If you're going to have a conference you might as well have it in a nice place :)

If you’re going to have a conference you might as well have it in a nice place 🙂

It took about three years but the first major international conference on long COVID – the “Keystone Long COVID and Post Acute Sequalae of SARS CoV 2 (PASC): Pathogenesis and Treatment” conference recently took place in Santa Fe, New Mexico at the El Dorado Hotel. Health Rising was there, kind of. (We got the online version).

For people with chronic fatigue syndrome (ME/CFS) many of the faces are new. We know of Avindra Nath and David Systrom but otherwise, the conference featured researchers new to the post-infectious field, some of whom have transitioned heavily into the long-COVID space such as Akiko Iwasaki, Tim Henrich, Michael Peluso, and Stephen Deeks.

We got glimpses at studies examining some ongoing long-COVID cohorts and initiatives such as the Outsmart Cohort, Tulanes ClinSeqSer Cohort, the Mount Sinai Yale Cohort, the ADAPT cohort, the LIINC cohort, and the German COVID-19 OMICS Initiative. We also had several mouse studies – something we rarely see in ME/CFS.

It was good to see Dr. Gary Gibbons, the director of the Heart, Lung, and Blood Institute (NHLBI) at the NIH and a leader of the NIH’s RECOVER Initiative, start things off. Gibbons made sense as COVID-19 affects the cardiovascular system. On the other hand, until now, NHLBI has shown zero interest in ME/CFS or post-viral illnesses. Maybe that will be changing.

Homeless at the NIH

Gibbons noted the many different institutes working together on COVID that never have worked before. That’s not surprising given the complex nature of post-infectious illnesses and it’s the need to do cross-institute work that has led the Solve ME Initiative to begin a long-term effort to create a new post-infectious disease institute. Indeed, ME/CFS is still homeless at the NIH largely because it, like long COVID, doesn’t fit well in any one Institute.

Dr. Stephen Deeks

Dr. Stephen Deeks – one of the organizers of the event – called the RECOVER Initiative “a great success”.

The Trans-NIH Working Group that guides ME/CFS research at the NIH is a unique cross-institute effort that has failed to receive much help, in large part, because it’s not associated with any one Institute. Hopefully, long COVID will help force the issue and create an entity that works for these complex, multi-system disorders.

Dr. Stephen Deeks – a respected researcher with a long track record who is a part of the RECOVER effort – underscored how new the long-COVID effort is by noting how many of the speakers had never met each other until now. He called RECOVER “a great success“! Indeed, despite the flack it’s received over the past year or two – the RECOVER Initiative came in for nothing but praise from many of the speakers – suggesting that we need to give it more time.

Yale’s Outsmart Long Cohort

The Outsmart Cohort moved quickly to collect samples from 70 people – most of whom were not hospitalized – within 48 hours of becoming ill and then a month later. Then they followed them for 24 months.

Note the requirement for inclusion – at least 1 symptom remaining for more than 90 days. Another study found that if you had one symptom, you probably had at least a few more, but we don’t know how many of the participants met the criteria for ME/CFS or fibromyalgia, POTS or IBS, for that matter.

People who took longer to clear the virus from the respiratory tract – and were presumably more symptomatic – tended to have brain fog and muscle pain. This makes sense with the Dubbo study finding in ME/CFS that the more symptomatic you were, the more likely you were to come down with a post-infectious fatigue syndrome.

A latent class analysis of long-term symptoms identified 3 groups characterized by:

  • Anxiety, headache, weakness
  • Body aches, joint pain
  • Brain fog, memory problems, insomnia.

Note that fatigue is not mentioned – perhaps because everyone had fatigue. Post-exertional malaise was clearly not on this group’s radar.

They did an extensive immunological evaluation (T-cell panel, myeloid, and B-cell panel) combined with markers of metabolic programming (fatty acid oxidation, glycolysis; TOM-20 – oxidative phosphorylation, mitochondrial mass)

They found increased numbers of myeloid-derived suppressor cells (also found in chronic infection, cancer, and obesity) in the anxiety, headache, and weakness group. On the other hand, they found increased levels of a lectin receptor (LOX-1) – which is also a suppressor (it suppresses T-cell proliferation) but is also associated with the blood vessels (endothelial cells, platelets, macrophages, smooth muscle cells). Either way, the immune system appeared to be trying to tamp down its response.

