The Effect of the Omicron Variant on T-cell Immunity

Bjarke Endel Hansen, Liselotte Brix and Dilek Inekci

Immudex, Copenhagen, Denmark

Introduction

The COVID-19 pandemic continues to affect billions of lives worldwide. The emergence of the highly transmissible SARS-CoV-2 B.1.1.529 (Omicron) variant has once again raised concerns about the effectiveness of the vaccine-induced immunity. Whereas the durability and breadth of protection against the newly circulating SARS-CoV-2 variant remain unknown, the findings highlight the need to continuously assess and quantify the level of immunity. In particular, the Omicron variant possesses numerous mutations in the Spike protein, increasing its likelihood to evade the neutralizing antibodies induced by the most common vaccines, Pfizer/BioNTech, Moderna, AstraZeneca, and Johnson & Johnson, which are all based on the Spike protein.

This has more than ever re-emphasized the importance of assessing the cellular immunity against SARS-COV-2 and variants. T-cell immunity may be less affected by the new variant than the antibody response and be an essential piece in unraveling the immunity puzzle as new variants emerge.??

While several studies have demonstrated robust T-cell responses against SARS-COV-2 in convalescents and vaccinated individuals, the antibody response is still the major focus area when assessing the immunity against variants. Besides limiting the assessment of the broad immunity to SARS-CoV-2 and variants, this tendency increases the risk of a deficient understanding of SARS-CoV-2-related immunity.

Immudex provides T-cell monitoring assays for SARS-CoV-2 based on the established Dextramer? technology, enabling detection and characterization of virus-specific T-cell responses. The technology relies on displaying virus-specific epitopes on major histocompatibility complex (MHC) molecules for recognition by virus-specific T-cells. In this analysis, we included SARS-CoV-2 CD8+ T-cell assays designed to cover eight of the most common class I human leukocyte antigen (HLA) alleles, including HLA-A*01:01, HLA-A*02:01, HLA-A*03:01, HLA-A*11:01, HLA-A*24:02, HLA-B*07:02, HLA-B*35:01, and HLA-B*44:02 complexed to epitopes from Spike and Non-Spike (Nucleocapsid, ORF1ab, and ORF3a) proteins of the Wuhan strain of SARS-CoV-2.

The assays cover several literature-reported epitopes tested in several cohort studies (9, 10, 15, 19) and in-house studies (not published). Among others, Nielsen et al. (2021) reported that in a study of 106 HLA-A2+?individuals, 90% showed a detectable SARS-CoV-2-specific CD8+?T-cell response using the Dextramer? assay. In-house data revealed a similar frequency (96%) of SARS-CoV-2 specific CD8+?T-cells in mild convalescent patients across eight HLA alleles.

Similarly, the SARS-CoV-2 CD4+ T-cell Dextramer? assays included in this analysis cover the alleles HLA-DRB1*01:01, HLA-DRB1*04:01, and HLA-DRB1*07:01 coupled with epitopes from Spike and Non-Spike proteins.

Here, we examined the conservation of the T-cell epitopes used in the Dextramer? assays across the SARS-CoV-2 variants Wuhan, Delta, and Omicron, to underline why investigating the cellular immunity may be more prominent in relation to evaluating the vaccine protection.?

Analysis

To examine the T-cell epitope conservation across Wuhan, Delta (B.1.617.1), and Omicron variants, protein sequences in FASTA format were retrieved from the National Center for Biotechnology Information (NCBI) database (Table 1). A multiple sequence alignment analysis was created for Spike, Nucleocapsid, ORF3a, and ORF1ab using CLC Sequence Viewer 8.0 (Qiagen). The multiple alignment was overlayed with the specific epitopes included in the SARS-CoV-2 Dextramer? assays to assess whether the epitopes are affected by the mutations shown in the Delta and Omicron variants (Table 2-3, Appendix A).??

Table 1. NCBI accession numbers for protein sequences used for multiple alignment.

Table 2. Conservation of Spike-specific CD8+ T-cell epitopes across Wuhan, Delta, and Omicron variants.

