Omicron-Specific Cytotoxic T-Cell Responses After a Third Dose of mRNA COVID-19 Vaccine Among Patients With Multiple Sclerosis Treated With Ocrelizumab

Key Points

Question  Are T-cell responses to the SARS-CoV-2 Omicron variant conserved in anti-CD20–treated patients with multiple sclerosis after COVID-19 messenger RNA vaccination?

Findings  In this cohort study of 20 patients treated with ocrelizumab, Omicron spike-specific CD4 and CD8 T cells were detectable in approximately half of patients 6 months after the second vaccine dose, and cytotoxic T-cell responses increased following the third dose. Frequencies of T cells specific to the Delta and Omicron variants were lower compared with the vaccine strain, both before and after receiving a booster dose.

Meaning  In this study of anti-CD20–treated patients with multiple sclerosis, the vaccine-induced T-cell responses were little affected by the mutations carried by Omicron and might prevent severe COVID-19 infection, and a third vaccine dose improved cytotoxic T-cell responses against Omicron.

Importance  The SARS-CoV-2 variant B.1.1.529 (Omicron) escapes neutralizing antibodies elicited after COVID-19 vaccination, while T-cell responses might be better conserved. It is crucial to assess how a third vaccination modifies these responses, particularly for immunocompromised patients with readily impaired antibody responses.

Objective  To determine T-cell responses to the Omicron spike protein in anti-CD20–treated patients with multiple sclerosis (MS) before and after a third messenger RNA COVID-19 vaccination.

Design, Setting, and Participants  In this prospective cohort study conducted from March 2021 to November 2021 at the University Hospital Geneva, adults with MS receiving anti-CD20 treatment (ocrelizumab) were identified by their treating neurologists and enrolled in the study. A total of 20 patients received their third dose of messenger RNA COVID-19 vaccine and were included in this analysis.

Interventions  Blood sampling before and 1 month after the third vaccine dose.

Main Outcomes and Measures  Quantification of CD4 and CD8 (cytotoxic) T cells specific for the SARS-CoV-2 spike proteins of the vaccine strain as well as the Delta and Omicron variants, comparing frequencies before and after the third vaccine dose.

Results  Of 20 included patients, 11 (55%) were male, and the median (IQR) age was 45.8 (37.8-53.3) years. Spike-specific CD4 and CD8 T-cell memory against all variants were maintained in 9 to 12 patients 6 months after their second vaccination, albeit at lower median frequencies against the Delta and Omicron variants compared with the vaccine strain (CD8 T cells: Delta, 83.0%; 95% CI, 73.6-114.5; Omicron, 78.9%; 95% CI, 59.4-100.0; CD4 T cells: Delta, 72.2%; 95% CI, 67.4-90.5; Omicron, 62.5%; 95% CI, 51.0-89.0). A third dose enhanced the number of responders to all variants (11 to 15 patients) and significantly increased CD8 T-cell responses, but the frequencies of Omicron-specific CD8 T cells remained 71.1% (95% CI, 41.6-96.2) of the responses specific to the vaccine strain.

Conclusions and Relevance  In this cohort study of patients with MS treated with ocrelizumab, there were robust T-cell responses recognizing spike proteins from the Delta and Omicron variants, suggesting that COVID-19 vaccination in patients taking B-cell–depleting drugs may protect them against serious complications from COVID-19 infection. T-cell response rates increased after the third dose, demonstrating the importance of a booster dose for this population.

The SARS-CoV-2 variant B.1.1.529 (Omicron) was designated a variant of concern in November 2021¹ and is spreading rapidly. The protection provided by current COVID-19 vaccines is not established. Preliminary studies suggest that antibodies neutralizing Omicron, which carries multiple mutations in the spike protein, critically wane in the months following heterologous infection or vaccination.^2,3 A third vaccine dose seems to boost neutralizing antibodies, although less efficiently than for the B.1.617.2 (Delta) variant.² Whether the mutations in Omicron spike protein affect T-cell recognition, which is known to be less affected than antibodies for other variants,⁴ is still under investigation.

T-cell responses have a role in protection against severe COVID-19, and their importance is further underlined when antibody responses to vaccination are defective. We and others have recently shown that in patients with multiple sclerosis (MS) taking anti-CD20 treatment, 2 doses of COVID-19 messenger RNA (mRNA) vaccines induce suboptimal antibody responses but robust and functional T-cell responses against the vaccine strain.^5,6 In the current situation and specifically for this vulnerable population, it is critical to understand if Omicron-specific T cells are elicited by 2 or 3 doses of mRNA vaccine, particularly because monoclonal antibodies that are given to these patients to alleviate symptoms are mainly ineffective against Omicron.³ Here, we report the T-cell responses to Omicron compared with the vaccine strain and Delta variant in anti-CD20–treated patients with MS before and following the third dose of COVID-19 mRNA vaccines.

