Recently, Health Rising posted a review of an Amy Proal – Tim Henrich interview which noted the formation of a highly active group of researchers at the University of California at San Francisco (UCSF) dedicated to solving long COVID. The group – called the LIINC (Long Term Impact of Infection with Novel Coronavirus) group – has participated in dozens of long-COVID papers over the past three years.
This group published two preprints recently on long COVID – demonstrating what an apparently well-funded research group at a major university can do. The first preprint, “Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2“, involved 30 UCSF researchers.
The Yin/Peluso study focused on one of the big guns of the immune system – the T-cells. T-cells are part of the adaptive immune system – the part of the immune system that’s tasked with tracking down and eliminating pathogens. (The first part of the immune system – the innate immune system – holds off the pathogens until the adaptive immune system kicks in a couple of days later.)
T-cell both track down pathogen cells and regulate the immune response, and are of major interest in chronic fatigue syndrome (ME/CFS). Mark Davis at Stanford received a rare NIH grant to study them, Derya Unutmaz at Jackson Labs has been very excited about the strange gut-associated mucosal-associated invariant T-cells he’s found, and Lissa Selin and Anna Gill got a big NIH grant (5-year, $2.5 million) to study T-cell exhaustion in ME/CFS.
Cytotoxic (CD8+) T-cells destroy virus-infected and cancerous cells and recruit other immune cells such as macrophages to help them in the attack. Helper T-cells (CD4) tell memory B cells that something is up, as well as activating more killer T-cells. Different subtypes of these cells exist.
Besides cytotoxic and helper T-cells, regulatory T-cells shut down the immune response and are responsible for ensuring that an autoimmune process doesn’t get initiated. Memory T-cells, natural killer T-cells, mucosal-associated invariant T-cells and other T-cells exist.
Since T-cells play such an important role in tracking down and destroying pathogen-infected cells, it makes perfect sense to check them out in long COVID. The longer it takes them to do that, for instance, the deeper the coronavirus could burrow into the tissues, or the more damage it could wreak.
Peluso and Henrich’s 2021 study found that some subsets of killer T-cells decayed more quickly in long-COVID patients; i.e. the killer T-cells tasked with finishing off the coronavirus disappeared at a quicker rate than in COVID patients who did not come down with long COVID.
This study combined “next-generation” T-cell characterization assays (CyTOF) with antibody studies (apparently “this-generation” :)), as well as gene expression (RNA-Seq (also “next generation” :)) and high-density plasma proteomics (yep, “next generation”) to attempt to figure out what the heck is going on with T-cells and the immune system in long COVID.
The analyses were done on 27 long-COVID and 16 recovered COVID patients 8 months after the infection. Note that this is not necessarily an ME/CFS-like subset. The only requirement for the long-COVID patients was that they have at least one COVID-19-attributed symptom that was new or had worsened since the infection, and was at least somewhat bothersome. Not the most stringent criteria! Most people, however, had at least several symptoms, and the number of symptoms tended to increase from 4-8 months. As this study occurred in 2020-21, nobody had been vaccinated.
The goal – “to identify clues to the immunologic processes that might drive long COVID” – was certainly achieved.
Ongoing Immune Response – First off, the study found “profound changes” in the distribution of t-helper (CD4+) T-cells with particularly high proportions of several subsets (tcm (memory), Tfh (b-helper), and Treg cells.) That indicated that an “ongoing immune response” was present in the long-COVID patients.
Epstein-Barr Virus Reactivation – The fact that the study did not find elevated T-cell responses to the SARS-CoV-2 coronavirus in the long-COVID patients suggested that the immune response was probably directed against another pathogen, such as a herpesvirus (perhaps Epstein-Barr virus), or an auto antigen (autoimmune response directed against a tissue).
Viral Reservoirs – They did, however, find evidence of exhausted SARS-CoV-2-specific CD8+ T-cells in the long-COVID patients. That and higher SARS-CoV-2 antibodies were consistent with a coronavirus viral reservoir that was present in the body. As noted earlier, Selin and Gill are studying T-cell exhaustion they believe could be driving everything in ME/CFS. Their preliminary findings seem pretty close to those found in long COVID and produced a nice tie-in with EBV reactivation – which seemed likely in this study.
In preliminary studies, Selin and Gil found that certain CD8 T-cells were altered in patients with chronic ME/CFS as compared to those who do not have ME/CFS. This suggests that an aberrant response to an immunological trigger, like infection, results in a permanently dysregulated immune system, as a result of CD8 T-cell exhaustion, a phenomenon they previously discovered in patients who developed ME/CFS following an infection with the Epstein-Barr virus.
At this point, two subsets of long COVID appeared to present themselves: one subset driven by high antibody (IgG) expression and another with low antibody expression. A nirmatrelvir-ritonavir clinical trial was underway to attempt to wipe out that reservoir.
- This study from the LIINC group at the University of California at San Francisco examined one of the big guns of the immune system – the T-cells. The T-cells track down virus-infected cells and destroy them, and regulate the adaptive immune response.
- With three large NIH-funded T-cell studies (Mark Davis at Stanford, Selin-Gill Harvard, Derya Unutmaz at Jackson labs) underway, T-cells are potentially a big deal in ME/CFS.
- The UCSF research team brought “next-generation” technology to bear in the T-cell characterization, gene expression, and plasma proteomics sections of the study. The study included long-COVID and recovered COVID-19 patients. The goal was “to identify clues to the immunologic processes that might drive long COVID“.
