Signal boost

[sathari]

mellowtigger has created a very straightforward and informative website about COVID and more to the point Long COVID, www.sars2.org/.

ETA: There is a very good discussion in the comments on the accuracy and presentation of some of the material at the linked site, which I recommend exploring. H/T in particular to rydra_wong for a comprehensive discussion of same.

Comments

[lightbird]

Thank you very much for this link.

[rydra_wong]

Okay, I need to put up my hand and say that based on all the reading I've done, some of this is inaccurate or presented in very misleading ways.

And I speak as someone who operates at very high levels of paranoia, still masks on public transport and in all indoor public spaces, and also spent much of my teens with CFS/ME so I am seriously not out to downplay the seriousness of long Covid. But I don't think this is helpful.

infection is permanent

Based on everything I know, this is wildly inaccurate.

Even if you have lingering viral infection after recovery in some cases, this is not the same as implying that all or even most cases are "permanent". Most people clear the infection.

This isn't HIV.

SARS-CoV-2 lab study suggests similar gastrointestinal system persistence, with viral rna found in gut mucosa 7 months after initial infection.

In 4 percent of cases.

Dr. Daniel Chertow, Head of Emerging Pathogens Section, Clinical Center, NIAID at NIH, reports viral persistence in autopsies they performed.

Assuming this is the same cohort of 44 autopsies discussed here (sorry, not watching an hour-long video to confirm) -- they all still had Covid when they died (almost all of them from Covid):

https://assets.researchsquare.com/files/rs-1139035/v1_covered.pdf?c=1640020576

They were all hospitalized and most of them on ventilators (also steroids, which are immunosuppressants). These are people who got extremely ill, stayed extremely ill but hung on for a long time due to massive medical intervention, and never managed to clear the infection before they died.

Not mentioning those rather important facts gives the impression that these are people who got Covid, recovered, then got hit by a bus 230 days later and turned out to have the virus persisting in their bodies. That's not what we're talking about.

infection causes immune system damage

The linked article discusses lymphocytopenia (decrease of white blood cells) as a phenomenon in patients who are ill with Covid, and its relation to outcomes.

Nothing in it says anything about permanent damage, which is what's being implied here.

Covid is bad enough without implying that it's airborne HIV or that anyone who gets it is doomed.

[sathari]

Hoo boy. Do you suggest I delete the post, or link to your comment with a disclaimer, or... something else entirely?

[rydra_wong]

Your post, your call how you want to handle it, I think.

[sathari]

And done. Thanks for taking the time and effort to address these concerns so comprehensively.

[rachelmanija]

Thank you, you said what I wanted to only with actual links.

[mellowtigger]

These are good criticisms about data selection, but how do you propose studying viral persistence, if not autopsies of sick people who failed to clear the infection, early during the pandemic? I don't expect otherwise healthy people will consent to brain sampling. I think your linked study is the correct one. It took almost a year for NIH to publish that information from the autopsies performed. The longer term information you're looking for may not yet be published, which doesn't negate the claim itself. It could negate it in the future, as more detailed information fails to confirm what's already been noticed during the early era. I've lost count of the studies documenting various late symptoms and then noting mysteriously near the end, "as if there's a viral reservoir" that remains in the body. They hint but don't declare. It remains the most plausible explanation. An alternative could exist, but it must explain a great many unusual features of Long Covid while establishing viral clearance.

Lymphocytopenia is relevant to the issue of being susceptible to additional infections due to active Covid infection. If the Covid infection is ongoing, then we can expect the immune suppression is too. The webpage doesn't even get into the superantigen effect (note it also says viral persistence), another immune system disruption. If there over half a dozen different plausible methods of persistence, why wait years for definitive proof? I was there in the 1980s, and I remember the same delays. Yes, I'm very much appealing to the precautionary principle here. You're right. The website is short on detail and differentiation. That's intentional, otherwise it becomes like the diatribes linked near the bottom.

"Most people clear the infection." But, people are getting Covid, recovering, then developing symptoms much later based on immune responses suggesting ongoing viral exposure. It is a pattern consistent with my proposal. Is it consistent with yours? I'm watching local wastewater data over time, since I would expect the troughs between waves to slowly rise each year, since more people would be shedding virus even without active illness. That's another signal that requires large amounts of time to develop. Like with people getting ornamental cold sores whenever a cold or flu disrupts their immune system, I would expect wastewater SARS-CoV-2 levels to increase during any local disease outbreak. The new waves have been too frequent, though, to tell what Covid inactivity looks like in wastewater.

[rydra_wong]

It remains the most plausible explanation. An alternative could exist, but it must explain a great many unusual features of Long Covid while establishing viral clearance.

As mentioned, I had CFS/ME -- a.k.a. post-viral fatigue -- for years. Viruses having long-term consequences even after the virus is cleared is not exactly an unknown phenomenon. See also post-polio syndrome, for example.

One of the possibilities I've seen discussed is that long Covid could be caused by long-term changes in immunological response that are something like an auto-immune illness.

Another possibility is that a major factor is micro-clotting in organs.

I've seen some people noting a strong overlap between the symptoms of long Covid and those of POTS, so it's possible that autonomic disruption could be important.

And then there are studies showing gut dysbiosis in people with long Covid.

There are a range of possibilities that each have some suggestive evidence behind them.

AFAIK, it's not been ruled out that there could be some kind of covert viral persistence in those people who do get long Covid. That possibility may still be on the table! And I believe Akiko Iwasaki has speculated about "viral ghosts" -- not the intact virus but lingering fragments.

But right now, we don't know what causes long Covid. The fact that you personally find one explanation to be the most compelling doesn't make it proven fact.

