Comprehensive molecular characterization of post-COVID condition: Immunoglobulin suppression and persistent...

Post-COVID condition (PCC), or long COVID, affects a significant proportion of individuals following SARS-CoV-2 infection, yet its molecular framework remains poorly understood. This study aimed to define the molecular profile of PCC by integrating broad proteomic analysis using Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) with targeted antigen quantification through targeted mass spectrometry (MRM/SRM).

Plasma and pellet fractions from 65 PCC patients, classified as symptomatic or asymptomatic, were analyzed using SWATH-MS with updated SARS-CoV-2 protein libraries (v2022 and v2024), enabling a comprehensive profiling of immune- and viral-related proteins. The presence of viral antigens, specifically spike and nucleocapsid proteins, was quantified using MRM/SRM. A protein-concentration-based severity metric using clustering analysis and dimensionality reduction methods was proposed to assess correlations between proteomic alterations and clinical symptoms.

A key finding in PCC patients, particularly in symptomatic cases, was a pronounced downregulation of immunoglobulins, including kappa and lambda light chains. SWATH-MS analysis identified six proteins (corresponding to UniProt entries Q8N5F4, LV147, KV311, KVD20, A0A5C2G1U0, and KV315) that strongly correlated with disease severity (R² > 0.9), highlighting their potential as biomarkers. In pellet samples, the protein G1SG72 (ABCE1) emerged as a marker associated with severity, suggesting possible alterations in antiviral responses. The severity metric proposed showed a strong correlation with clinical symptoms, providing a quantifiable measure of PCC severity and enabling effective patient stratification. Additionally, MRM/SRM analysis detected the persistent presence of SARS-CoV-2 antigens, specifically the Spike and Nucleocapsid proteins, in symptomatic PCC patients.

This study defines a molecular profile of PCC, marked by immunoglobulin downregulation and the persistence of SARS-CoV-2 antigens, which may contribute to ongoing immune alterations in PCC. The severity metric derived from proteomic profiling provides a tool for categorizing PCC patients based on symptom severity and could support future studies aimed at targeted interventions.