A Concerned Scientist @BE@qoto.org

Another article from @HelenBranswell today. This time with an interesting Q&A with the head of the CDC's influenza division.

https://www.statnews.com/2024/05/03/bird-flu-why-h5n1-keeping-awake-cdc-top-flu-scientist/

"It sounds like your team that was ready to go didn’t go. And it sounds like from what you’re telling me that CDC is very much in the back seat on this one. That it’s the states or local authorities who are running this.

They have the authority, right? CDC does not have the authority to go into a state. We have to have an invite from state public health.

Have any states invited CDC in?

No. Not officially yet. We’re speaking to these partners if not once a day, more than that."

"There has been a single human case in Texas. Has anybody done serology testing around that individual? That would be an obvious place to start, would it not?

I don’t know that that was consented to. You have to have consent from people to follow up. Certainly it was something that was on our radar for what we would like to have and request, but to my knowledge, serology was not performed. (A report on the case published Friday in the New England Journal of Medicine confirmed Dugan’s belief. The infected person and his contacts would not consent to have blood drawn.)"

@carstenfranke

Yeah, I did wonder about particularly state fairs and whether everyone was just going to go ahead with them, and I'm sure the answer is yes.

Catching up on my reading today and there's 4 new articles from StatNews.com that fit in this thread.

First, making the case for expanded wastewater surveillance:

https://www.statnews.com/2024/05/01/h5n1-bird-flu-hospital-wastewater-surveillance/

@HelenBranswell with another article about the USDA obfuscating data by labeling genomic sequences with simply "USA" and "2024":

https://www.statnews.com/2024/05/02/bird-flu-in-cows-h5n1-virus-changes-missing-data/

This one discusses a preprint

"The authors suggest the spillover event that started the spread in cattle may have happened in early December. The first detection that something was amiss with some cattle herds in the Texas panhandle dates to late January, but it took until March 25 before USDA confirmed the presence of H5N1 in a Texas herd."

https://www.biorxiv.org/content/10.1101/2024.05.01.591751v1.full.pdf+html

"Our genomic analysis
and epidemiological investigation showed that a reassortment event in wild bird populations preceded a5
single wild bird-to-cattle transmission episode. The movement of asymptomatic cattle has likely played a
role in the spread of HPAI within the United States dairy herd. Some molecular markers in virus populations
were detected at low frequency that may lead to changes in transmission efficiency and phenotype after evolution in dairy cattle. Continued transmission of H5N1 HPAI within dairy cattle increases the risk for
infection and subsequent spread of the virus to human populations."

The politics of public health is the topic of the next one, which is depressing:

https://www.statnews.com/2024/05/02/bird-flu-testing-dairy-state-politics-in-congress/

"Republican lawmakers have one big message on the avian flu outbreak in cows: Calm down."

No comment from me as I couldn't even get through it without having to take a walk.

And, finally, a little more info about the preprint paper from above and the recent data dump from the USDA:

https://www.statnews.com/2024/05/02/bird-flu-virus-in-cows-four-months-before-h5n1-outbreak-confirmed/

""These data support a single introduction event from wild bird origin virus into cattle, likely followed by limited local circulation for approximately 4 months prior to confirmation by USDA,” the authors wrote."

"In the last few years, H5N1 has spread from wild birds to a variety of carnivorous mammals, including foxes, bears, and seals, but in each of those instances, the virus has hit a dead end. The outbreak in dairy cows represents one of the first times that this bird flu virus has demonstrated the ability to efficiently transmit between mammals, said Thomas Mettenleiter, a virologist who served as the director of the Friedrich Loeffler Institut — Germany’s leading animal disease research center — from 1996 until he stepped down last year. The other instance was a number of outbreaks at mink farms in Spain and Finland in 2022 and 2023, respectively."

New article from StatNews again today, this time titled "Pasteurization inactivates H5N1 bird flu in milk, new FDA and academic studies confirm"

https://www.statnews.com/2024/05/01/bird-flu-pasteurization-inactivates-h5n1-in-milk/

I think the take home message in the article is:

"On Wednesday, the agency reported results from testing of a further 201 products, which included cottage cheese and sour cream, in addition to milk. Any PCR-positive samples were then injected into embryonated chicken eggs, to see whether any active virus could be grown — the gold standard test for assessing the viability of an influenza virus. None of the samples produced viable, replicating virus, Prater said."

