cell epitopes from all three encoded SARS-CoV-2-derived antigens and presented them on HLA alleles. Concatenating short segments of different SARS-CoV-2 proteins (antigens) gave rise to junctional epitopes not detectable in the SARS-CoV-2 proteome.

However, introducing a few amino acids most likely enhanced the cleavage of desired epitopes by the polyprotein and reduced the probability of junctional peptide formation.

HLA ligandomics analysis showed effective cleavage at ORF1ab epitopes nearby junctional peptides. Also, MS could not detect junctional epitopes at these sites. Further, BNT162b4 elicited robust, polyfunctional T-cell responses against three antigens in mouse models.

Its combination with BNT162b2 broadened the antigen-specificity of the T-cell repertoire but did not adversely impact the BNT162b2-induced nAb responses against the S glycoprotein.

Likewise, its co-administration with BNT162b2 did not impair the T-cell repertoire and phenotypic functions or frequency of SARS-CoV-2 S-specific T cells that BNT162b2 triggered.

However, its co-administration decreased cytokine secretion in SARS-CoV-2 N- and M-specific T cells, indicating some sought of rivalry between the responses to the N and M proteins vs. S glycoprotein.

Some possible explanations are differences in T-cell epitope abundance, preferential presentation of BNT162b2 vs. BNT162b4 epitopes, and immunodominant S-specific T cells.

Nevertheless, BNT162b4 broadened the cumulative T-cell responses to an extra set of SARS-CoV-2 antigens presented by BNT162b4.

The authors also found adequate evidence of low SARS-CoV-2 titers, improved lung pathology, and decreased weight loss in hamsters challenged with multiple SARS-CoV-2 variants when co-vaccinated with BNT162b4 and BNT162b2.

The test animals challenged by the ancestral strain or the Delta VOC had more pronounced BNT162b4-driven immune responses in nasal turbinates, indicating that it increased mucosal immunity, albeit immunoglobulin G accessibility in this area was restricted, which decreased the overall immune protection.

In challenge by the Omicron BA.1 subvariant, the authors could not detect reduced viral titers, most likely because Omicron has a lower overall viral burden and elicit a weaker inflammatory response.

Yet, according to the authors, the protection conferred in the upper respiratory tract by the co-administration of BNT162b4 via tissue-resident memory T cells or T-cell migration following infection showed promise, as it helped decrease SARS-CoV-2 transmission.

Conclusions

T cells play a critical role in protective immunity against severe COVID-19. However, the extent to which they prevent infections is unknown.

The current study's findings in a hamster model warrant further assessment in humans.

Accordingly, the potential effects of the BNT162b4 vaccine candidate in combination with Omicron BA.4/BA.5 S-adapted BNT162b2 is under clinical evaluation.