Granulocytic neutrophilic MDSC cells are similar to monocytes – which have gotten a lot of attention. People with more of these cells experience brain fog, memory problems, and insomnia. Interestingly, people with high CD20+, CD27-memory B-cells – and headache, anxiety weakness – also tend to have high numbers of PMN MDSC cells, as well as eotaxin-3 and IFN (1 and 3).

They don’t know what’s causing these unusual immune configurations to pop up, and are investigating more.

Thinking Bigger: the Immune Hormone Mix

Akiko Iwasaki –  “Thinking Beyond the Spike”


A great deal of focus is being concentrated on the spike protein – the yellow protuberances seen in the image – but Akiko Iwasaki – citing diseases like ME/CFS – feels we need to move beyond the spike.

Akiko Iwasaki did a sort of immunological overview, which didn’t appear to provide anything new but was notable in a sea of long-COVID talks for her emphasis that long COVID is one of many post-acute infection syndromes. She even mentioned a post-infectious disease paper she cowrote with Mady Hornig and an ME/CFS patient.

She said, “We need to think beyond the spike!” and thank god for that. So much attention is focused on the spike protein of the coronavirus – the part of the virus that sticks out and gains entry into the cell. Yes, the spike protein is clearly important, but Akiko reminded everyone that many other post-infectious illnesses exist that are not triggered by the coronavirus – and cannot be explained by the spike.

Health Rising covered her massive, 273-person “Distinguishing features of Long COVID identified through immune profiling” study in preprint form about a year ago. That paper – which set a high standard that, unfortunately, has rarely been met since then – made it to the big time. It was published in one of the most widely read scientific journals in the world – Nature – a couple of days ago.

The Hugely Predictive Factor for Long COVID…is also found in ME/CFS and Fibromyalgia: the IACFS/ME Conference II


The study found a number of themes – high levels of monocytes, dendritic cells, activated B-cells, exhausted T-cells, high antibody responses against EBV, and then there was the shocker – the main distinguishing factor – low cortisol. Speaking of hormones, the study also found low testosterone in females and reduced estradiol in males. The study’s rather unique combination of immune and hormonal factors allowed it to differentiate between people with and without long COVID with remarkable accuracy (96 %).

CNN reported that the cortisol finding “was one of the most exciting to the researchers because it makes some biological sense.” Akiko Iwasaki said, “When you have low levels of cortisol, you will get tiredness, nausea, vomiting, weight loss, weakness and pain. So lower levels of cortisol could be contributing to the symptoms.”

At the conference, Iwasaki pointed a finger at the HPA axis, and thyroid and female hormones – all of which have shown up in ME/CFS but which, aside from this paper, have pretty much been ignored in the rush to assess immune functioning in long COVID.

The few times the HPA axis has been assessed in long COVID, problems have shown up. A Japanese study found lower levels of cortisol, and free thyroxin (FT4). Another study found evidence of impaired pituitary functioning, but that’s pretty much it on assessing HPA axis functioning in long COVID. To anyone who’s followed ME/CFS research, the absence of HPA axis and hormonal research is pretty astonishing.

Cortisol and HPA axis

The HPA axis and cortisol have been news in ME/CFS for a long time yet have been virtually ignored in long COVID. Akiko Iwasaki’s study, however, suggested that they may play a critical role.

A review paper, “Protracted stress-induced hypocortisolemia may account for the clinical and immune manifestations of Long COVID“, did, however, pick up on Iwasaki’s findings and expanded on them. It reported – rather astonishingly – that Iwasaki’s study found that “the plasma cortisol levels in patients with Long COVID were almost half of those found in matched controls independently of age, sex, sample collection time, and body mass index”, and noted that machine learning tools found that “cortisol levels alone were the most significant predictor for Long COVID classification“.

The authors believe the HPA axis was first activated by the infection, but then suppressed, and that this suppression results in immune dysregulation and the “expression of sickness syndrome manifestations”; i.e. the “sickness behavior” we have heard so much about. They posited that whether someone comes down with an ME/CFS-like condition in part depends on how impaired their cortisol response becomes.

