A Concerned Scientist @BE@qoto.org

I don't know how to say this politely. If you take Leana Wen seriously, you're not serious and should probably keep your opinions to yourself.

I've also been asked a lot whether we're in panic mode here, and if we're running off to the homestead.

No, not at this point. We, obviously, already take airborne precautions. Please don't forget about COVID.

Last night my wife and I did make the decision to stop using grocery store milk. We really only buy 2 gallons a month. It's not a big deal to us, so it seems like an easy thing to do. We use it to make kefir, and kefir can, under some circumstances, harbor and facilitate the growth of viruses from what I've read. So the kefir grains are going to stop being fed for the moment. Sorry kefir grains.

If I bought a lot of ground beef from the store would I be worried? Hard to tell since it's not something we do, but, I guess I'd be cooking it to a higher temperature, at least.

Know your egg substitutes.

Crises precipitate change. Don't be afraid to be flexible as circumstances change.

Otherwise, we're just keeping up to date and seeing what goes on.

Who am I following on this? @HelenBranswell has a string of great articles at statnews.com.

https://www.statnews.com/2024/04/05/bird-flu-cdc-urges-doctors-watch-for-h5n1-in-farm-workers/

https://www.statnews.com/2024/04/18/h5n1-bird-flu-scientists-want-usda-genetic-data-faster/

https://www.statnews.com/2024/04/21/usda-releases-h5n1-bird-flu-genetic-data-eagerly-awaited-by-scientists/

https://www.statnews.com/2024/04/23/h5n1-bird-flu-genetic-analysis/

https://www.statnews.com/2024/04/23/h5n1-bird-flu-virus-particles-in-pasteurized-milk-fda/

https://www.statnews.com/2024/04/24/h5n1-bird-flu-vaccine-preparedness/

I follow a lot of people. 1,878 as of this morning. I also don't engage in any other social media. Never have, never intend to. Pretty much every other social media domain is blocked at our firewall level. I only looked at twitter(as it was called at the time) in December of 2019, for the first time in my life, to try to get fast breaking COVID news, and have access to scientists who would be ahead of the knowledge curve.

I'm only really here for one reason. To get good info, synthesize it, and redistribute it, often in different words, when I think it'll be helpful. Despite some truly "delightful" DMs I've received recently, I have no ulterior motive. No one's forcing you to believe that, and I take it as a badge of honor to be blocked, so, knock yourself out if you're so inclined.

I'm asking everyone, particularly scientists, to be careful with your words. There's been palatable rising tensions here in 2024. Some of it has to do with science(H5N1, WHO airborne) some of it doesn't(politics), but it's real.

I have seen some truly awful H5N1 takes as things ramp up. Particularly this morning. Nuance matters. If you want to be a prognosticator, be clear. "I think" or "I believe" instead of launching into what you want to say.

Here's a few things I've seen that should be discussed carefully:

- Pasteurization is completely effective against H5N1.

Here's what the FDA says about that:

The FDA believes the pasteurization process is “very likely” to inactivate H5N1, though they acknowledged that no studies have been done to test that.

Here's someone who knows better:

“Daniel Perez, an influenza researcher at the University of Georgia, is doing his own test tube study of pasteurization of milk spiked with a different avian influenza virus. The fragile lipid envelope surrounding influenza viruses should make them vulnerable, he says. Still, he wonders whether the commonly used “high temperature, short time” pasteurization, which heats milk to about 72°C for 15 or 20 seconds, is enough to inactivate all the virus in a sample.”

- It's already spreading person to person across the US.

The only reference I can find that would lead to that conclusion would be this:

"Only one human case linked to cattle has been confirmed to date, and symptoms were limited to conjunctivitis, also known as pink eye. But Russo and many other vets have heard anecdotes about workers who have pink eye and other symptoms—including fever, cough, and lethargy—and do not want to be tested or seen by doctors. James Lowe, a researcher who specializes in pig influenza viruses, says policies for monitoring exposed people vary greatly between states. “I believe there are probably lots of human cases,” he says, noting that most likely are asymptomatic."

Or, perhaps in conjunction with this:

"The genetic sequence from the human case, which occurred on an unidentified farm in Texas, is sufficiently different from the cattle sequences that it can’t be easily linked to them, he said. The differences suggest that the individual was either infected in a separate event — maybe not via a cow, but through contact with infected wild birds — or that there might have been another line of viruses in cattle early on and it has since died out."

I don't want to belabor the point, and I don't want to call out anyone. I just felt the need, after scrolling through my timeline this morning, to point out that language matters. Be careful. Don't spread misinformation. If you want to prognosticate, go ahead, but be clear it's your opinion. Your magic internet points don't matter.

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."