The PolyBio Research Foundation recently hosted its fall research symposium featuring project updates from some of the leading Long Covid scientists in the field, including Dr. Akiko Iwasaki, Dr. Michael VanElzakker, and Dr. Amy Proal.

Long Covid media outlet The Sick Times live-blogged the event and noted that the consortium “fosters collaboration between different scientific disciplines, with researchers sharing samples and methods across organizations.”

A recording of the event will be made available, and you can read our summary of the Symposium presentations below. 

Read Part One of our PolyBio Symposium coverage here.

Read other entries in our Solve Science Spotlight series here.

FALL 2024 POLYBIO SYMPOSIUM SCHEDULE – PART 2

Dr. Timothy Henrich (University of California San Francisco)

Dr. Henrich gave an update on tissue biopsies in the LIINC cohort and discussed his July 2024 paper: Tissue-based T cell activation and viral RNA persist for up to 2 years after SARS-CoV-2 infection.

He imaged 75 patients (Long Covid and fully recovered) looking for T cell activation. He noted that it has been difficult because Covid reinfection messes up the trajectory of damage over time since infection.

Dr. Henrich looked at:

• Colorectal imaging
• Gut biopsies
• Also looking in bone marrow
• He is characterizing viral proteins in tissues using PET imaging
• Used “spatial imaging” which looks like this (see slide): 

The proportion of NK cells with a mature and cytotoxic phenotype was significantly lower in people with LC compared with those who had fully recovered (see slide):

Dr. Henrich says 25% Long Covid patients had EBV (Epstein Barr Virus) in saliva, suggesting viral reactivation plays a role in persistent symptoms.

He has funding from Chan Zuckerberg and Merck as well as PolyBio and RECOVER.

He spoke about a new trial (INTERRUPT-LC) that is suppose to increase NK and T cell activity to clear lingering SARS COV2 virus using Anktiva (IL-15 based therapy).

Dr. Esen Sefik (Yale University)

Dr. Sefik stated that human neutrophils react to SARS COV2 in a way mice do not (mice are capable of this response in reaction to other stimuli – just not SARS COV2). 

She used mice to demonstrate the hyperinflammatory loop caused by SARS COV2 by inserting human macrophages into mice to show human macrophages house persistent viral replication whereas mice without human macrophages do not. The human macrophages in mice show SARS COV2 reservoirs, albeit at low levels, that can have a persistent inflammation cascade.

Dr. Sefik also looked at neutrophils, another human myeloid cell, which form NETS in response to a SARS COV2 infection, whereas mice neutrophils do not. NETS (short for “Netosis”) are histones and DNA secreted from the nucleus within Neutrophils and are called “Neutrophils Extracellular Traps” aka “NETs”. This has been described in acute Covid for its role in respiratory distress.

SARS COV2-infected neutrophils showed a lower amount of NETS in patients taking Paxlovid (due to lower viral replication overall) so you can improve the amount of NETs using antivirals that block the viral replication. NETs can be blocked better by “PAD inhibitors” and “Pefabloc” which are both “NETosis inhibitors.” PAD inhibitors work by blocking the enzyme PAD ”needed for circulation” and Pefabloc works by inhibiting protease. Both of these reduced presence of NETosis in SARS COV2 infected mice who had human neutrophils with high levels of NETosis beforehand.

Dr. Sefik found that the “human myeloid cells,” macrophages and neutrophils, are important human reservoirs of SARS-COV2. 

Dr. Michael VanElzakker (Harvard University)

Dr. VanElzakker (Solve Ramsay Research Grant class of 2019) stated that everything his lab does at Harvard includes Long Covid and pre-Covid ME/CFS patients.

He describes does a “dual MRI-PET” for neuroinflammation and neuroimaging and is now starting to do full body dual MRI-PET for Fibrin accumulation in organs and microclots in their blood (supported by PolyBio) particularly for patients with ongoing dyspnea and trouble breathing. Dr. VanElzakker has the patients wear an overnight sleep monitor for two nights before, do a pupillometry to measure pupil responses, and he takes blood and saliva samples — all to better understand imaging. 

Dr. VanElzakker just received a generous donation to study Long Covid and ME/CFS patients with craniocervical instability, or CCI, which he notes can be brought on by both infections or accidents. He will use an “MRI-safe” vagus nerve stimulator for the ear to probe vagus nerve function during imaging and also can measure cerebral spinal fluid flow velocity and volume. 

He also discussed another study that uses regular MRI and EEG for cognitive dysfunction, and the use of Pupillometry to measure autonomic function and intracranial pressure.  He is also doing multiple forms of blood plasma, whole blood, and saliva analysis using the consortium established with PolyBio, as well as neutrophil testing for “neutrophil activation” (seen in acute Covid). He says it is higher in patients with ME/CFS than healthy controls, and that you can see the neutrophils losing their DNA on their imaging.