- That goal appeared to have been met as the study found numerous and significant immune abnormalities. First off, the increased expression of three subsets of T-cells suggested that an ongoing immune process was occurring in the long-COVID patients which wasn’t present in the recovered patients.
- Several subsets of long COVID appear to be present: one was associated with high antibody (IgG) expression and another with low antibody expression. A highly inflammatory response to the virus that could be driving their symptoms was also found in a small group of long-COVID patients.
- Plus, high levels of a subset of activated cytotoxic T-cells in females suggested that increased inflammation could help explain their increased risk of coming down with long COVID.
- The most striking finding, though, was a massive disconnect between the humoral (B-cell) and cellular immune (T-cell) response in the long-COVID patients. These two systems should work together to take care of the virus: the B-cells attach themselves to viral particles to block the virus from entering the cell while the T-cells kill cells that get infected.
- These two systems were coordinated in the recovered COVID patients but not in the long-COVID patients. About half the long-COVID patients who produced coronavirus-specific T-cells produced no antibodies to the virus.
- Putting all the pieces together, the authors found a highly inflammatory state, probably driven by immune dysregulation or problems with immune regulation, was present in long COVID. They concluded the a viral reservoir, reactivation of other viruses, or an autoimmune process could be responsible.
- A second paper using a more effective technique than has been used before from the LIINC found no evidence that increased autoantibodies or an autoimmune issue was in play in long COVID.
Massive Immune Disconnect – The most striking finding, though, was a massive disconnect between the humoral (B-cell) and cellular immune (T-cell) response in the long-COVID patients. These two systems should work together to take care of the virus: the B-cells attach themselves to viral particles to block the virus from entering the cell, while the T-cells kill cells that get infected.
These two systems were coordinated in the recovered COVID patients but not in the long-COVID patients. About half the long-COVID patients who produced coronavirus-specific T-cells produced no antibodies to the virus. This dysregulation also showed up in the gene expression results: genes involved in both the T-cell and B-cell response were upregulated in the recovered COVID cohort but not in the long haulers. With half their adaptive immune response to the virus essentially missing, the long-COVID patients appeared to be trying to fight off the coronavirus with one hand tied behind their back.
The cause was unclear, but the authors posited that a “misalignment” between IL4 and IL5 production by Th2 cells might be the proximate cause, while the ultimate trigger might lie in a persistent coronavirus reservoir, the reactivation of other viruses, or an autoimmune response. The Th2 finding was interesting given indications that an augmented Th2 response is present in ME/CFS.
The Th1 response is focused on killing pathogens while the Th2 response is more skewed toward allergy. It’s been proposed that an overly active Th2 response in ME/CFS is thwarting the immune system from effectively taking care of pathogens such as Epstein-Barr virus (EBV).
Putting all the pieces together, the authors found a highly inflammatory state, probably driven by immune dysregulation or problems with immune regulation, was present in long COVID. Increased expression of heme genes in long-COVID patients also pointed a finger at possible clotting issues including microclots.
Autoimmunity Nixed – For Now
We’re not done with the LIINC group yet, though. They also recently produced another preprint, “Autoantigen profiling reveals a shared post-COVID signature in fully recovered and Long COVID patients“, that digs deep into the autoantibody/autoimmune question in long COVID. The large study (121 long COVID, 64 recovered COVID-19, 57 pre-COVID controls) assessed the levels of autoantibodies (antibodies with the ability to attack the body) present.
We know that acute COVID-19 (the initial response to the virus) provokes the production of many different autoantibodies. Whether those autoantibodies persist in long COVID – and could therefore be driving the illness – is unclear, and study results have been mixed.
The authors noted that methods that can “identify the full range of novel autoantibodies” have not been used thus far and that’s what they and their “high-throughput, unbiased, proteome-wide screens” brought to the table in this study.
Finding little difference between the autoantibodies found in the long-COVID patients and the recovered COVID-19 patients, and no evidence that any of the antibodies were associated with any of the long-COVID symptoms, the study put the brakes on the idea that autoantibodies were driving long COVID or that autoimmunity was present.
They did note that “complex conformational, post-translationally modified, or multimeric protein configurations” might be missed by their assay, thus the results do not completely rule out autoimmunity – and they asserted that more work needs to be done in this area. As of now, though, what appears to be the most rigorous assessment of autoimmunity yet in long COVID didn’t find evidence of it.
The fact that the study did not find elevated T-cell responses to the SARS-CoV-2 coronavirus in the long-COVID patients suggested that this immune response was probably directed against another pathogen, such as Epstein-Barr virus.
Evidence of exhausted SARS-CoV-2-specific CD8+ T-cells and higher SARS-CoV-2 antibodies in the long-COVID patients, were, however, consistent with the idea of a coronavirus viral reservoir being present. Note that T-cell exhaustion has been found in ME/CFS, and Selin believes it could be driving the symptoms in ME/CFS.
Numerous immune abnormalities were found in this T-cell/gene expression/antibody/proteome study. One wonders if the exhausted T-cells found in this study might mimic the exhausted T-cells thus far found in ME/CFS (which are the subject of a large NIH-funded study). The idea that reactivation to a herpesvirus might play a major role in long COVID notched up a bit when the study failed to find elevated T-cell responses to the coronavirus.
Several immune subsets appear to be present in long COVID, but the really big news was the disconnect between the T and B-cells. About half of the long-COVID patients who produced a T-cell-specific response to the coronavirus didn’t produce any antibodies to it.
Putting all the pieces together, the authors found a highly inflammatory state, probably driven by immune dysregulation or problems with immune regulation, was present. They concluded that a viral reservoir, reactivation of other viruses, or an autoimmune process could be responsible.
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