This prospective cohort study was initiated in March 2021 at the Geneva University Hospitals, Switzerland, according to the principles of Good Clinical Practice and approved by the Geneva Cantonal Ethics Commission (2021-00430). All study participants provided written informed consent. Participants who received their third dose of mRNA COVID-19 vaccine before November 1, 2021, were included in the analyses, and blood was sampled before and 30 days after vaccination. Study details, methods on peripheral blood mononuclear cells (PBMC) preparation, anti–SARS-CoV-2 nucleoprotein and receptor-binding domain (RBD) antibody measurement, and T-cell assays are found elsewhere⁵ and in the eMethods in the Supplement. Briefly, specific T cells were measured using the activation-induced marker (AIM) assay. PBMC were stimulated with peptide pools covering the different spike proteins, and specific T cells were identified by the expression of activation surface markers, such as 4-1BB, CD69, and OX40. This study followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guideline.

Statistical analysis was performed with GraphPad Prism version 8.0.2 (GraphPad). Quantitative variables were compared using Wilcoxon signed rank test either including the entire cohort or responders only, as indicated, and 2-tailed P values less than .05 were considered statistically significant.

Of 20 included patients with MS receiving anti-CD20 monotherapy (ocrelizumab), 11 (55%) were male and 9 (45%) were female, and the median (IQR) age was 45.8 (37.8-53.3) years. A total of 16 patients received a third dose of mRNA-1273 (Moderna; 100 μg) and 4 received a third dose of BNT162b2 (Pfizer-BioNTech), with a median (IQR) interval between the second and third dose of 26.7 (22.3-29.0) weeks. Before the booster dose, 11 patients were seropositive for anti-RBD antibodies, increasing to 13 patients 1 month after the third dose, and antibody levels rose significantly (geometric mean titer, 3.5 U/mL to 57.9 U/mL) (Table; eFigure in the Supplement). One patient had been infected before vaccination as witnessed by detectable anti-nucleoprotein antibodies (Table).

We first measured spike-specific CD8 T cells that have a role in the elimination of SARS-CoV-2–infected cells. These cytotoxic T cells, specific for the vaccine strain and the Delta and Omicron variants, were present before the booster dose in 12, 10, and 9 patients, respectively. Following the booster dose, the number of responders increased to 15 patients for the vaccine strain and to 14 for both variants. The frequencies of specific CD8 T cells were clearly enhanced after the third dose (Figure 1A and B) but were reduced for both variants compared with the vaccine strain before receiving a booster dose (Delta, 83.0%; 95% CI, 73.6-114.5; Omicron, 78.9%; 95% CI, 59.4-100.0) and after receiving a booster dose (Delta, 89.3%; 95% CI, 57.6-100.0; Omicron, 71.1%; 95% CI, 41.6-96.2) (Figure 1C). No difference was observed between levels of Delta-specific and Omicron-specific CD8 T cells (eFigure in the Supplement).

CD4 T cells are known to provide help to B cells, thereby enhancing the production of antibodies with improved neutralizing capacity. Before receiving the booster dose, 9 to 10 patients had detectable memory CD4 T-cell responses, increasing after the booster dose for the vaccine strain (in 15 patients) and for Delta (in 14 patients) but only little for Omicron (in 11 patients). Unlike CD8 T cells, no significant changes in the frequencies of specific CD4 T cells were detected after the booster dose (Figure 2A and B). Delta and Omicron spike-specific CD4 T-cell responses were significantly reduced compared with the vaccine strain to 83.5% (95% CI, 69.4-105.6) for Delta and to 72.3% (95% CI, 53.4-82.7) for Omicron after the booster dose compared with 72.2% (95% CI, 67.4-90.5) and 62.5% (95% CI, 51.0-89.0), respectively, before the booster dose. There was no significant correlation between antibody titers and CD4 or CD8 T-cell levels before or after the booster dose, irrespective of strain specificity (data not shown).

Last, we assessed the memory phenotype of spike-specific CD8 and CD4 T cells, as these cells are recalled on encounter with SARS-CoV-2. Spike-specific CD4 and CD8 T cells mostly had an effector phenotype independent of the variant, indicating their capacity to quickly respond in case of infection (eTable in the Supplement).

In anti-CD20–treated patients with MS, SARS-CoV-2–specific antibody titers are low or undetectable after 2 doses of mRNA vaccine^5-7 and are not restored after a third dose, as shown here and for patients with lymphoma.^5,8 Antibodies are crucial in the prevention of infection through inhibition of viral entry and in the elimination of infected cells through antibody-mediated killing. Even if antibody responses are largely impaired in anti-CD20–treated patients, T-cell responses after 2 vaccine doses developed similarly to immunocompetent individuals.⁹ Activated T cells have an important role in the clearance of infected cells and in the control of viral load, which may decrease duration and intensity of symptoms.¹⁰ With the emergence of variants such as Omicron that can evade neutralizing antibodies, even at high titers, T-cell responses become even more important, and their presence may still provide protection from the severe forms of COVID-19.

