A Concerned Scientist @BE@qoto.org

@trendless

I felt like my post on this paper was long enough already that 99% of people weren't going to read it, but, overall the liver and kidney(your filters) were where a lot of viral RNA and subgenomic RNA were found.

https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00171-3/fulltext

I'm also going to hammer the point endlessly, but, your body also has to try to remove microplastics and PFAs, so people's livers and kidneys probably weren't in the best shape before COVID.

Blaming it on drinking alone is lazy.

@PacificNic @Edelruth @NilaJones

I would HOPE, for example, that someone at the CDC has been in contact with, say, dairy farmers, to make sure that any sick people get reported, but, who knows?

@PacificNic @Edelruth @NilaJones

Sure, and I get the concern, especially because the latest spread in cows has been said to be asymptomatic when visually inspecting the cows.

I think it points out the holes in the system. Who determines that they should be testing pigs? Who pays for it? Do farmers have to have their pigs tested? At what point do we start mass-surveilling people looking for signs?

I've been looking for reports of lots of sick people without COVID wastewater numbers going up, for instance, but is there anyone at the USDA or CDC looking for such things? You just wouldn't know and it's unclear who would make that call. They're all fine questions that I don't think have great answers.

@PacificNic @Edelruth @NilaJones

From what I understand, so far H5N1 contaminated milk has been extremely viscous. I think the lack of concern is two-fold. One, pasteurization. Two, what they've seen so far wouldn't be palatable to people.

@NilaJones @PacificNic

Fair! I was imprecise. I was talking about H5N1 while saying "bird flu" and I would change "There's any number of zoonotic diseases that are a mutation or two away from infecting people" to "There's any number of zoonotic diseases that are a mutation or two away from mass infecting people."

For instance, one reason previous versions haven't taken off across people is because they are good at replication at 40C(bird respiratory tract), but don't replicate well at 32C(human respiratory tract).

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000424

I've pointed this one out a couple of times just to get thinking about how it's not just receptors. There's physical differences in different hosts that have to be overcome as well. It's a multi-step process for the virus.

"Bird flu" as a general term now, was first discovered in 1878. The next mutation could be the one, or it might not be. The step to more mammalian spread, first reported in 2022 and studied in 2023 was a big deal. We'll see what's next.

I had no scheduled time today for journal reading, but, when I saw this article I had to take a break from other stuff and give it a read. Apologies if I missed anything. As always, point out if I did, or if I misinterpreted anything.

https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00171-3/fulltext

I find this interesting, because next to a large-scale autopsy study(I do not know why this hasn't been done), this is probably the next best thing to look for viral persistence.

In their own words:

"This single-centre, cross-sectional cohort study was done at China–Japan Friendship Hospital in Beijing, China, following the omicron wave of COVID-19 in December, 2022. Individuals with mild COVID-19 confirmed by PCR or a lateral flow test scheduled to undergo gastroscopy, surgery, or chemotherapy, or scheduled for treatment in hospital for other reasons, at 1 month, 2 months, or 4 months after infection were enrolled in this study. Residual surgical samples, gastroscopy samples, and blood samples were collected approximately 1 month (18–33 days), 2 months (55–84 days), or 4 months (115–134 days) after infection. SARS-CoV-2 was detected by digital droplet PCR and further confirmed through RNA in-situ hybridisation, immunofluorescence, and immunohistochemistry. Telephone follow-up was done at 4 months post-infection to assess the association between the persistence of SARS-CoV-2 RNA and long COVID symptoms."

So, in short, what did they find? In patients who no longer tested positive via nasopharyngeal RT-PCR, a lot of viral persistence, in both "viral RNA" and "subgenomic RNA" but not universal viral persistence. Of course, they were unable to search all tissues in anyone's body, so that's not to eliminate the possibility that it was elsewhere in any test subject.

The big question to me here, and at least on my first read I think they were careful not to discuss it; was the viral RNA replicating? Given the lack of discussion on it in the article, let's just move on, but it's in the back of my mind.

