VIPER: A program to validate next-generation Long COVID diagnostic tests

To unlock treatments, we must first have the right tools to measure the disease. That is where VIPER –  the Viral Immunopathogenesis and Persistence Repeat Donor Cohort – comes in. VIPER is a next-generation diagnostics program that is:

• Validating the first diagnostic tests for persistent SARS-CoV-2 and other key drivers of Long COVID
• Opening the door for industry engagement, just as validated diagnostics transformed HIV research
• Laying the groundwork for broader next-generation diagnostics for other infection-associated chronic illnesses, like Chronic Lyme Disease

In short: VIPER is the catalyst. It creates the diagnostic infrastructure needed for targeted treatments, and ultimately cures, to reach patients.

The diagnostic assays prioritized and validated through the VIPER program represent a new generation of Long COVID molecular diagnostics designed to capture complex biological signals with far greater precision than conventional testing approaches. These next-generation tools rely on advanced, high-throughput technologies – including liquid biopsy platforms – that can generate rapid, precise, and comprehensive molecular insights for disease detection and personalized treatment.

By enabling multiplexed measurement of SARS-CoV-2 RNA and antigen, host transcriptional responses, immune activation markers, and other molecular signatures from accessible biofluids, these technologies provide a powerful framework for identifying active biological processes driving Long COVID and for tracking disease activity over time.

The strength of VIPER lies in its world-class team. The core team includes:

• Dr. Amy Proal (PolyBio Foundation, Mount Sinai) – Global leader in infection-associated chronic disease, architect of the $42M Long COVID Research Consortium.
• Dr. Steven Deeks (UCSF) – Legendary HIV researcher, now leading the first Long COVID clinical trials at UCSF.
• Dr. Michael Peluso (UCSF) – Infectious disease physician with extensive experience caring for Long COVID patients and translating clinical samples into discovery.
• Dr. Timothy Henrich (UCSF) – Global expert in virus persistence, tissue analysis, and experimental medicine.
• The Long Covid Research Consortium – A groundbreaking global network of scientists founded by PolyBio. LCRC members are developing innovative diagnostic platforms for Long COVID, which will be rigorously tested and validated through VIPER.

Dr. Amy Proal (PolyBio Foundation, Mount Sinai) – Global leader in infection-associated chronic disease, architect of the $40M Long COVID Research Consortium.

Dr. Steven Deeks (UCSF) – Legendary HIV researcher, now leading the first Long COVID clinical trials at UCSF.

Dr. Michael Peluso (UCSF) – Infectious disease physician with extensive experience caring for Long COVID patients and translating clinical samples into discovery.

Dr. Timothy Henrich (UCSF) – Global expert in virus persistence, tissue analysis, and experimental medicine.

The Long Covid Research Consortium – A groundbreaking global network of scientists founded by PolyBio. LCRC members are developing innovative diagnostic platforms for Long COVID, which will be rigorously tested and validated through VIPER.

1. Recruitment of Participants – 150 individuals with and without Long COVID are enrolled in UCSF’s Long-Term Infection with Novel Coronavirus (LIINC) Study.
2. Collection of Samples – A carefully curated set of blood, saliva, stool, and tissue samples is collected and stored in a professional biobank.
3. Cross-Lab Testing – Multiple top laboratories receive identical, de-identified samples and apply their most promising diagnostic platforms.
4. Head-to-Head Evaluation – VIPER’s data team compares results to identify the most accurate, scalable tests.
5. Path to Patients – The strongest diagnostics are fast-tracked into clinical trials at UCSF, Mount Sinai, and with pharma partners.

This collaborative, comparative design ensures transparency, rigor, and speed — producing results that regulators, industry, and clinicians can trust.

Insights and innovations from LCCI will not sit in academic journals. Rather they will be directly communicated to physicians, including those at the CoRE Clinic, where PolyBio’s Dr. Amy Proal serves as Scientific Director alongside Nash Family Director Dr. David Putrino. CoRE serves as a beta-testing site for novel Long COVID or chronic tick-borne/vector-borne infection diagnostic tests and treatment protocols informed by key PolyBio project findings. CoRE also powers a free medical education program, which recently released the first-ever Infection-Associated Chronic Disease Provider Manual. This landmark resource equips clinicians with practical guidance on diagnosis, multidisciplinary care models, and targeted treatments for patients with Long COVID and other complex chronic conditions.

VIPER is not just a scientific effort — it is designed from the start with commercialization in mind.

• Startup Creation: Promising diagnostic platforms emerging from VIPER will be incubated into new companies or integrated into existing biomedical start-ups. These include open source companies.
• Companion Diagnostics: Top assays will be positioned as “companion diagnostics” — the tools pharma uses to select trial participants and measure success, which drives FDA approval.
• Pharma Engagement: PolyBio leaders work directly with companies like Invivyd, ImmunityBio, and Enanta, ensuring that validated diagnostics are built into upcoming clinical trials
• Multi-Disease Platforms: Diagnostics validated in VIPER may be able to expand beyond Long COVID into Lyme, Epstein Barr, and other infection-driven diseases, multiplying impact.

This integrated pathway ensures that VIPER’s discoveries do not sit on the shelf — they reach patients quickly and sustainably.

Diagnostics are not the finish line for the LCCI — they are the key that unlocks pharma engagement and effective treatments.

• Patient Selection: Identifying which patients harbor persistent virus means clinical trials can enroll the right participants.
• Measuring Effectiveness: Diagnostics allow researchers to see if a drug is truly reducing viral persistence, making trials faster and more definitive.
• Targeted Care: Once validated, diagnostics empower physicians to prescribe antivirals, antibodies, or immune therapies with confidence.

Just as HIV diagnostics made it possible to test, refine, and ultimately approve life-saving drugs, VIPER diagnostics will pave the way for the first effective Long COVID treatments.

Learn more about the Long COVID Cure Initiative