SARS-CoV-2 Mpro protease as a biomarker and therapeutic target in Long COVID: a real-world prospective cohort study

SARS-CoV-2 Mpro protease as a biomarker and therapeutic target in Long COVID: a real-world prospective cohort study | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Brief Communication SARS-CoV-2 Mpro protease as a biomarker and therapeutic target in Long COVID: a real-world prospective cohort study Soraya Maria Menezes, Marc Jamoulle, Chenyu Liu, Elena Louazon, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7449833/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Long COVID affects 400 million people worldwide, for whom predictive biomarkers and effective therapies are urgently needed. Herein, we investigate SARS-CoV-2 viral RNAs as candidate biomarkers and therapeutic targets. Combining whole blood digital transcriptomics and plasma proteomics, viral RNAs significantly correlated with platelet-expressed genes/proteins and complement/coagulation pathways. Likewise, SARS-CoV-2 ORF3a, ORF8 , M and antisense RNAs were significantly enriched in purified platelets. Mpro viral RNA was increased in patients with lower self-reported fitness, which could be reverted by Paxlovid (Nirmatrelvir/Ritonavir) treatment. Using a novel, cloud-based real-time analysis of personalized symptom scores, we found significant clinical benefit of Paxlovid, parallelled by a rapid decline in neurodamage/astrogliosis markers (NFL/GFAP). Multivariate logistic regression revealed antiviral but not antiplatelet treatment as independent predictor of clinical recovery in a real-world Long COVID cohort with long-term follow-up. Platelet-expressed biomarkers of Paxlovid response ( IL12A/HDAC5) were validated in a placebo-controlled clinical trial (PROLIFIC). In conclusion, our results provide mechanistic and druggable links between major Long COVID disease mechanisms: viral persistence, platelet/coagulation defects, and neurodamage. Health sciences/Biomarkers/Predictive markers Health sciences/Medical research/Translational research Biological sciences/Molecular biology/Transcriptomics Health sciences/Pathogenesis/Infection Biological sciences/Microbiology/Virology/SARS-CoV-2 Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplTable1NatMedDec2025.xlsx Suppl.Table2NatMedDec2025.xlsx Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7449833","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Brief Communication","associatedPublications":[],"authors":[{"id":562517058,"identity":"1c7e2a76-9fc8-4a6a-92ed-45140158ec00","order_by":0,"name":"Soraya Maria Menezes","email":"","orcid":"https://orcid.org/0000-0003-4519-8682","institution":"Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU 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Herein, we investigate SARS-CoV-2 viral RNAs as candidate biomarkers and therapeutic targets. Combining whole blood digital transcriptomics and plasma proteomics, viral RNAs significantly correlated with platelet-expressed genes/proteins and complement/coagulation pathways. Likewise, SARS-CoV-2 \u003cem\u003eORF3a, ORF8\u003c/em\u003e, \u003cem\u003eM\u003c/em\u003e and antisense RNAs were significantly enriched in purified platelets. \u003cem\u003eMpro\u003c/em\u003e viral RNA was increased in patients with lower self-reported fitness, which could be reverted by Paxlovid (Nirmatrelvir/Ritonavir) treatment. Using a novel, cloud-based real-time analysis of personalized symptom scores, we found significant clinical benefit of Paxlovid, parallelled by a rapid decline in neurodamage/astrogliosis markers (NFL/GFAP). Multivariate logistic regression revealed antiviral but not antiplatelet treatment as independent predictor of clinical recovery in a real-world Long COVID cohort with long-term follow-up. Platelet-expressed biomarkers of Paxlovid response (\u003cem\u003eIL12A/HDAC5)\u003c/em\u003e were validated in a placebo-controlled clinical trial (PROLIFIC). 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