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

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.