Post-acute COVID-19 is characterized by gut viral antigen persistence in inflammatory bowel diseases, 2022, Zollner et al

[LarsSG]

Abstract

Background and aims:
The coronavirus disease 2019 (COVID-19) pandemic affects populations, societies and lives for more than two years. Long-term sequelae of COVID-19, collectively termed the post-acute COVID-19 syndrome, are rapidly emerging across the globe. Here, we investigated whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) antigen persistence underlies the post-acute COVID-19 syndrome.

Methods:
We performed an endoscopy study with 46 inflammatory bowel disease (IBD) patients 219 days (range: 94-257) after a confirmed COVID-19 infection. SARS-CoV-2 antigen persistence was assessed in the small and large intestine by qPCR of four viral transcripts, immunofluorescence of viral nucleocapsid and virus cultivation from biopsy tissue. Post-acute COVID-19 was assessed by a standardized questionnaire, and a systemic SARS-CoV-2 immune response was evaluated by flow-cytometry and ELISA at endoscopy. IBD activity was evaluated by clinical, biochemical and endoscopic means.

Results:
We report expression of SARS-CoV-2 RNA in the gut mucosa ~7 months after mild acute COVID-19 in 32 of 46 patients with IBD. Viral nucleocapsid protein persisted in 24 of 46 patients in gut epithelium and CD8+ T cells. Expression of SARS-CoV-2 antigens was not detectable in stool and viral antigen persistence was unrelated to severity of acute COVID-19, immunosuppressive therapy and gut inflammation. We were unable to culture SARS-CoV-2 from gut tissue of patients with viral antigen persistence. Post-acute sequelae of COVID-19 were reported from the majority of patients with viral antigen persistence, but not from patients without viral antigen persistence.

Conclusion:
Our results indicate that SARS-CoV-2 antigen persistence in infected tissues serves as a basis for post-acute COVID-19. The concept that viral antigen persistence instigates immune perturbation and post-acute COVID-19 requires validation in controlled clinical trials.

Preprint PDF

From the Discussion:
We argue that viral antigen persistence reflects incomplete clearance of SARS-CoV-2 rather than subclinical (latent or persistent) infection, as we were unable to replicate virus from biopsy derived tissue. In line with this, we usually detected only some (but not all) viral transcripts in biopsies from the same patient. Our experimental data rather suggest that immunosuppressive therapy with or without genetic predisposition (affecting the immune system) may promote incomplete viral clearance.

In our report, only patients with gut antigen persistence (determined by qPCR) reported post-acute COVID-19 symptoms. In contrast, none of the patients without evidence for antigen persistence in the gut reported symptoms of post-acute COVID-19. This observation strongly argues for a role of viral antigen persistence in post-acute COVID-19 and it appears plausible that SARS-CoV-2 antigen persistence, possibly in infected tissues beyond the gut, could impact host immune responses underlying the post-acute COVID-19 syndrome.

Note: They asked patients about post-Covid symptoms, but it isn't clear to me if they asked patients specifically if they had symptoms that appeared or persisted post-Covid or asked them if they had symptoms in general, which they classified as post-Covid symptoms.

 

[Hutan]

Thanks @LarsSG
Seems like an important finding.

 

[Boba]

Interesting. They didn’t find any active virus, but remnants with all patients experiencing LC symptoms and the other way around didn’t find any remnants in the patients without LC symptoms. No healthy controls obviously. Would be interesting to see if really healthy controls don’t show remnants as well.

Would explain why postvax long haulers have symptoms. They should check those as well for particles. Then obviously the question of pathology connected to those particles.

 

[Hutan]

To me, this idea makes some sense. I think the strongest argument I've heard against this idea of persistence of pathogen antigens is that the antigens would break down over time, the body would recycle and eliminate them. So, perhaps it might work for an illness of months or even a few years, but it becomes less likely for illnesses lasting 5 years or decades. That's when the idea of smouldering infections that periodically flare up gets invoked.

I thought the paper was good. They were looking at biopsies of patients with a previous diagnosis of IBD, so perhaps their gut lining was a bit fragile or unusual, although it sounded as though many were in remission at the time of the biopsies. It would have been good to have a bit more clarity around symptoms regarded as indicative of Long Covid.

