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

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.

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

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.

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.

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.