Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals

Authors: Grifoni A, Weiskopf D, Ramirez SI …. Smith DM & Crotty S.

Link to paper: https://www.cell.com/cell/fulltext/S0092-8674(20)30610-3

Journal/ Pre-Print: Cell

Tags: Immunology/Immunity, Bioinformatics, Clinical/ Diagnostics, Vaccines Virology

Research Highlights 

1. By stimulating lymphocytes from recovered patients from mild COVID-19 with well-characterised SARS-CoV-2 peptide pools, the authors detect virus-specific CD4+ T cell responses that predominantly target the Spike, M and N proteins. Low frequencies of T cells reactive to nsp and ORF proteins were also detected.

2. Patients who recovered from mild COVID-19 infection generated robust antibody responses (IgG, IgM and IgA) that correlated with the frequency of virus-specific T cells.

3. All healthy donors had IgG against common coronaviruses, but not SARS-CoV-2. 4/11 of these same donors had T lymphocytes reactive against non-spike SARS-CoV-2 peptides, suggesting cross-reactive immunity towards coronaviruses.

Summary

This study aims to evaluate whether SARS-CoV-2 infection triggers specific/protective immunity in patients who have recovered from confirmed mild/moderate COVID-19 disease compared to healthy unexposed donors. Through the development and use of HLA epitope predicted and antigen-specific peptide megapools, 10/10 recovered patients demonstrated detectable functional virus-specific T CD4+ cells (able to secrete cytokines after ex vivo activation). The spike, M and N proteins are the targets of 27%, 21% and 11% of CD4+ T cells responses, in addition to low frequencies of nsp3, nsp4 and ORF8 specific CD4+ T cell response. This diversity in antigen-reactivity is greater than in other coronavirus infections. Specific CD8+ T cell responses were also detected, with a different pattern of antigen reactivity. Comparatively, the healthy blood donors had no SARS-CoV-2 IgG, but 4/11 donors had detectable reactive CD4+ T cells towards non-spike SARS-Cov-2 peptides suggesting some cross-reactivity between coronaviruses that might explain the variability in disease manifestation across patients.

Impact for SARS-CoV2/COVID19 research efforts

Understand the immune response to SARS-CoV2/COVID19

Develop a vaccine for SARS-CoV2/COVID19

Study Type

· In silico study / bioinformatics study

· In vitro study

Strengths and limitations of the paper

Novelty:

1. The scale and design of the viral peptide pools generated emphasize the significance of spike protein in CD4+, CD8+ and antibody responses, but it also reveals that immune responses are not restricted to this protein. The M and N proteins are targeted by a significant portion of virus-specific cells in COVID-19 patients.

2. A number of healthy patients with no SARS-CoV-2 exposure have virus-antigen specific T cells specifically targeting ORF1ab proteins.

Standing in the field: This is an exciting evolution on earlier work using the megapools to evaluate antigen-specific responses (https://www.medrxiv.org/content/10.1101/2020.04.11.20062349v1.article-info)

Appropriate statistics: Yes, appropriate for the small sample size

Viral model used: Megapools of SARS-CoV2 virus peptides selected for HLA class I or II binding epitopes and individual peptide pools covering distinct viral antigens.

Translatability: By describing the targeted peptide landscape in CD4+ and CD8+T cell responses against SAR-CoV2 they suggest and open the way to vaccine design which can better mimic the natural SARS-Cov2 CD4 T cell response triggered.

Main limitations:

- Supplementary data is not yet available online

- Small sample size: the antigen-specific studies were only conducted on 10 COVID-19 patients and 11 healthy donors.

- Only focus on early recovered patients from mild/ non-hospitalized patients

- Would have been informative to look at the functional status of T cells before stimulation (exhaustion, proliferation etc.)

- Would have been useful to have more information about the antigen-specificity of the IgG, IgA and IgM antibodoes. Whether they share the same antigen-specificity as the CD4+ T cells and whether they can be used as markers of a protective immune response