SARS-CoV-2 spike may impair antigen presentation by CD8 T cells

As the coronavirus disease 2019 (COVID-19) pandemic continues to sweep the world, no effective treatment has been identified so far. Host immunity is thus a significant contributor to viral clearance. A new preprint explores how some variants of the spike protein expressed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19 can impair the antigen presentation responses required to marshal cell-mediated immunity against the virus.

Both neutralizing antibodies and effector T cells are required to clear the virus from COVID-19 patients. Such cells are activated by T cell epitopes. A new study published on the bioRxiv* preprint server aims to identify specific viral epitopes on the spike protein from various regions of the spike protein and the T cell responses they evoke. The researchers draw on the already identified pool of peptides from convalescent COVID-19 patients located on viral domains not susceptible to mutations.

Identification of T cell epitopes

The researchers first predicted 15 potential HLA-A2 restricted CD8+ T cell epitopes of four pathogenic coronaviruses, namely, SARS-CoV-2, SARS-CoV, MERS-CoV and Coronavirus OC43. These were confirmed to be presented by HLA-A2 on the antigen-presenting cells (APC). All showed moderate to strong binding to HLA-A2 except for n-Sp5 and s-Sp12.

They then generated pMHC tetramers with all the peptides to see if they were specific for antigen-reactive CD8 T cells from 31 convalescent COVID-19 patients. They found tetramers of n-Sp1, 2, 6, 7, 11, 13, and 14 were capable of detecting such antigen-specific CD8+ T cells.

Next, they showed that n-Sp1, 2, and 7 had the capability to activate CD8+ T cells, with n-Sp1 inducing the most robust response in the shape of CD69 expression. The researchers here used an artificial antigen-presenting cell (aAPC) system, namely, the T2A2 cell line, for reasons of safety and convenience, coupled with accuracy and the capability to stimulate CD8+ T cells.

They found that APCs presenting these novel mixed epitopes could activate T cells from healthy donors, demonstrating T-cell mediated T2A2 killing and apoptosis, as well as CD8+IFN-γ+ expression. Such epitopes could be used to develop vaccines one day.

They demonstrated that n-Sp1 based pMHC tetramers demonstrated the highest proportion of antigen-specific CD8+ T cells in convalescent patients, the highest HLA-A2 binding capability, and T cell activation, indicating it is the dominant CD8+ T cell epitopes on the SARS-CoV-2 spike protein.

Immune response

Among the many SARS-CoV-2 variants in circulation, 614D>G, 613Q>H in n-Sp6 and 5L>F in n-Sp1 were the top three most frequently observed.

For the dominant n-Sp1, the mutant 5L>F, n-Sp1-m1 showed only a mild decrease in pMHC binding capability, but with a higher expression of CD69, indicative of T cell activation. It was also capable of antigen-specific CD8+ T cell generation, though somewhat less than the wild-type strain. It is essential to consider that the wild-type n-Sp1 tetramer was incapable of recognizing the mutant n-Sp1-induced antigen-specific CD8+ T cells.

Again, the 8L>V, n-Sp1-m2 mutant showed a significant decrease in pMHC binding. When both the above mutations were present, there was a further decline in binding capability.

The n-Sp2 and n-Sp6 mutants showed decreased binding as well, at various levels.

Overall, these results indicated that these variations might have caused a deficiency in the antigen presentation of the dominant epitopes, which was required to rebuild a new CD8+ T cell immune response in COVID-19 patients.”

Regional variation

The researchers found that of the three common variants, 614D>G and 613Q>H in n-Sp6, and 5L>F in n-Sp1, the second was a less potent T cell activator. The first variant is the dominant strain globally, but the mutation does not appear to have altered T cell activation markedly relative to the wild-type strain.

This could be because the mutant binds with greater strength to the host cell receptor, the angiotensin-converting enzyme 2 (ACE2), but does not take part in inducing T cell immunity. This is supported by the finding that the variant is associated with higher viral loads but not increased disease severity.

Finally, the third variant does activate T cells but could not detect antigen-specific T cells from convalescent patients. It could be that these patients were infected with the original strain, and the mutant needed to elicit a new CD8 + T cell immune response.

The n-Sp1 8L>V mutation displayed lower binding to HLA-A2 as well as detecting much fewer n-Sp1-specific CD8+ T cells, both of which might lead to the virus escaping the immune response.

What are the implications?

Thus, this study showed that variants in a dominant epitope of the spike protein could lead to impaired antigen presentation, thus making it necessary to reconstruct a CD8 T cell response in COVID-19 patients.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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