# Persistent Immune Dysregulation during Long COVID is Manifested in Antibodies Targeting Envelope and Nucleocapsid Proteins

**Authors:** Marcin Kwissa, Manikannan Mathayan, Satyajeet S. Salunkhe, Velavan Bakthavachalam, Zijing Ye, Mark A. Sanborn, Samantha Condo, Aditi Upadhye, Athulith Nemakal, Haoyang Wang, James Chan, Justin M. Richner, Sanjib Basu, Richard M. Novak, Jeffrey R. Jacobson, Balaji B Ganesh, Martha Cerda, Hassan Brim, Nathaniel B Erdmann, Bruce D. Levy, Gailen D. Marshall, Grace A McComsey, Torri D Metz, Megumi J. Okumura, Michael J. Peluso, Tiffany Walker, Paul J. Utz, Jerry A. Krishnan, Bellur S. Prabhakar, Jalees Rehman

PMC · DOI: 10.21203/rs.3.rs-8302624/v1 · Research Square · 2026-01-08

## TL;DR

The study finds that people with Long COVID have persistent immune issues, including high antibody levels against certain SARS-CoV-2 proteins and elevated immune cell activity.

## Contribution

The study identifies specific immune markers and antibody patterns that persist in Long COVID patients over six months.

## Key findings

- LC participants showed elevated IgG titers against SARS-CoV-2 Envelope and Nucleocapsid proteins for up to 6 months.
- LC patients had higher levels of circulating T follicular helper cells and mucosa-associated invariant T cells.
- LC participants exhibited elevated serum cytokines and higher rates of autoantibodies compared to convalescent individuals.

## Abstract

Long COVID (LC) or Post-Acute Sequelae of SARS-CoV-2 infection (PASC) syndrome represents a widespread health challenge that necessitates the development of novel diagnostic approaches and targeted therapies that can be readily deployed. Immune dysregulation has been reported as one of the hallmarks of LC, but the extent of LC immune dysregulation in patients over time remains unclear. We therefore assessed SARS-CoV-2-specific antibody responses, peripheral immune cell profiles, autoantibody profiles and circulating cytokines for up to 6 months in participants with a SARS-CoV-2 infection who either convalesced or developed LC. Compared to convalescent, LC participants with a broad range of LC phenotypes exhibited persistently elevated IgG titers for SARS-CoV-2 Envelope and Nucleocapsid proteins over the 6 months of study duration. In contrast, the IgG responses to Spike protein were significantly lower in the LC cohort with predominantly IgG1 and IgG3 class-switched bias. Using CyTOF analysis we show elevated numbers of circulating T follicular helper cells (cTFH) and mucosa-associated invariant T cells (MAIT), which also correlated with high anti-Envelope IgG titers. Persistent immune activation was accompanied by augmented serum cytokine profiles with LIF, IL-11, Eotaxin-3, and HMGB-1 in LC participants, who also demonstrated significantly higher rates of autoantibodies. These findings highlight the persistence of immune dysregulation in LC, underscoring the need to explore targeted therapies addressing viral persistence, dysregulated antibody production, and autoimmunity.

## Linked entities

- **Proteins:** LOC124901580 (endogenous retrovirus group K member 6 Env polyprotein), CHMP5 (charged multivesicular body protein 5)
- **Diseases:** Post-Acute Sequelae of SARS-CoV-2 infection (MONDO:0100233)