In any case, even if there is some kind of covert viral persistence in people who get long Covid, that's completely different from claiming that "infection is permanent" in anyone who gets it, whether they get long Covid or not.

but how do you propose studying viral persistence, if not autopsies of sick people who failed to clear the infection, early during the pandemic? I don't expect otherwise healthy people will consent to brain sampling.

If you want to establish viral persistence in the brains of people who have apparently recovered, then yes, you need to wait for enough otherwise healthy people to get hit by buses.

(Of course, if you'd settle for tissue other than the brain, you'd probably have much better luck getting consent for biopsies. The onus is on people who believe that there's viral persistence in otherwise healthy people to do those studies and find it.)

But showing viral persistence in people who are still in hospital dying of Covid does not say anything about viral persistence in otherwise healthy people.

What the paper does show is further evidence that Covid is a weird and scary virus that can potentially get into pretty much every organ system. Like, the stuff we do know is concerning enough! Ditto the stuff we know about long Covid! We don't need to overplay it.

If there over half a dozen different plausible methods of persistence, why wait years for definitive proof? I was there in the 1980s, and I remember the same delays. Yes, I'm very much appealing to the precautionary principle here.

Because there is nothing that suggests that "infection is permanent" in everyone who gets Covid, or that everyone who gets Covid has permanent immune damage.

Even if you think that we should behave as if those things were known to be true, just in case it turns out they are, presenting them as proven fact is misinformation.

I was there in the '80s too (I was wiping tables in the London Lighthouse cafe as a teenager circa '90/91). The immune devastation caused by AIDS was not subtle.

The webpage doesn't even get into the superantigen effect (note it also says viral persistence), another immune system disruption.

That link goes to a paper from the Journal of Medical Hypotheses (rather ironically under the circumstances, given its track record with AIDS denialism in particular):

https://en.wikipedia.org/wiki/Medical_Hypotheses

It is literally just speculating, and in a "not-conventionally-peer-reviewed" way at that.

[mellowtigger]

"But right now, we don't know what causes long Covid. The fact that you personally find one explanation to be the most compelling doesn't make it proven fact."

Yes, although that argument cuts both ways. Discounting the earliest/sickest cases in favor of some future explanation seems a bit circular, somewhat like saying, "The virus is persistent only for those people in which it persists." Viral persistence in some people has been demonstrated in multiple ways. (You don't seem to be claiming that every paper stating viral persistence is wrong.) Are there other permanent infections that, in the reverse way, some people are known to escape without persistence themselves?

The problem with the cases involving otherwise healthy people (like this one, which closes with "Certainly, further studies are needed...") is that they're still anecdotes. They exist, but they're disconnected from larger population studies, which everyone finds more convincing. Doctors like that one are seeing the problem, noting it, and calling for additional study... which takes more time.

But, back to here, it's clear that the website is failing to convince detractors. I was hoping to convince someone now rather than wait 2.5 more years to see what happens. If the only thing that will convince people is a study which does not yet exist, then the website is a doomed effort.

[rydra_wong]

If the only thing that will convince people is a study which does not yet exist, then the website is a doomed effort.

If you want to convince people of a claim that is not proven, then yes, you need a study (multiple studies, in fact) that does not yet exist.

If you are going to make huge claims (that Covid infection is "permanent", and that everyone who gets it has permanent immune damage) which contradict large amounts of what scientists currently believe to be the case, then you need to be able to prove them.

And presenting it as if these things are proven fact is misinformation.

calling for additional study... which takes more time.

That is how science works, yes. The research has to actually take place.

[mellowtigger]

Then I'll stick with the claim of misinformation. You're welcome to do what you wish with the mention here on Dreamwidth. I found the Head of Emerging Pathogens at NIH talking about persistence to be convincing (repeatedly mentioning immune privilege in sites where they found virus), but that was a study critiqued here. I'll definitely look into the other problem with the gut persistence seeming to contradict itself. That's as bothersome as the doctor speaking on CNN whose words seem to be inconsistent to the expressed message.

I accept that the website itself is short on information. That's intentional, otherwise it looks like this document from a doctor who collected literally hundreds of studies about various forms of persistence that have been found. I didn't even include the adipose tissue reference that's mentioned there. (Chalk up yet another route to persistence.) I may include a link to the doctor's list on the webpage, since the chosen links there now aren't sufficiently convincing for many people. I know that even doctors make mistakes, but disputing every paper about persistence seems to require a whole lot of doctor mistakes about many different routes to persistence. These results convinced me. I hope, for all our sakes, that your skepticism is the right call.

[rydra_wong]

SARS-CoV-2 lab study suggests similar gastrointestinal system persistence, with viral rna found in gut mucosa 7 months after initial infection.

In 4 percent of cases.

Okay, to be pedantic at myself here: that 4 percent refers to the first article linked in that sentence.

The second linked article (specifically on patients with IBD) found much higher rates of viral RNA in gut tissue, but N.B.:

"We were unable to culture SARS-CoV-2 from gut tissue of patients with viral antigen persistence."

Also:

"Our findings indicate that viral antigens, but not infectious virions, persist in the gut mucosa long beyond mild acute COVID-19 in patients with IBD."

Antigen persistence =/= viral persistence.

[mellowtigger]

"Antigen persistence =/= viral persistence."

Agreed. Are the authors contradicting themselves? They also say:
"SARS-CoV-2 RNA was detected in 32/46 patients using qPCR. Viral RNA was detected in 1 biopsy in 19 patients, in 2 biopsies in 9 patients, and in all 3 biopsies collected in 4 patients. Detection was unrelated to the intestinal location and viral RNA was detected in 15/46 duodenal, 10/46 ileal, and 13/46 colonic samples."

RNA =/= antigen also, so... I admit to being confused here. I thought PCR was used to detect viral code, not antigen.