There's the potential confounding of reinfections, possibly asymptomatic reinfections. That's going to confound other similar studies looking at even longer periods since the initial infection unless it's possible to identify specific variants from the viral fragments.

 

[FMMM1]

To me, this idea makes some sense. I think the strongest argument I've heard against this idea of persistence of pathogen antigens is that the antigens would break down over time, the body would recycle and eliminate them. So, perhaps it might work for an illness of months or even a few years, but it becomes less likely for illnesses lasting 5 years or decades. That's when the idea of smouldering infections that periodically flare up gets invoked.

I thought the paper was good. They were looking at biopsies of patients with a previous diagnosis of IBD, so perhaps their gut lining was a bit fragile or unusual, although it sounded as though many were in remission at the time of the biopsies. It would have been good to have a bit more clarity around symptoms regarded as indicative of Long Covid.

There's the potential confounding of reinfections, possibly asymptomatic reinfections. That's going to confound other similar studies looking at even longer periods since the initial infection unless it's possible to identify specific variants from the viral fragments.

Only scanned a bit of your post but I recall that OMF highlighted that you can identify virus from fragments - so a persistent, low level, viral infection should be relatively easy to identify (PCR?)? OMF did look for viral fragments but nothing found & Ian Lipkin?
Only thing that I recall to argue against this is Prusty's work which (from memory) seemed to find low level infections --- consequence or cause though?

Surely GWAS would find relevant genes i.e. if it were common [EDIT - cause of ME]?

 

[Andy]

Merged thread

Background & Aims
The coronavirus disease 2019 (COVID-19) pandemic has affected populations, societies, and lives for more than 2 years. Long-term sequelae of COVID-19, collectively termed the postacute COVID-19 syndrome, are rapidly emerging across the globe. Here, we investigated whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen persistence underlies the postacute COVID-19 syndrome.

Methods
We performed an endoscopy study with 46 patients with inflammatory bowel disease (IBD) 219 days (range, 94–257) after a confirmed COVID-19 infection. SARS-CoV-2 antigen persistence was assessed in the small and large intestine using quantitative polymerase chain reaction of 4 viral transcripts, immunofluorescence of viral nucleocapsid, and virus cultivation from biopsy tissue. Postacute COVID-19 was assessed using a standardized questionnaire, and a systemic SARS-CoV-2 immune response was evaluated using flow cytometry and enzyme-linked immunosorbent assay at endoscopy. IBD activity was evaluated using clinical, biochemical, and endoscopic means.

Results
We report expression of SARS-CoV-2 RNA in the gut mucosa ∼7 months after mild acute COVID-19 in 32 of 46 patients with IBD. Viral nucleocapsid protein persisted in 24 of 46 patients in gut epithelium and CD8+ T cells. Expression of SARS-CoV-2 antigens was not detectable in stool and viral antigen persistence was unrelated to severity of acute COVID-19, immunosuppressive therapy, and gut inflammation. We were unable to culture SARS-CoV-2 from gut tissue of patients with viral antigen persistence. Postacute sequelae of COVID-19 were reported from the majority of patients with viral antigen persistence, but not from patients without viral antigen persistence.

Conclusion
Our results indicate that SARS-CoV-2 antigen persistence in infected tissues serves as a basis for postacute COVID-19. The concept that viral antigen persistence instigates immune perturbation and postacute COVID-19 requires validation in controlled clinical trials.

Open access, https://www.gastrojournal.org/article/S0016-5085(22)00450-4/fulltext

 

[Hutan]

Austrian paper.
The indications that persistence of pathogenic material might be causing ME/CFS (including post-Covid-19 ME/CFS and post-Ebola ME/CFS) keep coming.

Viral nucleocapsid protein persisted in 24 of 46 [IBD] patients in gut epithelium and CD8þ T cells.

Studies with intestinal epithelial organoids confirmed that SARS-CoV-2 infects human epithelium, triggering an interferon (IFN) signature.

