Assessment of T-cell Reactivity to the SARS-CoV-2 Omicron Variant by Immunized Individuals

Abstract

Importance: The emergence of the highly contagious Omicron variant of SARS-CoV-2 and the findings of a significantly reduced neutralizing potency of sera from individuals with previous SARS-CoV-2 infection or vaccination highlights the importance of studying cellular immunity to estimate the degree of immune protection to the new SARS-CoV-2 variant.

Objective: To determine T-cell reactivity to the Omicron variant in individuals with established (natural and/or vaccine-induced) immunity to SARS-CoV-2.

Design, setting, and participants: This was a cohort study conducted between December 20 and 21, 2021, at the Santa Lucia Foundation Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy, among health care worker and scientist volunteers. Lymphocytes from freshly drawn blood samples were isolated and immediately tested for reactivity to the spike protein of SARS-CoV-2.

Main outcomes and measures: The main outcomes were the measurement of T-cell reactivity to the mutated regions of the spike protein of the Omicron BA.1 SARS-CoV-2 variant and the assessment of remaining T-cell immunity to the spike protein by stimulation with peptide libraries.

Results: A total of 61 volunteers (mean (range) age, 41.62 (21-62) years; 38 women [62%]) with different vaccination and SARS-CoV-2 infection backgrounds were enrolled. The median (range) frequency of CD4+ T cells reactive to peptides covering the mutated regions in the Omicron variant was 0.039% (0%-2.356%), a decrease of 64% compared with the frequency of CD4+ cells specific for the same regions of the ancestral strain (0.109% [0%-2.376%]). Within CD8+ T cells, a median (range) of 0.02% (0%-0.689%) of cells recognized the mutated spike regions, while 0.039% (0%-3.57%) of cells were reactive to the equivalent unmutated regions, a reduction of 49%. However, overall reactivity to the peptide library of the full-length protein was largely maintained (estimated 87%). No significant differences in loss of immune recognition were identified between groups of participants with different vaccination or infection histories.

Conclusions and relevance: This cohort study of immunized adults in Italy found that despite the mutations in the spike protein, the SARS-CoV-2 Omicron variant was recognized by the cellular component of the immune system. It is reasonable to assume that protection from hospitalization and severe disease will be maintained.

Figure 1.. T-cell Responses to the Ancestral and Omicron Spike Protein of SARS-CoV-2

Representative flow cytometry plots gated on CD4⁺ or CD8⁺ T cells showing upregulation of activation markers (CD69 and CD40 ligand [CD40L] for CD4⁺ cells and CD69 and CD137 for CD8⁺ cells) following overnight stimulation with a pool of overlapping peptides covering the whole spike protein from the ancestral vaccine strain (Pool_S), a peptide pool covering only the mutated regions of the Spike protein from the Omicron variant (Pool_Mut) or a peptide pool covering the same regions as Pool_Mut, but from the ancestral strain (Pool_Ref). Ctr indicates unstimulated control; numbers, percentages of activation induced marker cells within each gate.

Figure 2.. Frequency of Participants in Each Group Presenting Spike-Specific Responses

2 Doses indicates individuals with 2 doses of vaccine; 3 Doses, 3 doses of mRNA vaccine; AIM indicates activation induced marker; COV-VAC, individuals who had contracted and recovered from SARS-CoV-2 and were subsequently vaccinated; HET, heterologous vaccination with adenoviral vector followed by an mRNA vaccine; Pool_Mut, pool of 83 peptides covering only the mutated regions of the spike protein from the Omicron variant; Pool_Ref, peptide pool covering the same regions as the mutated Omicron regions, but from the ancestral strain; Pool_S, an overlapping peptide pool spanning the entire spike protein from the ancestral vaccine strain; and VAC-COV, individuals who had been vaccinated and who had subsequently been infected with SARS-CoV-2.

Figure 3.. Reduced Recognition of Mutated Regions of the Spike Protein in the Omicron Variant

Freshly isolated lymphocytes were incubated with peptide pools encompassing the mutated regions of the spike protein in the Omicron variant (Omicron), and with the reference peptide pool of the same region in the ancestral vaccine strain (Vaccine). Activated CD4⁺ (A) (CD69⁺ and CD40 ligand⁺) and CD8⁺(B) (CD69⁺ and CD137⁺) cells were identified by flow cytometry, and interferon (IFN)-γ production was measured in the supernatants (C). Background T-cell activation in paired unstimulated cultures was subtracted. Dotted lines indicate the threshold for positivity (median − 75th percentile of values from unstimulated cultures). Differences were assessed using Friedman rank sum test with Omicron exposure (vaccine / Omicron) as the random effect and participant ID (points) as the random effect.

Figure 4.. Remaining Immunity to the Spike Protein of the Omicron Variant

Fraction of preserved CD4⁺ (A) and CD8⁺ (B) reactivity to the whole spike protein in each group, after having subtracted loss of reactivity to the mutated regions. 2 Doses indicates individuals with 2 doses of vaccine; 3 Doses, 3 doses of mRNA vaccine; COV-VAC, individuals who had contracted and recovered from SARS-CoV-2 and were subsequently vaccinated; HET, heterologous vaccination with adenoviral vector followed by an mRNA vaccine; and VAC-COV, individuals who had been vaccinated and who had subsequently been infected with SARS-CoV-2.