Dr. VanElzakker does “microclot quantification” to compare Long Covid patients with healthy controls–measuring endocrine measures, a spike protein assay, and tests antibody function and history.

With a focus on brain fog, Dr. VanElzakker developed a hypothesis based on a neuroimaging study that looked at brain response in the general population to inflammation and found one region, the anterior midcingulate–of interest for its role in cognitive control to focus on a task during discretion. Previous studies in ME/CFS show activation in this region on fMRIs.

A sleep quality study on Long Covid and ME/CFS showed similar worse sleep quality than in healthy controls.

He also discussed pupillometry (a quick burst of light that measures pupil contractio) in pre-Covid ME/CFS patients, Long Covid patients, and healthy controls and found:

• Long Covid and ME/CFS patients had smaller pupil diameters relative to healthy controls prior to light burst.
• Long Covid patients had stronger constriction after light burst than healthy controls. ME/CFS was the same as healthy controls.
• ME/CFS had a much slower response time (“constriction velocity”) than healthy controls or Long Covid patients (Dr. VanElzakker said that this is what you’d expect to see in concussion patients).

Dr. Petter Brodin (Karolinska Institutet)

Dr. Brodin is currently looking for genetic determinants of Long Covid by doing whole genome sequencing on 110 severe Long Covid patients. He is checking for genetic variants in antiviral immunity that could lead to viral persistence underlying severe Long Covid. 

Dr. Brodin has been looking at the sex hormone differences in men and women as they relate to immune response. He says that the known delayed/failed interferon responses in men is what causes worse outcomes (also in Covid) to acute infection. 

The predominance of TNF alpha in men leads to a cytokine storm and death (which was seen more in males during the pandemic).

Dr. Brodin looked at a Sep 2024 publication to investigate the role of sex hormones in the immune system to testosterone increase during gendering-affirming therapy (Immune system adaptation during gender-affirming testosterone treatment): 

• Testosterone therapy was given to patients assigned female sex at birth and transitioning to males.
• Increased testosterone, which lowered estradiol and progesterone, stopping the menstrual cycle, caused a shift in Interferon 1 (decreased) and TNF alpha (increased) which is the expected state for men. 
• Dr. Brodin said the immune system adapted to its new hormone environment while its genetics did not change.

Dr. Brodin looked broadly at immune response using whole blood transcriptomics and saw two large scale changes:

• Group of genes associated with type 1 infereon DECREASED
• Group of genes associated with proinflammatory response (IL6, TNF, etc) INCREASED  

Plasmacytoid dendritic cells (PMDC) seemed to be some sort of sensor to sex hormone shifts and regulate the Interferon and TNF alpha balance accordingly. 

Dr. Brodin mentioned that we know blocking the TNF pathway will upregulate Interferon and create a “Lupus-like sort of disease.”

He also said that we know TNF higher levels result in bad pregnancy and implantation outcomes while Interferon 1 is beneficial for pregnancy. He said TNF is used for muscle repair and growth and may be more prevalent in men for evolutionary reasons. He noted that Interferon 1 can lead to muscle wasting.

He also noted that females show higher rates of bad vaccine responses than men, higher incidence of autoimmunity, whereas males have higher acute infection and mortality rate to infection.  

Dr. Lael Yonker (Harvard University)

Dr. Yonker described a study looking at neutrophils in children and comparing the results to healthy controls and children with MIS-C. She said its looks like Long Covid and MIS-C are the same illness on a spectrum with MIS-C being a more severe form of disease on the spectrum. 

She said that children with Long Covid had higher neutrophil activation and was higher in those who still had spike protein in their blood. Children also have increased cytokines compared to healthy controls (MIS-C populations were even higher). She calls MIS-C the “most severe form of PASC.” 

Dr. Yonker is also working on spike antigen detection, neutrophil profiling, microclot quantification, endothelial activation, cytokine detection, and antibody profiling.

She wonders what sets children apart from adults in PASC, so far does not see a difference.  She stated that she would like to see children included in medicine intervention trials, and that the only studies including children are only for behavioral interventions or studies using devices.

Dr. Yonker mentioned that she is also running a Larazatide study in children. 

Dr. Marcelo Freire (J. Craig Venter Institute, “JCVI”, San Diego)

Dr. Freire looked at oral tissues, saliva, and blood for biomarkers and noninvasive testing options using Salivary Proteome, which is a free community website anyone can use (see slide). He found upregulation of Fibrin and Neutrophils and vascular  dysregulation. Multiple neutrophil markers increase in saliva during Covid (see slide below). 