## Full-text entities

- **Genes:** IGHA1 (immunoglobulin heavy constant alpha 1) [NCBI Gene 3493] {aka IgA1}, IL18 (interleukin 18) [NCBI Gene 3606] {aka IGIF, IL-18, IL-1g, IL1F4}, S (surface glycoprotein) [NCBI Gene 43740568] {aka spike glycoprotein}, IGHG1 (immunoglobulin heavy constant gamma 1 (G1m marker)) [NCBI Gene 3500], JCHAIN (joining chain of multimeric IgA and IgM) [NCBI Gene 3512] {aka IGCJ, IGJ, JCH}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, CD27 (CD27 molecule) [NCBI Gene 939] {aka S152, S152. LPFS2, T14, TNFRSF7, Tp55}, HMGB1 (high mobility group box 1) [NCBI Gene 3146] {aka HMG-1, HMG1, HMG3, SBP-1}, IGLV@ (immunoglobulin lambda variable cluster) [NCBI Gene 3546] {aka IGLV}, LTA (lymphotoxin alpha) [NCBI Gene 4049] {aka LT, TNFB, TNFSF1, TNLG1E}, LIF (LIF interleukin 6 family cytokine) [NCBI Gene 3976] {aka CDF, DIA, HILDA, MLPLI}, GAD1 (glutamate decarboxylase 1) [NCBI Gene 2571] {aka CPSQ1, DEE89, GAD, GAD-67, SCP}, IL24 (interleukin 24) [NCBI Gene 11009] {aka C49A, FISP, IL10B, MDA7, MOB5, ST16}, IL12B (interleukin 12B) [NCBI Gene 3593] {aka CLMF, CLMF2, IL-12B, IMD28, IMD29, NKSF}, B3GAT1 (beta-1,3-glucuronyltransferase 1) [NCBI Gene 27087] {aka CD57, GLCATP, GLCUATP, HNK1, LEU7, NK-1}, NCAM1 (neural cell adhesion molecule 1) [NCBI Gene 4684] {aka CD56, MSK39, NCAM}, IL7R (interleukin 7 receptor) [NCBI Gene 3575] {aka CD127, CDW127, IL-7R-alpha, IL-7Ralpha, IL7RA, IL7Ralpha}, IGK (immunoglobulin kappa locus) [NCBI Gene 50802] {aka IGK@}, IGHA2 (immunoglobulin heavy constant alpha 2 (A2m marker)) [NCBI Gene 3494], CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, IGHM (immunoglobulin heavy constant mu) [NCBI Gene 3507] {aka AGM1, MU, VH}, IL11 (interleukin 11) [NCBI Gene 3589] {aka AGIF, IL-11}, CXCL5 (C-X-C motif chemokine ligand 5) [NCBI Gene 6374] {aka ENA-78, SCYB5}, PTPRC (protein tyrosine phosphatase receptor type C) [NCBI Gene 5788] {aka B220, CD45, CD45R, GP180, IMD105, L-CA}, IGHG4 (immunoglobulin heavy constant gamma 4 (G4m marker)) [NCBI Gene 3503], M (membrane glycoprotein) [NCBI Gene 43740571], IGHG3 (immunoglobulin heavy constant gamma 3 (G3m marker)) [NCBI Gene 3502] {aka IgG3}, IL3RA (interleukin 3 receptor subunit alpha) [NCBI Gene 3563] {aka CD123, IL-3R-alpha, IL3R, IL3RAY, IL3RX, IL3RY}, IGKV@ (immunoglobulin kappa variable cluster) [NCBI Gene 3519] {aka IGKV, IGKV1, IGKV1@, IGKV2, IGKV2@, IGKV3}, IGL (immunoglobulin lambda locus) [NCBI Gene 3535] {aka IGL@}, ITGAX (integrin subunit alpha X) [NCBI Gene 3687] {aka CD11C, SLEB6}, TNFSF13B (TNF superfamily member 13b) [NCBI Gene 10673] {aka BAFF, BLYS, CD257, TALL-1, TALL1, THANK}, IFNB1 (interferon beta 1) [NCBI Gene 3456] {aka IFB, IFF, IFN-beta, IFNB}, CXCL10 (C-X-C motif chemokine ligand 10) [NCBI Gene 3627] {aka C7, IFI10, INP10, IP-10, SCYB10, crg-2}, IL23A (interleukin 23 subunit alpha) [NCBI Gene 51561] {aka IL-23, IL-23A, IL23P19, P19, SGRF}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, IL17A (interleukin 17A) [NCBI Gene 3605] {aka CTLA-8, CTLA8, IL-17, IL-17A, IL17, ILA17}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, IL2RA (interleukin 2 receptor subunit alpha) [NCBI Gene 3559] {aka CD25, IDDM10, IL2R, IMD41, TCGFR, p55}, CXCR5 (C-X-C motif chemokine receptor 5) [NCBI Gene 643] {aka BLR1, CD185, MDR15}, CD28 (CD28 molecule) [NCBI Gene 940] {aka