Multi-layered deep immune profiling, SARS-CoV-2 RNAemia and inflammation in unvaccinated COVID-19 individuals with persistent symptoms

Long-COVID immunopathogenesis involves diverse factors. We longitudinally characterize hospitalized COVID-19 patients, examining the role of SARS-CoV-2 RNAemia and inflammation in immune dysregulation. Hospitalized patients are evaluated during acute infection (T0), 3 months post-symptom onset (T1), and 3 years if symptoms persisted (T2). Immune profile includes characterization of SARS-CoV-2-specific/non-specific T/B cells (flow cytometry) and antibodies (ELISA, neutralization, ADCC). RNAemia and cytokines are quantified (RT-PCR, cytometric beads array) and correlated. Statistics: non-parametric cross-sectional, longitudinal and correlation analyses. Here we show 48 hospitalized individuals during acute COVID-19, 38 exhibit early persistent symptoms (EPS+) 3 months post-symptoms onset, 10 do not (EPS−). Groups are comparable for age, sex, co-morbidities. The EPS+ shows fatigue, dyspnoea, anosmia/dysgeusia, diarrhea, chronic pain, mnestic disorders. Over time, they show a reduction of neutralization ability and total SARS-CoV-2-specific CD4 T cells, with increased total CD4 TEMRA, and failure to increase RBD-specific B cells and IgA+ MBCs. EPS+ patients show higher levels of T0-IFN-γ + CD4 TEMRA, T1-IL-2 + CD4 TEM and T1-TNF-α + CD4 cTfh. In EPS+, baseline SARS-CoV-2 RNAemia positively correlates with CD4 TEMRA, follow-up SARS-CoV-2 RNAemia with ADCC. Among 38 EPS+ individuals at T1, 33 are evaluated 3 years after infection, 5 are lost at follow-up. 10/33 EPS+ show long-term symptoms (late persistent symptoms, EPS + LPS+), whereas 23/33 fully recover (EPS + LPS−). Antibodies, RNAemia, and cytokines show no differences between/within groups at any time point. Early persistent symptoms are associated with multi-layered SARS-CoV-2-specific/non-SARS-CoV-2-specific immune dysregulation. The shift towards non-Ag-specific TEMRA and ADCC trigger in EPS+ may relate to SARS-CoV-2 RNAemia. Early immune dysregulation does not associate with long-term persistent symptoms. Further research on SARS-CoV-2 RNAemia and early immune dysregulation is needed. After COVID-19 resolution, many individuals continue experiencing symptoms such as fatigue, shortness of breath, and cognitive issues, which limit their daily activities. The causes of persistent symptoms remain unclear, but poor immune control of infection is plausible. Our research examined two key elements in driving poor immune control, including the presence of virus in the blood and inflammation. For severely ill, hospitalized, unvaccinated individuals with long-lasting symptoms beyond three months after infection, our findings show a weak immune response against the virus that causes COVID-19. The presence of the virus in the blood may contribute to this issue. Understanding these mechanisms moves us closer to finding better treatments. Rovito et al. conduct deep immune profiling of hospitalized and unvaccinated individuals with persistent symptoms three months post COVID-19. They explore the role of SARS-CoV-2 RNAemia and peripheral inflammation in driving immune dysregulation, finding impaired responses in the humoral arm partially linked to RNAemia.