Green = no mutations in epitope, Red = mutations in epitope

Table 3. Conservation of Non-Spike-specific CD8+ T-cell epitopes across Wuhan, Delta, and Omicron variants.

Green = no mutations in epitope, Red = mutations in epitope

Discussion

The multiple alignment analysis of Spike across the SARS-COV-2 variants Delta and Omicron showed a conservation of 13 and 14 out of 17 investigated CD8+ T-cell epitopes, respectively, corresponding to 76% and 82%. Similarly, all investigated Non-Spike CD8+ T-cell epitopes were conserved across the three variants (100%).

Analysis of SARS-CoV-2 specific CD4+ T-cell epitopes also showed a high degree of conservation between the Wuhan, Delta, and Omicron variants (data not shown). Thus, the Delta sequence showed a conservation of 17 out of 17 Spike epitopes (100%) and 12 out of 12 Non-Spike epitopes (100%) derived from Nucleocapsid, Envelope, and ORF1ab. The Omicron sequence showed a conservation of 13 out of 17 Spike epitopes (76%) and a conservation of 12 out of 12 Non-Spike proteins (100%).

The high degree of conservation across SARS-CoV-2 T-cell epitopes in the three major variants, Wuhan, Delta, and Omicron, is promising for the disease course of individuals that have previously encountered SARS-COV-2 and/or been vaccinated. Based on the observations, we hypothesize that the level of T-cell responses will yield good protection against Omicron in convalescent and likely also vaccinated individuals. Moreover, the present data verify the applicability of our current SARS-CoV-2 Dextramer? assay to monitor the T-cell immunity across variants.

In the future, virus strains with mutations affecting key T-cell epitopes may appear. However, our highly adaptable technology allows a rapid development of SARS CoV-2 Dextramer? assays tailored to any new variant.