IMD123, Tp44}, E (envelope protein) [NCBI Gene 43740570], LOC102723407 (immunoglobulin heavy variable 4-38-2-like) [NCBI Gene 102723407] {aka IGHV4, IGHV4-30, IGHV4-38-2, IGHV4-39, IGHV4-b, IGVH4-39}, N (nucleocapsid phosphoprotein) [NCBI Gene 43740575], CCL26 (C-C motif chemokine ligand 26) [NCBI Gene 10344] {aka IMAC, MIP-4a, MIP-4alpha, SCYA26, TSC-1}, CD19 (CD19 molecule) [NCBI Gene 930] {aka B4, CVID3}, CD14 (CD14 molecule) [NCBI Gene 929], IGHG2 (immunoglobulin heavy constant gamma 2 (G2m marker)) [NCBI Gene 3501], IGHV3-69-1 (immunoglobulin heavy variable 3-69-1 (pseudogene)) [NCBI Gene 28402] {aka IGHV3-H, IGHV3H}
- **Diseases:** hepatitis (MESH:D056486), dyspnea (MESH:D004417), neurological, cardiovascular, musculoskeletal or respiratory complications (MESH:D012140), nerve problems (MESH:D019973), Immune Dysregulation (OMIM:614878), chest pain (MESH:D002637), arrhythmia (MESH:D001145), immune abnormalities (MESH:D007154), swelling legs (MESH:D004487), chronic inflammation (MESH:D007249), IgG4 (MESH:D000077733), disease (MESH:D004194), sleeping problems (MESH:D012893), cardio-pulmonary, musculoskeletal, neuropsychiatric, (MESH:D009140), muscle pain (MESH:D063806), LC (MESH:D000094024), back pain (MESH:D001416), cough (MESH:D003371), anxiety (MESH:D001007), dysautonomia (MESH:D054969), heart problems (MESH:D006331), skipped beats (MESH:D005117), tissue injury (MESH:D017695), joint pain (MESH:D018771), Infection (MESH:D007239), COVID-19 (MESH:D000086382), head pain (MESH:D006261), brain fog (MESH:D005222), weakness in arms or legs (MESH:D018908), HIV (MESH:D015658), loss of or change in smell or taste (MESH:D000086582), autoimmune reaction (MESH:D001327), sleep apnea (MESH:D012891), excessive fatigue (MESH:D005221), viral infection (MESH:D014777), chronic diseases (MESH:D002908), Cardio-pulmonary2 (MESH:D059347)
- **Chemicals:** FA (MESH:C030544), ABC (MESH:C106538), sulfuric acid (MESH:C033158), Alexa 647 (MESH:C569686), urea (MESH:D014508), Citric acid (MESH:D019343), Trypan blue (MESH:D014343), water (MESH:D014867), H2O2 (MESH:D006861), Methylcellulose (MESH:D008747), His (MESH:D006639), metal (MESH:D008670), Tween 20 (MESH:D011136), NaN3 (MESH:D019810), CyTOF (-), PBS (MESH:D007854), paraformaldehyde (MESH:C003043), DTT (MESH:D004229), acetonitrile (MESH:C032159), Na2CO3 (MESH:C005686), NaHCO3 (MESH:D017693), formaldehyde (MESH:D005557), nitrogen (MESH:D009584)
- **Species:** herpesvirus [taxon 39059], Severe acute respiratory syndrome coronavirus 2 (no rank) [taxon 2697049], Severe acute respiratory syndrome-related coronavirus (no rank) [taxon 694009], Homo sapiens (human, species) [taxon 9606], Cavia porcellus (domestic guinea pig, species) [taxon 10141], human gammaherpesvirus 4 (Epstein Barr virus, no rank) [taxon 10376]
- **Cell lines:** MAIT — Homo sapiens (Human), Telomerase immortalized cell line (CVCL_AT83), Vero E6 — Chlorocebus sabaeus (Green monkey), Spontaneously immortalized cell line (CVCL_0574)

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12803341/full.md

## Figures

5 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12803341/full.md

## References

68 references — full list in the complete paper: https://tomesphere.com/paper/PMC12803341/full.md

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Source: https://tomesphere.com/paper/PMC12803341