Abstract

Long COVID (LC) involves a spectrum of chronic symptoms after acute severe acute respiratory syndrome coronavirus 2 infection. Current hypotheses for the pathogenesis of LC include persistent virus, tissue damage, autoimmunity, endocrine insufficiency, immune dysfunction and complement activation. We performed immunological, virological, transcriptomic and proteomic analyses from a cohort of 142 individuals between 2020 and 2021, including uninfected controls (n = 35), acutely infected individuals (n = 54), convalescent controls (n = 24) and patients with LC (n = 28). The LC group was characterized by persistent immune activation and proinflammatory responses for more than 180 days after initial infection compared with convalescent controls, including upregulation of JAK-STAT, interleukin-6, complement, metabolism and T cell exhaustion pathways. Similar findings were observed in a second cohort enrolled between 2023 and 2024, including convalescent controls (n = 20) and patients with LC (n = 18). These data suggest that LC is characterized by persistent activation of chronic inflammatory pathways, suggesting new therapeutic targets and potential biomarkers of disease.

Discussion

In this study, we found that individuals with LC were characterized by persistent activation of chronic inflammatory pathways compared with CCs. These pathways included proinflammatory cytokine signaling, complement activation, metabolic dysregulation and immune exhaustion and persisted for more than 180 days. These findings suggest that chronic inflammation may contribute to the pathogenesis of LC and define potential new therapeutic targets.

We observed that participants with LC exhibited reduced granzyme B and cytotoxic T cell signaling and increased immune exhaustion, suggesting dysregulated cross-talk between the innate and adaptive immune responses. Our findings are consistent with prior reports that the IL-6 and JAK-STAT signaling pathways were upregulated in individuals with LC, particularly in those with cardiorespiratory or multisystem symptoms. We also found that chronic upregulation of IFNγ signaling was associated with LC and correlated with signatures of reduced T cell activation and increased T cell exhaustion, suggesting that chronic immune stimulation may lead to functional impairment of T cells. These findings are consistent with prior observations and suggest the potential role of T cell dysregulation and exhaustion in LC pathogenesis.

Our study also confirms and extends prior reports of metabolic dysregulation in LC. We observed a decrease in amino acid metabolism and an increase in corticotropin-releasing hormone signaling, leptin signaling, fatty acid metabolism, bile acid and beta-alanine metabolism in LC. Moreover, these metabolic pathways correlated with proinflammatory pathways in the LC group, suggesting a link between metabolic dysregulation and chronic inflammation. We also observed decreased activity of the telomere maintenance and DNA damage recognition and repair pathways, chromatin regulation and DNA methylation in the LC group. Impaired telomere maintenance could be associated with premature cellular senescence or apoptosis that may impede tissue repair processes.

Our study is limited by relatively small cohorts of individuals with LC who were predominantly female and with symptom clusters that primarily involved fatigue, brain fog and pain. Larger studies from more diverse populations will be required to assess the generalizability of our findings. Nevertheless, we observed good concordance between the 2020–2021 initial cohort and the 2023–2024 validation cohort. Another limitation is the use of bulk RNA-seq, which limits more detailed resolution of pathways at the cellular level. Therefore, future studies should use single-cell transcriptomic and T cell profiling technologies to provide higher-resolution data. Nevertheless, our observations suggest potential therapeutic targets for LC that could be explored in clinical trials. Because the IL-6 and JAK-STAT pathways were among the top upregulated pathways in participants with LC in both the 2020–2021 and the 2023–2024 cohorts, we have initiated a clinical trial to evaluate the therapeutic efficacy of the JAK1 inhibitor abrocitinib for LC (NCT06597396).

In conclusion, our data demonstrate that LC is characterized by chronic inflammation, immune exhaustion and metabolic dysregulation. Current therapeutic efforts are largely focused on antiviral agents to address potential residual viral replication. However, the lack of efficacy of nirmatrelvir-ritonavir in treating LC highlights the need to explore alternative therapeutic strategies. Our data suggests that the JAK-STAT and IL-6 pathways, and the IFN and metabolic pathways, are potential therapeutic targets that could be evaluated for LC.