References

1. Shomuradova, A. S. et al. (2020). SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors. Immunity. doi:10.1016/j.immuni.2020.11.004
2. Peng, Y. et al. (2020). Broad and strong memory CD4(+) and CD8(+) T-cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat Immunol. doi:10.1038/s41590-020-0782-6
3. Grifoni, A. et al. (2020). A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell Host Microbe. doi:10.1016/j.chom.2020.03.002
4. Chour, W. et al. (2020). Shared Antigen-specific CD8+ T-cell Responses Against the SARS-COV-2 Spike Protein in HLA-A*02:01 COVID-19 Participants. MedRxiv. doi:10.1101/2020.05.04.20085779
5. Nelde, A. et al. (2020). SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T-cell recognition. Nat Immunol. doi:10.1038/s41590-020-00808-x
6. Ferretti, A. P. et al. (2020). Unbiased screens show CD8+ T-cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein. Immunity. doi:10.1016/j.immuni.2020.10.006
7. Sekine, T. et al. (2020). Robust T-Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19. Cell. doi:10.1016/j.cell.2020.08.017
8. Schulien, I. et al. (2020). Characterization of pre-existing and induced SARS-CoV-2-specific CD8(+) T-cells. Nat Med. doi:10.1038/s41591-020-01143-2
9. Adamo, S. et al. (2021) Signature of long-lived memory CD8+ T-cells in acute SARS-CoV-2 infection. Nature. https://doi.org/10.1038/s41586-021-04280-x
10. Minervina, A. A. et al. (2021) Convergent epitope-specific T-cell responses after SARS-CoV-2 infection and vaccination. MedRxiv. doi: 10.1101/2021.07.12.21260227
11. Gangaev, A. et al. (2021). Identification and characterization of a SARS-CoV-2 specific CD8(+) T-cell response with immunodominant features. Nat Commun. doi:10.1038/s41467-021-22811-y
12. Habel, J. R. et al. (2020). Suboptimal SARS-CoV-2-specific CD8(+) T-cell response associated with the prominent HLA-A*02:01 phenotype. Proc Natl Acad Sci U S A. doi:10.1073/pnas.2015486117
13. Saini, S. K. et al.?(2021). SARS-CoV-2 genome-wide T-cell epitope mapping reveals immunodominance and substantial CD8(+) T-cell activation in COVID-19 patients. Sci Immunol. doi:10.1126/sciimmunol.abf7550
14. Kared, H. et al.?(2021). SARS-CoV-2-specific CD8+ T-cell responses in convalescent COVID-19 individuals. J Clin Invest. doi:10.1172/JCI145476
15. Nielsen, S. S. et al.?(2021). SARS-CoV-2 elicits robust adaptive immune responses regardless of disease severity. EBioMedicine. 103410. doi:10.1016/j.ebiom.2021.103410
16. Sahin, U. et al.?(2021). BNT162b2 vaccine induces neutralizing antibodies and poly-specific T-cells in humans. Nature. doi:10.1038/s41586-021-03653-6
17. Rha, M. S. et al.?(2021). PD-1-Expressing SARS-CoV-2-Specific CD8(+) T-Cells Are Not Exhausted, but Functional in Patients with COVID-19. Immunity. doi:10.1016/j.immuni.2020.12.002
18. Tarke, A. et al.?(2021). Comprehensive analysis of T-cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. Cell Rep Med. doi:10.1016/j.xcrm.2021.100204
19. Schreibing, F. et al. (2021). Dissecting CD8+ T-cell pathology of severe SARS-CoV-2 infection by single-cell epitope mapping. bioRxiv. doi:10.1101/2021.03.03.432690
20. Heide, J. et al. (2021). Broadly directed SARS-CoV-2-specific CD4+ T-cell response includes frequently detected peptide specificities within the membrane and nucleoprotein in patients with acute and resolved COVID-19. PLoS Pathog. doi:10.1371/journal.ppat.1009842
21. Mallajosyula, V. et al. (2021). CD8(+) T-cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients. Sci Immunol. doi:10.1126/sciimmunol.abg5669
22. Ma, T. et al. (2021). Protracted yet Coordinated Differentiation of Long-Lived SARS-CoV-2-Specific CD8(+) T-cells during Convalescence. J Immunol. doi:10.4049/jimmunol.2100465
23. Zhang, H. et al. ?(2021). Profiling CD8(+) T-cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants. Cell Rep. doi:10.1016/j.celrep.2021.109708
24. Nagler, A. et al. (2021). Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics. Cell Rep. doi:10.1016/j.celrep.2021.109305
25. Rowntree, L. C. et al.?(2021). SARS-CoV-2-specific CD8(+) T-cell responses and TCR signatures in the context of a prominent HLA-A*24:02 allomorph. Immunol Cell Biol. doi:10.1111/imcb.12482
26. Juno, J. et al.?(2021). Tracking the kinetics and phenotype of spike epitope-specific CD4 T-cell immunity in the context of SARS-CoV-2 infection and vaccination. Research Square. doi:10.21203/rs.3.rs-957030/v1
27. Low, J. S. et al. (2021). Clonal analysis of immunodominance and cross-reactivity of the CD4 T-cell response to SARS-CoV-2. Science. doi:10.1126/science.abg8985
28. Loyal, L. et al. (2021). Cross-reactive CD4+ T-cells enhance SARS-CoV-2 immune responses upon infection and vaccination. Science. doi:10.1126/science.abh182300000000000000
29. Swadling, L. et al. (2021). Pre-existing polymerase-specific T-cells expand in abortive seronegative SARS-CoV-2 infection. medRxiv. doi:10.1101/2021.06.26.21259239
30. Lu, X. et al. (2021). Identification of conserved SARS-CoV-2 spike epitopes that expand public cTfh clonotypes in mild COVID-19 patients. J Exp Med. doi:10.1084/jem.20211327
31. Brunk, F. et al. (2021). SARS-CoV-2-reactive T-cell receptors isolated from convalescent COVID-19 patients confer potent T-cell effector function. Eur J Immunol. doi:10.1002/eji.202149290
32. Pan, K. et al. (2021). Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs. Proc Natl Acad Sci U S A. doi:10.1073/pnas.2111815118

Appendix A

Multiple alignment analysis of the Spike protein sequences from SARS-COV-2 variants Wuhan, Delta, and Omicron. The specific CD8+ T-cell epitopes included in the SARS-CoV-2 Dextramer? assays are overlayed with orange arrows, demonstrating a conservation of most epitopes.