The review paper also reported that the three major findings of “low cortisol levels, T-cell exhaustion and augmented reactivity to Epstein-Barr virus has been also observed in patients with myalgic encephalomyelitis/chronic fatigue (ME/CFS) syndrome”.

That simply confirms what patients, doctors, and researchers in the ME/CFS know very well – that these are complex diseases that require a multi-systemic approach. We need big, multidimensional studies like the Yale study in order to tease out what’s going on. We’re not getting a lot of them. We also need researchers like Akiko Iwasaki who’ve taken the time to check out ME/CFS findings and apply them. They seem to be in fairly short supply!

David Putrino MD, who is right in the thick of things and was part of the study, stated, “There is no ‘silver bullet’ for treating long COVID, because it is an illness that infiltrates complex systems such as the immune and hormonal regulation. Complex illnesses require complex treatment solutions and we need more rapid research to better understand long COVID and discover new and promising therapies.”…Thank you!

Julio Silva – Yale – Testosterone is a key differentiator of sex-specific immune profiles and symptomology in long COVID

Iwasaki’s group appears to have jumped on the hormone findings as another Yale researcher dug deep into them. Silva reported that testosterone was lower in females and estradiol was lower in males with long COVID. This time, the top predictor of long Covid was lower testosterone.

That’s pretty interesting given that Hilary White has been using testosterone to treat fibromyalgia in women for quite some time, and estradiol is connected to testosterone and plays a role in pain inhibition.

Male Trouble: the Testosterone Connection in Fibromyalgia

Differences in immune functioning were found between males and females. Females had significantly higher NK cell levels, produced more cytokines, and displayed higher reactivity to EBV. Males displayed more dysregulated monocytes and dendritic cells. Both had low cortisol.

The Viral Persistence Talks

Viral persistence – the idea that the virus (or, more likely, pieces of the virus) is persisting in the body and triggering an immune reaction – is all the rage. There’s certainly now plenty of evidence that pieces of the coronavirus are persisting in people with long COVID. Whether they are causing long COVID is another question.

Michael Peluso UCSF

Michael Peluso of UCSF presented the findings from a nice, big (800-person) LIINC study. As with other LIINC studies, most of the participants (80%) were not hospitalized. They found a lot of evidence of viral persistence. Not the virus itself but components of the virus – mostly from the spike and nucleocapsid protein – persist in blood up to a year after infection.

People with higher antigen levels; i.e. higher levels of viral proteins – were worse off over time. A correlation appeared to be present between levels of the spike and nucleocapsid proteins and gut and musculoskeletal symptoms. Plus, coronavirus spike RNA (genetic material) was found in gut biopsy up to two years after the infection. Interestingly, given the interest in connective tissues in these diseases, the spike protein was always found in the connective tissue layer but never in the epithelial tissues that line the gut.

However…not everyone with long COVID was found to have coronavirus antigens (proteins) in their blood, and it was possible that some people had simply been re-infected again.

Are they triggering an inflammatory or autoimmune response that’s causing long COVID, or are they just hanging around? Avindra Nath has pointed out that we all carry viruses in our bodies, most of which do no harm.

Answering the viral persistence question is pretty straightforward – remove the virus – and see if the symptoms improve. If the patient recovers, you have your answer, and antiviral studies of Paxlovid are underway. (Time will tell how effective it is in removing the virus and pieces of the virus. The one report I saw did not find Paxlovid effective with long COVID, but larger studies are underway.)

The 30-person Outsmarting Long COVID Monoclonal Antibody Trial 

There is another way, though. In yet another Peluso/Deeks/Henrich study from the very active and creative UCSF LIINC group – the 30-person Outsmarting Long COVID study – is using an antiCOVID monoclonal antibody called AER002. Unlike antivirals, which attempt to stop a virus from replicating or infecting other cells – but don’t kill it – monoclonal antibodies can actually clear infected cells from the body. The study is supported by the PolyBio Research Foundation.