Dr. Freire is working with David Price to get samples to run proteomics in Long Covid. He says he is seeing clusters that are higher in saliva samples in Long Covid samples. He is looking more to see if he can find out whether changes in saliva are a consequence or a driver of disease. He says you can see a more robust IgA response to Covid in saliva than blood (see slide below).

Dr. Freire says too much IgA in saliva can actually induce an inflammatory response, itself. Prior to Covid, Dr Freire had been working on NETs using saliva proteomics. He is now learning that spike proteins are some of the biggest drivers in NETs. He wants to induce NETs using IgA purified from saliva and see if it drives NETosis. He is calling this the “IgA-Induced Pathogenesis Model” (see slide):

Link to PolyBio site with Dr Freire’s projects.

Dr. Rigel Chan (UMass Chan Medical School)

Dr. Chan thinks that the impact of viruses vary over time and found:

• Short-term adverse outcomes: cough, fever, chills, fatigue, shortness of breath, diarrhea, headache
• Mid -term adverse outcomes: brain fog, extreme tiredness, migrain, lot of taste and smell, memory loss
• Long-term adverse outcomes: cancer, autoimmune disease, dementia

Dr. Chan used cerebral organelles to make mini brain models to test in his lab using human cells. He used RNA sequencing to see changes in response to virus infections: his model shows that HSV-1 (Herpes Simplex Virus-1) is a risk factor for Alzheimer’s disease, though not flu. He does not see changes in Alzheimer’s related genes with Covid like he does with HSV (Herpes Simplex Virus). 

In a Covid model, he sees astrocytes being infected, proliferating, and dying. He thinks astrocytes have a unique ability to curb SARS COV2 replication and wants to consider ways to harness this for other cells.

He wonders if Covid might increase harm from HSV (Herpes Simplex Virus) or EBV (Epstein Barr Virus) which do have a correlation to Alzheimer’s.

Link to PolyBio site with Dr Chan’s work.

Dr. Zian Tseng (University of California San Francisco)

Dr. Tseng is an electrophysiologist who studies Sudden Cardiac Death (SCD). He is currently conducting the COVID POST SCD (Postmortem Systematic Investigation of Sudden Cardiac Death) Study. He only gets reports from SCD that go to hospitals, and gets tissues from SCD from patients who died at home.  Dr. Tseng now wonders if SCD is caused by viruses, and mentioned his collaborator Ellan Moffat.

Dr. Tseng explained he has two subsets of tissue – the ones that suddenly die (who died before 911 can intervene and whose tissue expression are stopped in time until they arrive to Dr. Tseng) have a very different expression than ones that survive (those who make it to the emergency room and go on to live in the ICU for a week before their tissue samples are collected and sent to Dr. Tseng). 

He is now looking at those SCD in patients who had had Long Covid.

Link to PolyBio site with Dr Tseng’s work.

Dr. Gene Tan (J. Craig Venter Institute, “JCVI”, San Diego)

Dr. Tan is also working with David Price and is making chimeric models of SARS COV1 and 2 viruses in his lab to observe immune responses. He is working to develop assay to measure antibodies that neutralize seasonal coronavirus. 

Dr. Tan found a higher response to IgG to EBV (Epstein Barr Virus) in females with Long Covid than males with Long Covid. Wonders if EBV affect on B cells could have something to do with its link to Long Covid whereas other herpes virus (eg ZVZ) do not.  

PolyBio link to Dr. Tan’s work.

Dr. Chiara Giannarelli (NYU Grossman School of Medicine)

Dr. Giannarelli looked at patients who died of Covid-19 and found a range of different stages of cardiovascular manifestations (she noted that all of them had predisposition of cardiovascular issues that put them at high risk for bad Covid outcomes). She used “Spatial Cell Single AI” to look for SARS COV2 in coronary (aka arteries) autopsies and found the majority in macrophages within the vascular walls of the arteries and even more active in “foam cells.”

Dr. Giannarelli infected vascular tissues and looked at inflammatory response. She said they found a pro-inflammatory response and noted that Neuropilin-1 (NRP1), which is in these tissues, is a host factor for SARS-COV2, and that NRP1 is more expressed in foam cells than macrophages. When she “silenced NRP1 in macrophages, the expression of SARS COV2 lessened. She is looking to find a way to lessen poor vascular outcomes in acute Covid. Also looking at the clearance ability of the virus from these particular types of tissue and what is going on with these tissue types in patients with Long Covid.  

Link to PolyBio site with Dr Giannarelli’s projects.

