Long COVID patients maintain robust immune memory two years after infection

Even after two years, individuals with long COVID display resilient immune responses, offering hope for long-term protection against reinfection.

In a recent study published in the journal Proceedings of the National Academy of Sciences, researchers defined severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific B- and T-cell responses in individuals with long COVID.

Long COVID is an ongoing global health burden; it impacts multiple organ systems, with affected people reporting diverse symptoms that persist from 12 weeks to two years or longer after SARS-CoV-2 infection. Fatigue, myalgia, impaired concentration, and chest pain are the most common symptoms.

Long COVID may be attributed to multiple non-mutually exclusive mechanisms that cumulatively account for the large spectrum of symptoms, including immune perturbations, viral persistence, and inflammatory pathways.

SARS-CoV-2-specific cluster of differentiation 8⁺ (CD8⁺) and CD4⁺ T cells have a major role in viral clearance and recovery. However, T cell recruitment and persistence in long COVID are less clear.

Long COVID can last weeks, months, or even years, affecting multiple organ systems with a wide range of symptoms, including fatigue, cognitive dysfunction, and chest pain.

Further, the introduction of vaccines complicated efforts to understand long COVID. Although vaccination reduced the risk of infection, it also boosted certain T-cell responses and altered immunodominance hierarchies, though it did not reduce long COVID rates.

This study provides critical insights into the long-term persistence and functionality of SARS-CoV-2-specific immune responses in individuals with long COVID, highlighting the role of robust T-cell memory pools in potential protection against subsequent infections, even in the presence of viral mutations.

The study and findings

The present study defined SARS-CoV-2-specific B- and T-cell responses over two years in individuals with long COVID.

The researchers analyzed 31 persons with long COVID for up to two years post-SARS-CoV-2 infection. Participants were recruited in Melbourne and Hong Kong between February and October 2020. Meanwhile, 19 persons with no ongoing symptoms served as non-long COVID (non-LC) controls.

The most commonly reported symptoms were headache, fatigue, memory issues, mental fog, confusion, tremors, dizziness, balance issues, loss of smell/taste, paresthesia, and problems speaking.

Notably, two-fifths of the sample reported complete recovery by the study endpoint.

They used SARS-CoV-2 peptide–human leukocyte antigen (HLA) tetramers to examine T cell responses against 11 CD8⁺ and two CD4⁺ viral epitopes.

They observed robust prototypical populations of viral epitope-specific CD8⁺ and CD4⁺ T cells at all time points in long COVID subjects and non-LC controls.

The frequency of spike-specific CD8⁺ T cells increased 3.7-fold between three months and 18 months post-infection in long COVID subjects. Meanwhile, spike-specific CD4⁺ T cell responses were stable in long COVID subjects and non-LC controls over time.

Next, the team examined the temporal changes in ex vivo phenotype and activation of SARS-CoV-2 tetramer-specific T cells and the impact of vaccination on activation and memory phenotypes.

While vaccination did not significantly alter the overall activation state of T cells, it was associated with a stable phenotype of SARS-CoV-2-specific T cells over time, underscoring the persistence of these immune responses in both long COVID and non-LC groups.

Total CD4⁺ and CD8⁺ populations of T_naïve, T central memory (T_cm), T effector memory (T_em), T_em cells re-expressing CD45RA (T_emra), and T stem cell memory (T_scm) subsets were not significantly different from acute infection to later time points in long COVID and control groups.

Among non-spike- and spike-specific CD8⁺ T cells, the T_cm phenotype was predominant (> 65%) at the acute time point but decreased (to 30% to 50%) at convalescent time points in the long COVID group. These convalescent T-cell phenotypes were stable from three months post-infection or after vaccination. Spike-specific CD4⁺ T cells were of T_cm and T_em phenotypes at the acute time point in the long COVID group.

However, spike-specific CD4⁺ T cells were of the T_cm phenotype from three months post-infection or after vaccination.

Further, both groups had low spike- and nucleocapsid-specific CD19⁺ immunoglobulin D^- (IgD^-) B cells during acute infection. Nevertheless, spike-specific B cells increased during convalescence in long COVID subjects.

Following the resolution of acute infection, the frequency of nucleocapsid-specific B cells remained stable over time, but spike-specific B cells increased at 18 and 24 months due to vaccination.

This increase highlights the lasting impact of vaccination on the immune system's ability to generate and maintain protective B-cell responses.

Long COVID and non-LC control groups had a higher frequency of spike-specific IgG⁺ B cells post-vaccination. Finally, the team investigated the T-cell receptor (TCR) signatures of antigen-specific CD4⁺ and CD8⁺ T cells.

To this end, 424 SARS-CoV-2-specific T cells from 16 long COVID subjects and four controls were single-cell sorted and sequenced at different time points.

They found that long COVID TCR clonotypes were evenly interspersed with control TCR clonotypes. Both groups exhibited two clusters based on CD4⁺ and CD8⁺ T cell epitopes.

Treatment for long COVID is largely symptomatic, focusing on managing individual symptoms due to the lack of a definitive cure.

The presence of key TCR signatures and their persistence across the two-year period suggest that individuals with long COVID, similar to fully recovered individuals, maintain functional T-cell memory that could be critical for long-term immunity.

The researchers compiled all individuals given the overlap of TCRαβ repertoires between the two groups.

The team generated alluvial plots per epitope to determine whether the same clonotype, TCRβ, or TCRα sequence was observed within individuals at multiple time points.

They observed a high degree of sharing within individuals for the TCRα and TCRβ chains across distinct epitopes, even after vaccination.

They identified seven CD4⁺ and 13 CD8⁺ TCRαβ clones within individuals across time points, suggesting clonal persistence in both groups.

Conclusions

Together, the findings indicate that SARS-CoV-2-specific T and B cells are established in long COVID and maintained over two years, similar to those in non-LC controls.

The results also demonstrate the establishment and persistence of antigen-specific T cell memory populations in long COVID at two years post-infection.

These findings provide essential insights into the immune landscape of long COVID, suggesting that despite the ongoing symptoms, individuals are equipped with immune memory that could protect against future infections.

Overall, the study provided key insights into CD4⁺ and CD8⁺ T cell responses in long COVID subjects and fully recovered persons.

Journal reference:

• Rowntree LC, Audsley J, Allen LF, et al. SARS-CoV-2-specific CD8+ T cells from people with long COVID establish and maintain effector phenotype and key TCR signatures over 2 years. Proceedings of the National Academy of Sciences, 2024, DOI: 10.1073/pnas.2411428121, https://www.pnas.org/doi/suppl/10.1073/pnas.2411428121