Peluso’s group is also doing gut biopsies, and they hope to check out cervical lymph nodes. Peluso said a good biomarker would be completely transformative. It was a good biomarker that jumpstarted HIV research and quickly led to good treatments. Speaking of biomarkers…

Ella Warburg – Harvard – “Uncovering the link between antigen persistence and post-acute sequelae”

Ella Warburg used assays with high sensitivity to three coronavirus antigens in RECOVER and other cohorts in an attempt to find a biomarker. She indeed found high SARS-CoV-2 antigen levels over time, and was able to correlate symptoms with the presence of the antigen.

The implications of the viral persistence hypothesis for ME/CFS are unclear. First, you’d have to identify the source of the immune activation – something that no one has yet been able to do. Of course, there is the Epstein-Barr virus (EBV) connection, but as yet we lack good antivirals for that virus. One would hope, though, that a positive viral persistence result would spur more interest in developing better drugs.

Choutka – Identification of elevated and altered humoral responses to EBV in long COVID

Mount Sinai Yale MY-LC cohort – Iwasaki group again… One study asked whether people with long COVID had been exposed – prior to long COVID – to different pathogens than people who recovered from COVID-19. Something called “original antigenic sin” can occur when our immune systems target a new infection with an old and not very effective immune response against a prior infection.

Original Sin? Could a Cold Virus Be Causing Long COVID? (or Other Post-Infectious Illnesses?)

People with long COVID had similar exposures to common pathogens, as did the healthy controls, but the elevated antibody binding to EBV and varicella zoster virus found in the long-COVID patients suggested that their immune system was reacting more strongly to these herpes viruses than the immune systems of those who recovered.

While they did not find evidence of EBV in the blood, or reactivation of IgM antibodies, they did find that one increased EBV antibody was correlated strongly with specific activated T-cells and increased cytokines (IL-4; IL-6 – gp42) levels. This seemed like a nice package of immune activation and they will surely follow up on that.

Finally! The German COVID-19 OMICS Initiative Targets ME/CFS-like Long COVID

Next came something very different and welcome! While ME/CFS has been mentioned a bit, nobody has actually analyzed an ME/CFS long-COVID subset. Instead, they’ve looked at general long-COVID groups (mostly not hospitalized, to be sure), which may or may not resemble ME/CFS. Even if they do resemble ME/CFS, they might have the full package. This group did.

This study, done in collaboration with Carmen Scheibenbogen’s Charite group, required that the participants meet the Canadian Consensus Criteria for ME/CFS.

The findings from the 60-patient study were interesting indeed. Up popped the innate Immune system – and monocytes! Monocytes have suddenly gotten really interesting in both ME/CFS and long COVID. While the alterations in the gene expression of the major immune cells were found, the most “striking” changes were found in the monocytes. Intrigued by that finding, they really dug in and subsetted the monocytes into their different states and stages of activation.

Move Over NK, T and B-cells. Are Monocytes the Real Problem in ME/CFS?


They then did the same with natural killer cells (NK), a major emphasis in ME/CFS research, and found evidence of increased inflammatory subtypes (cytotoxicity/ activation).

They also found increased levels of CD16+ T-cells, which can damage the endothelial cells lining the blood vessels, and noted that Carmen Scheibenbogen found markers of endothelial damage in both ME/CFS and long COVID.

All in all, it was good to see quite an immune overlap between ME/CFS and long COVID once they focused on the ME/CFS-like group of long COVID.

Digging Deep…

What came next, though, was even more interesting. While it doesn’t break any new ground in long COVID or ME/CFS, the next study by this group demonstrates how deeply a research team can dig when it has the resources.

We saw this with the recent WASF3 study where an NIH team took a single finding from an ME/CFS patient – kept exploring it  – and uncovered a potentially groundbreaking mitochondrial finding which they are already attempting to mount a clinical trial for. That study shows that given enough interest and resources, things can happen very quickly!

WASF3 – NIH Researchers Find New Mitochondrial Abnormality in ME/CFS

The question was why some severely ill COVID-19 patients benefited from dexamethasone – an immune suppressant – while others didn’t. They found that dexamethasone mainly altered the expression of monocytes (there they are again…) as well as B cells and CD4 T-cells.

The researchers were surprised to find that only a specific subset of monocytes responded to dexamethasone. When they did respond, though, they downregulated alarmin genes that raise the alarm in the immune system.

In the people who died, dexamethasone failed to downregulate that specific subset of monocytes and failed to downregulate their alarmins. An epigenetic analysis found the same thing; their monocytes remained in an epigenetic pro-inflammatory state.