It's not clear to me yet (just part the way though the paper so far) how many of the patients who were attending this IBD outpatient unit already had IBD (mostly Crohn's disease) before getting Covid. Perhaps the pre-existing disease made their digestive system tissue more prone to infection?


Check out Table 2 - excerpt in thumbnail below. It really is remarkable how the people whose gut mucosa tested negative to SARS-CoV-2 RNA all reported no post-acute COVID symptoms, whereas over half of the people whose gut mucosa tested positive reported fatigue.

 

[Hutan]

Here's the Table 2 information presented in graphical form. Sorry, I'm making a dog's breakfast of this commentary.

Patients recruited in this study had acute COVID-19 (PCR-confirmed SARS-CoV-2 infection) 219 days (range, 94–257) before endoscopy, which was performed to evaluate disease activity of an established IBD (ie, we did not select for patients with postacute COVID-19).

So, it sounds like people might have had established IBD before infection, rather than as a consequence of the Covid infection. It was noted that over half were in remission at the time of the biopsy.

This looks like a solid study to me, with multiple methods employed to verify the persistence of viral material. They used positive and negative controls for some analyses, like testing some biopsies taken in 2017 to check they weren't getting false positives.


It's interesting that, for a single patient, a biopsy in one part of the gut could be positive, whereas a biopsy in another the part of the gut was negative. It seems like the viral antigen persistence can be quite localised.



Regarding whether pre-existing conditions or treatment for the conditions make these people more likely to have viral antigen persistence:

Viral antigen persistence occurred in patients with and without immunosuppressive therapy (ie, azathio- prine, anti-TNF therapy, or vedolizumab; Figure 3C) and was unrelated to gut inflammation indicated using fecal calprotectin

 

[Hutan]

Andreas Zollner ∗
Robert Koch ∗
Almina Jukic
Alexandra Pfister
Moritz Meyer
Annika Rössler
Janine Kimpel
Timon E. Adolph
Herbert Tilg §

Seems like there has been some good research coming out of Austria on Long Covid. I'm not sure to what extent the researchers overlap.

In the discussion, they suggest that immunosuppressive therapy may have played a part in the frequency of viral antigen persistence

We argue that viral antigen persistence reflects incomplete clearance of SARS-CoV-2 rather than subclinical (latent or persistent) infection because we were unable to replicate virus from biopsy-derived tissue. In line with this, we usually detected only some (but not all) viral transcripts in biopsy specimens from the same patient. Our experimental data rather suggest that immunosuppressive therapy with or without genetic predisposition (affecting the immune system) may promote incomplete viral clearance.

This observation strongly argues for a role of viral antigen persistence in postacute COVID-19 and it appears plausible that SARS-CoV-2 antigen persistence, possibly in infected tissues beyond the gut, could impact host immune responses underlying the post- acute COVID-19 syndrome.1 This notion is supported by an influenza mouse model, demonstrating that ineffective viral clearance modulates adaptive immune responses and the formation of memory T cells in draining lymph nodes of the lung.

Our findings could be applicable to patients without IBD because viral antigen persistence has been reported in the gut 2 months after COVID-19 in patients without IBD or immunosuppression.15 Whether the re- ported link between gut viral antigen persistence and postacute COVID-19 is applicable to patients without IBD warrants controlled clinical trials. Our findings are also consistent with a growing body of evidence showing that COVID-19 does not affect gut inflammation in IBD.

Collectively, we provide evidence for SARS-CoV-2 anti- gen persistence in the gut as a basis for immune perturba- tion in postacute COVID-19. Whether viral antigen persistence (in and beyond the gut) underlies the patho- physiology of postacute COVID-19 warrants further clinical trials to tackle this rapidly emerging disorder across the globe.

I hope that there will be more studies of viral (antigen) persistence in various biopsy types.

 

[Hutan]

Ha. We had a duplicate thread on this, merged now. I got to be a bit excited about it all over again. At least I was consistent.

 

[SNT Gatchaman]

Follow-up: Clearance of gut mucosal SARS-CoV-2 antigens and post-acute COVID-19 after two years in patients with inflammatory bowel disease (2024, Gastroenterology)