Preprint Systems Immunology of Long Covid: Insights from the STOP-PASC Clinical Trial, 2025, Maestri, Bonilla+

[SNT Gatchaman]

Systems Immunology of Long Covid: Insights from the STOP-PASC Clinical Trial

Spoiler: Authors / Stanford

Evan Maestri; Woo Joo Kwon; Hong Zheng; Tyler Prestwood; Haley Hedlin; Jane W Liang; Holly McCann; Blake Shaw; Lu Tian; Ben Jones; Rufei Lu; Graham Wiley; Emily Haraguchi; Oliver Wirz; Jumana Afaghani; Brandon Lam; Dlovan F D Mahmood; Nicole A Phillips; Martha Ms Sim; Jeremy P Wood; James R Heath; Scott D Boyd; Joel Guthridge; Upinder Singh; Hector Bonilla; Prasanna Jagannathan; Pj Utz; Linda N Geng; Purvesh Khatri

BACKGROUND
Post Acute Sequelae of COVID-19 (PASC), also referred to as Long COVID, is an infection-associated chronic syndrome with heterogenous symptom profiles that occurs in a subset of people following SARS-CoV-2 infection. Despite proposed viral persistence mechanisms, no therapeutic benefit was observed in two randomized placebo-controlled trials of nirmatrelvir/ritonavir (NMV/r) in adults with Long COVID, including the Selective Trial of Paxlovid for PASC (STOP-PASC) and PAX LC. This systems immunology analysis aimed to characterize immune profiles of participants during clinical trial intervention, identify biomarkers associated with patient-reported outcomes, and investigate potential mechanisms underlying Long COVID.

METHODS
We performed comprehensive immunological profiling of 152 STOP-PASC trial participants using plasma proteomics (Olink® Explore HT 5400 panel), autoantigen arrays, viral serology, and microclot assays at baseline, day 15, and week 10. We assessed associations between immune features and patient-reported outcomes. We also conducted meta-analysis of nine independent Long COVID proteomics cohorts (n=590 total samples) to identify conserved inflammatory signatures.

RESULTS
NMV/r treatment at day 15 compared with baseline induced transient changes in plasma proteins that normalized by week 10, primarily impacting myeloid cell/monocyte, lysosome, and complement activation pathways. Cardiovascular symptoms were negatively associated with SARS-CoV-2 antibody levels at baseline. No widespread differences in autoantibody profiles, Epstein-Barr virus (EBV) reactivation, or microclotting were observed between STOP-PASC Long COVID participants, pre-pandemic controls, and individuals without Long COVID. Meta-analysis of publicly available Olink® data from Long COVID cohorts identified a conserved 60-protein Long COVID Signature (LCS) score revealing multi-compartment immune activation involving monocyte, neutrophil, and T/NK cell modules.

CONCLUSIONS
These findings advance our understanding of Long COVID immunology and may help direct future proteomic biomarker endpoints for Long COVID clinical trials.

Web | DOI | PDF | Preprint: MedRxiv | Open Access

 

[SNT Gatchaman]

Microclots were detected only in a small subset of STOP-PASC LC participants at baseline and the standardized mean differences (SMD) suggest that differences between groups are generally small.

By week 10, the proteome returned to baseline states with no significant changes identified. Overall, a 15-day treatment of NMV/r induced transient changes in the plasma proteome that are known to modulate immune pathways associated with mounting effective antiviral responses, and these changes return to baseline levels by week 10.

we sought to identify proteins that were associated with the severity of the core PROs reported by the participants in the STOP-PASC study. […] 110 proteins demonstrated consistent patterns (p<0.05) with the trend present in three or more PROs. For example, leptin (LEP), coagulation factor VII (F7), and coagulation factor XII (F12) were positively associated with fatigue and heart/cardiovascular symptoms; CD38 was negatively associated with dyspnea, and Interleukin 1 Receptor Like 1 (IL1RL1) and Interleukin 1 Receptor Type 2 (IL1R2) were negatively associated with post exertional malaise.

we turned to external publicly available LC cohorts. […] identified 60 proteins that were differentially regulated in the same direction in independent cohorts (FDR<5%, effect size >0.5, proteins measured in ≥3 cohorts). We defined a LC Signature (LCS) score as the geometric mean of 60 upregulated proteins

Our results suggest that measurement of PRO severity in LC aligns with meaningful underlying inflammatory signaling and biology. We observed leptin (LEP) was significantly associated with increased fatigue and several other PROs

Our analysis did not identify differences in IgG antibody levels against EBV viral capsid antigen (VCA), nuclear antigen 1 (EBNA-1), early antigen (EA), or CMV glycoprotein B between STOP-PASC LC participants and individuals without LC. Our serological assessment at this later timepoint (protracted LC symptom duration) suggests that persistent herpesvirus reactivation was not a dominant feature in established LC, at least in our mostly vaccinated study population.

While AAb repertoire changes return to homeostatic conditions after the acute phase in most patients, some with LC have detectable patterns of autoreactivity that could be associated with neurological sequela. We did not observe widespread evidence of autoimmunity against traditional autoantigens in STOP-PASC LC participants. However, a subset of participants in our cohort showed reactivities against specific antigens (CENP A, fibrillarin, and PDC-E2).

