Memory T cell reactivity to a broad range of conserved SARS-CoV-2-derived ORF1ab epitopes in first wave COVID-19 convalescents.

Abstract

Introduction: Understanding T cell responses to SARS-CoV-2 is crucial for developing effective vaccines. Memory T cells, including CD8⁺ cytotoxic and CD4⁺ helper T cells, play key roles in controlling viral infections. The open reading frame 1ab (ORF1ab) region of SARS-CoV-2, essential for viral replication, is highly conserved.

Objective: This study aims to analyze whether memory T cell responses against ORF1ab derived HLA class I peptides are present in convalescent individuals.

Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from 53 staff members, including 20 healthy and 33 convalescent subjects, in September 2020 during the first wave of COVID-19 at the Faculty of Medicine, Airlangga University, and Soetomo Hospital, Surabaya, Indonesia. The frequency of interferon gamma (IFNγ)-producing T cells in response to SARS-CoV-2 peptides was assessed using the ELISpot assay. Flow cytometry characterized memory T cell populations, including activation and exhaustion markers on CD8⁺ and CD4⁺ T cells.

Results: Significant increases in IFNγ production were observed in four out of ten ORF1ab-derived peptides tested: WSMATYYLF (p = 0.002), YVFCTVNAL (p = 0.007), LMIERFVSL (p = 0.011), and YLITPVHVM (p = 0.019). Convalescent subjects with prior mild and moderate COVID-19 exhibited significantly higher IFNγ responses to WSMATYYLF compared to controls. Correlation analyses showed that IFNγ responses to several peptides positively correlated with both infection and post-infection intervals. Flow cytometry analysis revealed significant increases in peptide-induced IFNγ production in CD8⁺ memory T cells, including central and effector memory subsets among convalescent subjects, along with notable differences in the exhaustion marker PD-1 compared to controls.

Conclusion: SARS-CoV-2 ORF1ab-derived HLA class 1 peptides, particularly WSMATYYLF, YVFCTVNAL, and LMIERFVSL, induce durable memory CD8⁺ T cell responses in COVID-19 convalescents. The correlation between T cell responses and the time since infection supports the persistence of ORF1ab-specific T cell immunity. This finding may potentially contribute to non-spike-based COVID-19 vaccine strategies and T cell-based immunomonitoring.