This study demonstrates that even a small subset of an immune cell type can have a very powerful impact. This group is involved in 6 large studies, some of which are focusing on long COVID-related ME/CFS; one of them – a national clinical study group led by Charite – contains 1,000 patients…Nice!

Australian ADAPT Cohort Looks for Immune Dysregulation and Finds It Doesn’t Tell the Whole Story


  • Day one of the first international conference on Long COVID suggested:
  • Pieces of the virus appear to be persisting for several years in long-COVID and perhaps in recovered patients. It’s not clear, though, that they are causing long COVID. We should know more about that in the not-too-distant future as numerous trials are underway that are attempting to wipe out the virus in long COVID.
  • Multidimensional studies that include both the immune system and hormones – are exceedingly rare in long COVID – but appear to be more effective than studies that focus entirely on the immune system. The long COVID field might want to take a note from the ME/CFS field and check out the HPA axis and cortisol more.
  • Monocytes – a virtually unexplored area of focus in ME/CFS until quite recently – are showing up big time in both ME/CFS and long COVID. The only study to assess long COVID patients who met the criteria (CCC) for ME/CFS found “striking” changes in monocytes.
  • The focus on the spike protein that infects cells is understandable in long COVID but given the similarities between long COVID and ME/CFS and other post-infectious diseases which do not feature the coronavirus, researchers need to “go beyond the spike” and look deeper.
  • Small parts of the immune system -such as monocyte subsets – that might have been missed in ME/CFS or long COVID could have major implications for the diseases – and if, found, could move the field forward quickly.
  • Most immune dysregulations that show up say 8 months later in long COVID disappeared two years later even in people for whom long COVID persisted.
  • Instead of smushing them together in one study, the long COVID field needs to differentiate the different types of long COVID present. The RECOVER Initiative could make a big impact here.
  • Despite the bad press that the NIH’s RECOVER Long COVID Initiative has received it got excellent reviews from several presenters. Let’s not count RECOVER out just yet.

The  Australian ADAPT long COVID cohort did extensive immune, serology, and gene expression testing of 100 mostly not hospitalized people over 6-time points over two years. Again we see very general criteria (greater than 1 persistent symptom; shortness of breath, fatigue/malaise, chest pain or tightness lasting for more than 90 days) for inclusion.

The study was particularly interesting in what it did not find. While it found altered levels of antibodies to COVID-19, B-cell response, exhausted T-cells, monocytes, and cytokines over the first 8 months or so, all of those issues resolved over two years – yet long COVID remained. (Some cytotoxic T-cell activation was still present.)

An analysis that used machine learning to predict which participants still had long COVID at 8 months plucked out some immune factors (IFN-B, Pentaxin-3, IFN-y, IL-6). Note, though, that the assessment was only 80% accurate at identifying who had long COVID. Compare that to the 96% accuracy in the Iwasaki study which added hormones to the immune mix and it seems pretty clear that immune analyses by themselves are probably not going to do it.

The one really interesting finding, though, again involved, yes, monocytes. CD4 monocytes were still more activated in the long-COVID patients at 24 months.


While the first day of the Keystone long-COVID conference suggested a couple of things, it’s pretty clear that pieces of the virus have persisted for several years in long-COVID and perhaps in recovered patients. It’s not clear, though, that the virus is causing long COVID. We should know more about that in the not-too-distant future as numerous trials are underway that are attempting to wipe out the virus in long COVID.

Multidimensional studies that include both the immune system and hormones appear to be more effective (and long-COVID researchers might want to catch up on their ME/CFS research). Monocytes – a virtually unexplored area of focus in ME/CFS until quite recently – are showing up more and more. Small parts of the immune system that might have been missed in ME/CFS or long COVID could have major implications for the diseases.

Particularly from the ME/CFS perspective, but also from the long-COVID perspective, we desperately need to differentiate the different types of long COVID found. The fact that several different types of long COVID are probably being smushed together in most of these studies must surely undercut their effectiveness. A general approach was understandable in the beginning, but three years in, one would hope studies would start focusing on subsets. This is where RECOVER – which was praised several times – on the first day – could make a big difference.

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