Dr. Christopher Dupont (J. Craig Venter Institute, “JCVI”, San Diego)

Dr. Dupont looked at lesser studied tissues (endometriosis, ligaments from CCI, skin, lung, intestinal, oral plaque) for viral reservoirs. Putting together a “tissue catalog.” Doing RNA sequencing, spatial transcriptomics and other methods to recover DNA and RNA viruses.

Dr. Dupoint is also cataloging the human gut microbiome and virome and working with industry to improve capture techniques. Dr. Dupont wants to work with David Price to look at lung samples. Link to PolyBio site with Dr Dupont’s work.

Dr. Benjamin Readhead (Arizona State University Biodesign Institute)
Dr. Readhead links transverse colon to Alzheimer’s through a vagal nerve connection. He has found a potential cytomegalovirus-based biomarker for Alzheimer’s clinical trials. 

Dr. Readhead’s team found that Alzheimer’s-associated CD83(+) microglia are linked with increased immunoglobulin G4 and human cytomegalovirus in the gut, vagal nerve, and brain. They’re now wondering about a clinical trial of antivirals in CD83(+) Alzheimer’s subjects and looking at blood-based biomarkers for CD83(+)/HCMV. 

Dr. Matthew Frank (University of Colorado, Boulder

Dr. Frank was looking at neuroinflammatory properties of SARS-CoV-2 antigens. He found that glucocorticoids (cortisol), which is supposed to mediate inflammation, is reduced in the serum of Long Covid patients. Link to PolyBio site with Dr Frank’s work.

Dr. Max Qian (J. Venter Craig Institute, JVCI, San Diego)

Dr. Qian is using machine learning to identify different subsets of Long Covid patients using symptoms and questionnaires from 615 Mount Sinai patients on 44 symptoms. They were able to find one groups which includes pulmonary, neurological, and cardiovascular problems, and a second group which includes sensory, hormonal, and gastrointestinal problems. Dr. Qian is trying to validate the endotypes using assay data and identifying global and local patterns. Link to Dr Qian’s work with PolyBio.

Dr. Nadia Roan (Gladstone Institutes / UC San Francisco)
Dr. Roan presented on SARS-CoV-2 persistence and T-cell activity in the female reproductive tract. She acknowledged that women, particularly pre-menopausal women, are more likely than men to experience Long COVID. There are sex differences in immune responses, which could be driven by chromosomal and hormonal factors. In an upcoming study that just began and is currently recruiting, their team is hoping to interrogate T-cell responses against SARS-CoV-2 and other similar diseases, knowing the endometrium might be a unique tissue to study SARS-CoV-2-specific T-cells.

Dr. Alessio Fasano (MASS General)
Dr. Fasano discussed the peptide larazotide in the treatment of SARS-CoV-2 spike protein translocation, and ”leaky gut” — his team found that SARS-CoV-2 reservoir can leak viral spike proteins from the gut to the blood, driving hyperinflammation. Fasano’s team worked on a clinical trial using a larazotide with “open-label compassionate use” and double-blind placebo trial for multisystem inflammatory syndrome (MIS-C). The trial is being adapted now for Long COVID. 

Dr. Sara Cherry (Penn Medicine)
Dr. Cherry talked about defining a viral reservoir in the GI tract with regard to Long Covid. In bronchial cultures and kinetic cultures, Cherry’s team saw the kinetics were different in terms of their persistence. They looked at cellular responses to SARS-CoV-2 infection. They found the genes induced in the gut were different than the ones induced in the lung. Aside from trying to find out how SARS-CoV-2 alters the gastrointestinal tract, her team is also trying to find out the effectiveness of varying antivirals. 

Dr. Amy Proal (PolyBio Research Foundation / CoRE at Mount Sinai)
Dr. Proal talked about the Long COVID low-dose rapamycin clinical trial starting at CoRE now. The clinical trial is double-blind, randomized, and placebo-controlled, and enrolls 80 Long COVID participants in a dose of 6 mg once-weekly that they’ll titrate up to. There will be whole blood, saliva, and EndoPAT data analyses measured once before the study, once at week 12, and once at 24. It “might help us design a larger trial of more tightly phenotyped participants,” Proal said, and hopefully it will grant people “a read on how well this dose is tolerated.”

Dr. David Putrino (Mt Sinai / CoRE)
Dr. Putrino shared that there are a number of clinical trials underway and planned for 2024/2025. In particular, he talked about an in-human trial in partnership with Humanity Neurotech around cognitive impairment. Roughly 60% of people with Long COVID report cognitive impairment significant enough to affect daily function, he said, and that scale of measurement is “aligned with the same level of impairment we would see in traumatic brain injuries.” Of particular note is a trial with low-frequency radiation with a company called Humanity Neurotech.