Despite considerable heterogeneity in LC, we have demonstrated via multicohort meta-analysis conserved dysregulation in inflammatory immune pathways. The proteins in the LCS Score which are consistently elevated in LC in multiple cohorts are associated with inflammation (IL6), monocyte (SIGLEC1/10) and neutrophil activation/granules (AZU1, PGLYRP1), and T/NK cell granzymes (GZMH, GZMA) suggesting a persistent dysregulated immune response.

 

[V.R.T.]

This looks really interesting.

A fair few cells/molecules come up here that have been discussed before.

Interleukin 1 Receptor Like 1 (IL1RL1) and Interleukin 1 Receptor Type 2 (IL1R2) were negatively associated with post exertional malaise.

Have we seen these come up before?

Interesting that this came from the STOP-PASC cohort.

 

[V.R.T.]

Large scale phenotyping of long COVID inflammation reveals mechanistic subtypes of disease

Spoiler: Multiple Authors, esp National Heart and Lung Institute, Imperial College

Felicity Liew; Claudia Efstathiou; Sara Fontanella; Matthew Richardson; Ruth Saunders; Dawid Swieboda; Jasmin K. Sidhu; Stephanie Ascough; Shona C. Moore; Noura Mohamed; Jose Nunag; Clara King; Olivia C. Leavy; Omer Elneima; Hamish J.C. McAuley; Aarti Shikotra; Amisha Singapuri; Marco Sereno; Victoria C Harris; Linzy Houchen-Wolloff; Neil J Greening; Nazir I Lone; Matthew Thorpe; A. A. Roger Thompson; Sarah L. Rowland-Jones; Annemarie B. Docherty; James D. Chalmers; Ling-Pei Ho; Alexander Horsley; Betty Raman; Krisnah Poinasamy; Michael Marks; Onn Min Kon; Luke Howard; Daniel G. Wootton; Jennifer K. Quint; Thushan I. de Silva; Antonia Ho; Christopher Chiu; Ewen M Harrison; William Greenhalf; J. Kenneth Baillie; Malcolm G. Semple; Rachael A. Evans; Louise V. Wain; Christopher Brightling; Lance Turtle; Ryan S. Thwaites; Peter J.M. Openshaw; ISARIC4C Investigators and the PHOSP-COVID collaborative group

One in ten SARS-CoV-2 infections result in prolonged symptoms termed ‘long COVID’, yet disease phenotypes and mechanisms are poorly understood. We studied the blood proteome of 719 adults, grouped by long COVID symptoms.

Elevated markers of monocytic inflammation and complement activation were associated with increased likelihood of all symptoms. Elevated IL1R2, MATN2 and COLEC12 associated with cardiorespiratory symptoms, fatigue, and anxiety/depression, while elevated MATN2 and DPP10 associated with gastrointestinal (GI) symptoms, and elevated C1QA was associated with cognitive impairment (the proteome of those with cognitive impairment and GI symptoms being most distinct).

Markers of neuroinflammation distinguished cognitive impairment whilst elevated SCG3, indicative of brain-gut axis disturbance, distinguished those with GI symptoms. Women had a higher incidence of long COVID and higher inflammatory markers. Symptoms did not associate with respiratory inflammation or persistent virus in sputum. Thus, persistent inflammation is evident in long COVID, distinct profiles being associated with specific symptoms.

Link | PDF (Preprint: MedRxiv)

Link to published article here

I found the above for IL1R2

Highlights

• PGE2 is necessary to elevate sST2 levels in the lung with type 2 lung inflammation
• Intraepithelial mast cells are the principal source of PGE2-driven lung sST2 production
• Deficiency of mast-cell-derived sST2 exaggerates type 2 lung inflammation
• PGE2 alters the mast cell transcriptome and promotes short Il1rl1 expression

Summary
Severe asthma and sinus disease are consequences of type 2 inflammation (T2I), mediated by interleukin (IL)-33 signaling through its membrane-bound receptor, ST2. Soluble (s)ST2 reduces available IL-33 and limits T2I, but little is known about its regulation.

We demonstrate that prostaglandin E2 (PGE2) drives production of sST2 to limit features of lung T2I. PGE2-deficient mice display diminished sST2. In humans with severe respiratory T2I, urinary PGE2 metabolites correlate with serum sST2. In mice, PGE2 enhanced sST2 secretion by mast cells (MCs). Mice lacking MCs, ST2 expression by MCs, or E prostanoid (EP)2 receptors by MCs showed reduced sST2 lung concentrations and strong T2I. Recombinant sST2 reduced T2I in mice lacking PGE2 or ST2 expression by MCs back to control levels. PGE2 deficiency also reversed the hyperinflammatory phenotype in mice lacking ST2 expression by MCs. PGE2 thus suppresses T2I through MC-derived sST2, explaining the severe T2I observed in low PGE2 states.

LINK

And this for IL1RL1

I wonder if anyone more knowledgable thinks their association with PEM here (and IL1R2 being associated with fatigue in the first study I linked) could make some sort of mechanistic sense?