In this study, 6 months after the second vaccine dose, memory T-cell responses to Delta and Omicron were detectable in around half of patients, in line with the durability of the response in healthy individuals.⁹ The number of responders increased for both CD4 and CD8 T cells after the third vaccine dose, showing that those with undetectable memory response after the primary vaccine series can be boosted. Importantly, a third dose increased the frequency of cytotoxic CD8 T cells, which are particularly important in viral defense, irrespective of the SARS-CoV-2 variant. Yet both before and after the booster dose, their frequencies were lower against Omicron, similar to the moderate decrease observed in healthy individuals 5 to 6 months after 2 doses.¹¹ This could indicate that the recognition of T cells may be partially compromised as mutations accumulate in variants of concern.

This study has limitations. The interpretation of our results is limited by the low sample size and the lack of comparison with other treatments or control populations. Given that the level of vaccine-specific T-cell responses in anti-CD20–treated patients with MS is similar to healthy controls after 2 doses, one could expect comparable levels after a third dose. Accordingly, others have reported similar levels of Omicron-specific T cells in healthy individuals.¹¹ Furthermore, the postvaccination follow-up is limited. The monitoring of breakthrough infections in this population is needed to confirm the benefit of vaccination, in particular against Omicron.

In this cohort study of patients with MS treated with ocrelizumab, a COVID-19 mRNA booster vaccination induced robust T-cell responses to both Delta and Omicron. However, their frequencies were lower compared with the vaccine strain, and the clinical implications of these findings need to be assessed.

Accepted for Publication: January 28, 2022.

Published Online: February 25, 2022. doi:10.1001/jamaneurol.2022.0245

Corresponding Author: Christiane S. Eberhardt, MD (christiane.eberhardt@unige.ch), and Arnaud M. Didierlaurent, PhD (arnaud.didierlaurent@unige.ch), Centre Médical Universitaire, rue Michel-Servet 1, 1211 Genève 4, Switzerland.

Author Contributions: Drs Didierlaurent and Eberhardt had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis. Drs Madelon and Heikkilä contributed equally to the manuscript.

Study concept and design: Madelon, Heikkilä, Sette, Siegrist, Lalive, Didierlaurent, Eberhardt.

Acquisition, analysis, or interpretation of data: Madelon, Heikkilä, Sabater Royo, Fontannaz, Breville, Lauper, Goldstein, Grifoni, Siegrist, Finckh, Lalive, Didierlaurent, Eberhardt.

Drafting of the manuscript: Madelon, Heikkilä, Breville, Lauper, Goldstein, Finckh, Didierlaurent, Eberhardt.

Critical revision of the manuscript for important intellectual content: Madelon, Heikkilä, Sabater Royo, Fontannaz, Lauper, Grifoni, Sette, Siegrist, Finckh, Lalive, Didierlaurent.

Statistical analysis: Madelon, Heikkilä, Breville, Eberhardt.

Obtained funding: Siegrist, Finckh, Didierlaurent, Eberhardt.

Administrative, technical, or material support: Sabater Royo, Fontannaz, Breville, Lauper, Goldstein, Grifoni, Sette, Siegrist, Lalive.

Study supervision: Madelon, Siegrist, Lalive, Didierlaurent, Eberhardt.

Conflict of Interest Disclosures: Dr Lauper has received personal fees from Pfizer, Celltrion, and Viatris outside the submitted work. Dr Sette is a consultant for Gritstone Bio, Flow Pharma, Arcturus Therapeutics, ImmunoScape, CellCarta, Avalia, Moderna, Fortress, and Repertoire. Dr Didierlaurent has received personal fees from Speranza; personal fees from Roche paid to his institution; and is chairman for the World Health Organization Technical Advisory Group on Emergency Use Listing of COVID-19 vaccines (no personal fees). The La Jolla Institute for Immunology has filed for patent protection for various aspects of T-cell epitope and vaccine design work. No other disclosures were reported.

Funding/Support: This work was supported by the HUG Private Foundation (Drs Eberhardt, Siegrist, and Didierlaurent) and by the Giorgi-Cavaglieri Foundation (Dr Didierlaurent). This work was additionally funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under contracts 75N93021C00016 and 75N9301900065 (Dr Sette).

Role of the Funder/Sponsor: The funders had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Additional Contributions: We thank Sandra Fernandes Oliveira, Olivia Studer, Sandrine Bastard, and colleagues at the Clinical Research Center, University Hospital of Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland, for their involvement in patient recruitment and sample collection; Chantal Tougne, Yves Donati, MSc, Wafae Adouan, and Sophie Coudurier for their contributions to processing the clinical samples and support in experimental work; and Myriam Ventura-Lehnis for her administrative support. None of these contributors were compensated for their work. We thank the team from the flow cytometry core facility for their technical support. We thank all colleagues who have provided support to participant recruitment, sample collection, and experimental work. We are grateful to all volunteers for their participation in the study.