Project Team

Michael Peluso, MD, Assistant Professor, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco

Tim Henrich, MD, Associate Professor, Division of Experimental Medicine, Department of Medicine, University of California San Francisco

Steven Deeks, MD, Professor, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco

Jeffrey Martin, MD, Professor and Chief of the Division of Clinical Epidemiology and Health Services Research, Department of Epidemiology & Biostatistics, University of California San Francisco

Chia-Ching (Jackie) Wang, MD, Associate professor in Department of Hematology-Oncology at Zuckerberg San Francisco General Hospital, University of California San Francisco

Ma Somsouk, MD, Craig Endowed Chair in Gastrointestinal Medicine, Professor of Medicine in Residence, University of California San Francisco

Felicia Chow, MD, Associate Professor of Neurology and has a joint appointment in the Department of Medicine, Division of Infectious Diseases, University of California San Francisco

Carlo De La Sancha Verduzco, MD, Assistant Professor of Pathology, University of California San Francisco School of Medicine

Steven Long, MD, Clinical Professor of Pathology, University of California San Francisco School of Medicine

Priscilla Hsue, MD, Maurice Eliaser Jr MD Distinguished Professor of Medicine, Chief of Cardiology, UCSF at Zuckerberg San Francisco General Hospital

Matt Durstenfeld, MD, Assistant Professor of Cardiology, University of California San Francisco Department of Medicine

David Walt, PhD, Hansjörg Wyss Professor of Biologically Inspired Engineering, Harvard Medical School, Professor of Pathology, Department of Pathology-Brigham and Women’s Hospital

Project Summary:

PASC Tissue co-lead Dr. Michael Peluso

The PASC Tissue Program is the first in the world to comprehensively sample multiple tissues including gut, lymph node, cerebrospinal fluid, and bone marrow to test the hypothesis that tissue-based viral persistence drives Long COVID and can be altered via interventions targeting viral reservoirs. The Program builds on the existing PolyBio-supported UCSF LIINC clinical core to determine the relationship between Long COVID symptoms, markers of SARS-CoV-2 persistence in blood and tissue, and tissue function using measures of blood vessel health (EndoPAT) and physical performance (cardiopulmonary exercise testing). The Program is also leveraging existing or planned Long COVID clinical trials targeting mechanisms of viral persistence (e.g. the Aerium monoclonal antibody trial and the Shionogi antiviral trial) to support deep assessment of the impact of such interventions on measures of viral persistence. While much of the science is being conducted via the existing network of LIINC collaborators, tissue samples are also being made available to collaborators within the Long COVID Research Consortium and beyond who are conducting complementary research. This is allowing the LIINC PASC Tissue Program to serve as a core for tissue biospecimen sharing just as LIINC serves as a clinical core for multiple collaborators studying Long COVID.

Project Background:

The University of California San Francisco Long-term Impact of Infection with Novel Coronavirus (LIINC) cohort program is a thriving post-acute COVID-19 study supported via the PolyBio Long Covid Research Consortium. It includes longitudinal biospecimen banking and clinical phenotyping to support basic and translational research to determine the underlying causes of Long COVID. Built upon the LIINC infrastructure are several PolyBio-supported projects aimed at visualizing inflammation and the potential SARS-CoV-2 reservoir using novel PET imaging techniques, as well as both ongoing and planned interventional trials targeting viral reservoirs as drivers of Long COVID. This work has made it clear that SARS-CoV-2 RNA and spike protein persist in the gut wall for up to 2.5 years following acute infection and that nearly ten percent of people have circulating spike protein in their blood at any given time months to years following COVID-19. These data, along with similar results from other investigators, suggest that Long COVID is a disease of tissue viral persistence.

Data by the project team: Imaging showed T cell activation to be higher in brain stem and spinal cord tissues up to 1.8 years after COVID-19.

The project team has also documented T cell activation in body sites such as the bone marrow, brainstem, spinal cord, gut wall, and lymph node tissue of Long COVID patients. The bone marrow plays an important role in systemic immune responses and inflammation in many viral infections such as Cytomegalovirus, Parvovirus B19, and HIV. Bone marrow from children with MIS-C demonstrates SARS-CoV-2 RNA and protein associated with macrophage activation syndrome, which can lead to profound immune dysregulation. Increased frequencies of megakaryocytes were also observed. These cells are the precursors for platelets and play an important role in coordinating inflammatory responses. These data suggest that SARS-CoV-2 infection in bone marrow may be a cause of immune cell activation, systemic inflammation, and overall immune exhaustion and dysfunction in Long COVID, and perhaps even disorders of clotting.