Viral RNA was found, overall, in 30% of solid tissue samples collected at one month, 27% of those at two months, and 11% of those at 4 months. Further, additional subgenomic RNA was detected in 61% of samples that had viral RNA.

Also, viral RNA was detected in blood plasma, white blood cells, and peripheral blood mononuclear cells(think T cells and B cells here) of 9 patients, all of whom were immunocompromised, but none in 10 patients who were immunocompetent. Of course, everyone is immunocompetent until they're not.

Importantly, "Detection of viral RNA in recovered patients was significantly associated with the development of long COVID symptoms" and "Patients with higher virus copy numbers had a higher likelihood of developing long COVID symptoms."

There's an awful lot here, but a few other things were interesting to me:

- An even split, essentially, in long COVID between men and women.

- 78% of the patients with long COVID had 3 vaccine doses(I'm sorry, vaccination does not mean you can't get long COVID and it can't be said enough) while 86% without long COVID had 3 vaccine doses. Only 6% were unvaccinated in both the long COVID and no long COVID cohorts.

- 46% of the long COVID cohort were given one of oseltamivir, baloxavir, nirmatrelvir–ritonavir, famciclovir, and ganciclovir, while 52% of the no long COVID group were.

- Viral RNA was found in:

liver, kidney, stomach, intestine, brain, blood vessel, lung, breast, skin, and thyroid

but not pancreas, gallbladder and appendix.

- "Furthermore, to explore whether any difference in viral load was due to different concentrations of the SARS-CoV-2 receptors ACE2 and TMPRSS2, we compared the expression levels of ACE2 and TMPRSS2 in tumour tissues and paratumour tissues, and the results showed that the mRNA levels of ACE2 (p=0·83) and TMPRSS2 (p=0·49) were not significantly different"

- "Long COVID symptoms at 4 months were significantly associated with viral persistence at 1 month and 2 months post-infection but not at 4 months."

- "The host cell dysfunction caused by viral persistence might be a crucial aspect of long COVID pathogenesis."

@Edelruth @PacificNic @NilaJones

No argument there. That would be another significant step.

@ScienceCommunicator

You make some fantastic points, and I think that, genuinely, the average person(talking US here as I'm not knowledgable about how this translates worldwide) doesn't know better. They've been told by capitalist industries that if they slap a few solar panels on their McMansion, buy an electric car and recycle that they'll save the world.

@PacificNic

Overall I like your alarmist TED talk. I can't blame anyone for worrying about this.

Here's the deal, to me. There's any number of zoonotic diseases that are a mutation or two away from infecting people. Before COVID I would say 99.9% of people never gave them a second thought. They will only increase as human population digs deeper into forests and whatnot, and with climate change.

On bird flu itself, I'm moderately alarmed, but, I was moderately alarmed a year ago, and the cows thing hasn't QUITE moved me beyond that.

https://jamanetwork.com/journals/jama/article-abstract/2801499

Mammals, in general, was what moved it from mild to moderate, at least for me.

But here's the thing. That last step, or a few steps, into virulent spread in humans might be tomorrow or it might be the 2120 pandemic. These things have a tendency to not happen on anyone else's schedule.

I think I mentioned this recently, and you've talked about COVID precautions overlapping with H5N1 precautions, but where we're at in our family is that we did a fresh mask fit test a week or two ago. I read the WHO and USDA updates, and, yes, the USDA is being super sketchy about this, which has piqued my curiosity. It's hard to tell if they're purposefully hiding something, if they're just totally in bed with industry, or if they're incompetent.

Prepare, not panic. I think @NilaJones mentioned stocking up on meat from a local farm, and while I thought that was brave with all the vegans lurking around, it was good advice for the meat eaters amongst us. Know your egg substitutes.

@atthenius @pvonhellermannn

Very much appreciated!

@atthenius @pvonhellermannn

I sincerely appreciate that offer! If she were still working in the brick and mortar classroom I bet she'd take you up on it.

She, however, works at a school that's been doing virtual school for decades for a few years now. She has over 100 kids, each of whom she works with individually, one on one, so there's no classroom to talk to.