SARS-CoV-2 spike protein can also accumulate in spaces adjacent to the meninges (membranes that encase the brain and spinal cord), or may cross the blood-brain barrier via the skull lymphatic system. In addition, spike protein can directly interact with fibrinogen, inducing structurally abnormal clots and microglial activation through fibrin-mediated pathways. In LIINC participants undergoing lumbar punctures, the team has documented a variety of cerebrospinal fluid abnormalities in Long COVID suggestive of ongoing immune responses. They have also detected increases in markers of inflammation and astrocyte turnover as well as viral persistence in neural-derived exosomes among those with Long COVID. These data suggest that SARS-CoV-2 persistence could induce neuroinflammation either through the direct presence of viral products in the central nervous system or via mechanisms based in the periphery that induce central nervous system inflammation.

To build on this knowledge the PASC Tissue Program has three central components:

Image by the project team showing SARS-CoV-2 RNA 158 days post-COVID-19 In gut tissue obtained from a Long COVID patient

1. To test the hypothesis that SARS-CoV-2 persistence in body sites including bone marrow, cerebrospinal fluid, gut wall, and lymph node is a driver of Long COVID. To do this the team is collecting the following samples via biopsy. In all biopsy studies analysis involves cutting-edge Digital Spatial Omics platforms to simultaneously determine SARS-CoV-2 RNA and protein burden, immune cell phenotypes and host gene responses to infection with single-cell resolution:

Bone Marrow: They are sampling bone marrow in individuals with and without Long COVID to determine if SARS-CoV-2 persists in bone marrow-resident cells, such as myeloid immune cells or megakaryocytes, leading to systemic inflammation and abnormal immune responses.

Cerebrospinal fluid (CSF): They are sampling CSF in people with and without Long COVID to determine if SARS-CoV-2 proteins are present in CSF and associate with distinct proteomic signatures of microglial immune cell activation in people with neurocognitive Long COVID symptoms. They are using Simoa to identify potential SARS-CoV-2 proteins in the CNS compartment. They are also performing metagenomic next-generation sequencing of SARS-CoV-2 RNA within the CSF, and looking for pathogenic B cells in order to determine if they may play a role in Long COVID as they do in other neurological disorders such as multiple sclerosis.

Gut wall: They are expanding the current gut biopsy program to determine if the gut is a primary site of SARS-CoV-2 persistence. Biopsies are being performed on individuals with and without Long COVID, including various Long COVID phenotypes. They are also searching for the presence of other persistent viruses thought to be important in the biology of Long COVID in gut tissue samples, including Epstein-Barr virus (EBV) and cytomegalovirus (CMV), which will also be tested in bone marrow.

Lymph node: They are developing a collaboration to test if the lymph node chains that drain these regions can be sampled to assess for the direct presence of viral components in these tissues as well as immunologic responses suggestive of viral persistence. Genetic material, proteins, and immune responses towards other pathogens important in the biology of Long COVID will also be measured.

2. To determine the relationship between markers of SARS-CoV-2 persistence in blood and tissue and the physiologic function of tissues using measures of endothelial function (EndoPAT) and physical performance (cardiopulmonary exercise testing).

If Long COVID is a disease of tissues, SARS-CoV-2 tissue persistence and resultant immune dysfunction should be reflected in tissue physiology, which may manifest as changes in parameters like endothelial function, blood flow, or oxygen extraction. In this part of the project, the team is measuring tissue physiologic function in participants using technologies such as EndoPAT (a device that measures endothelial function) and cardiopulmonary exercise testing (an exercise challenge that captures changes in oxygen extraction). Data obtained from this testing will be correlated with SARS-CoV-2 persistence markers to determine if endothelial dysfunction and/or reduced exercise capacity are associated with blood- and/or tissue-based antigen persistence.

3. To determine the impact of therapeutic approaches targeting mechanisms of viral persistence on tissue biologic and physiologic function.

The team has implemented a robust Long COVID clinical trials program focused on interventions to target tissue-based viral persistence. For example, they have launched a clinical trial of investigational SARS-CoV-2 specific monoclonal AER002, and a trial of Shionogi’s antiviral ensitrelvir. Future collaborations may include trials of therapeutics capable of targeting related viruses that may contribute to Long COVID (e.g., EBV). During each of these proof-of-concept clinical trials, funded separately from this project, samples (e.g., blood, nasal swabs) are being collected and banked at various timepoints before, during and after intervention. This initiative supports analysis of such samples for spike protein and other metrics of viral persistence. It also supports gut and lymph node tissue biopsies and SARS-CoV-2 measurement on trial participants. This is allowing each trial to function as an experimental medicine study, in which a deep understanding of therapeutic efficacy in clearing SARS-CoV-2 components from different reservoir sties is gained.