"In addition, several samples of retail powdered infant formula as well as other powdered milk products. All PCR results from these products were negative. The agency did not disclose when it plans to make its full analysis, including which products were purchased from which states, available to the public."

"Bolstering the FDA’s data, academic researchers at the Ohio State University and St. Jude Children’s Research Hospital told STAT Tuesday night that their own study of 58 PCR-positive milk samples taken from Texas, Kansas, and eight other states in the Midwest also failed to turn up any evidence that H5N1 can survive the pasteurization process."

@QuietLurker

That's the truth!

@QuietLurker

I'm never offended by questions, although I'm definitely not an expert. Just someone with a science background who reads a lot, and used to have a head cheese maker roommate for years :)

I know you didn't really ask about eggs, but, you mentioned them. I put eggs and chicken in the same category for now, personally. I don't see any substantial change in their situation just because cows got H5N1. There's something like 430 billion birds in the world and 90 million cows in the US. It's not a huge reservoir overall, although, any new viral reservoir can lead to new and often unpredictable mutations.

Sour cream's a great question and I don't have a great answer beyond making sure it's made with pasteurized milk/cream.

I did read somewhere recently that a lot of Mexican-style soft cheeses are sometimes allowed to use unpasteurized milk. I haven't dug into the subject deeply, but, if that's true, I'd say the same thing about your cheese. Just make sure it's from pasteurized milk.

Somewhere in the thread above was a mention that something like 4% of people supposedly drink raw milk more than 1 time per year. If that's true, that would be something like 13 million people. That seems impossibly large to me, but, let's assume it's correct for the moment. If even 10% of them were currently sick with bird flu, that would be over a million people. I think we'd know. I'm not saying that there's no risk at all. Clearly, we've made some changes just to be on the safe side, but, to date, I don't see any evidence that there's a lot of people with bird flu, unless it's simply not distinguishable from COVID.

@QuietLurker

I've addressed this a little last week, but, I think it still stands today. It sucks, but, you're not wrong about the track record. You have to make your own decisions until a different track record is established.

We don't drink milk, but we did buy some to make kefir with every couple of weeks, and we quit doing that for now. That said, it should be safe if properly pasteurized.

We eat cheese and haven't stopped. I'm far from an expert, but, from what I know from personal experience cheese makers know if something is growing in their cheese and throwing off the chemistry, pH, etc.

We don't buy grocery store beef, so, I haven't given it too deep of thought. Off the top of my head, we've lived with bird flu theoretically infecting any given chicken for years now, and if cooked above 165 it should be safe. I would think the same applies to beef, but, I know we are a nation of medium/medium rare beef. Since there's really no science on infectious dose from eating infected meat it's hard to intelligently discuss.

If it were me, I might wait until we have some more information on that, specifically the USDA's ground beef testing. But that's easy for me to say when it doesn't affect us, personally. If you live on a beef diet you might have a different outlook on that.

@QuietLurker

I don't think the poultry outlook has substantially changed since bird flu was first introduced to North America ~2021.

The USDA has started testing ground beef, but only in the 9 states officially recognized as having bird flu in dairy cows, from what I understand.

There's a new article on StatNews today from @HelenBranswell with a Q&A format about what we know, and don't know, at this point about this outbreak.

https://www.statnews.com/2024/04/30/h5n1-bird-flu-virus-cows-and-risk-to-people/

Wear a mask makes an early appearance, so that's a plus. There's some discussion of asymptomatic and presymptomatic spread.

Some quotes of note:

- "The U.S. Department of Agriculture has said few tests from the respiratory tracts of infected cows have come back positive — and those that did showed there wasn’t a lot of virus present. But there is at least some evidence that H5N1 is on occasion getting deep into the respiratory tracts of cows."

- "While the contribution of respiratory transmission is still in question, there appears to be little doubt that a lot of spread is happening in milking parlors, where cows are strapped into the milking machines, and that in dairy cows, H5N1 seems to be primarily infecting mammary glands. The amount of virus in the udders of infected cows is off-the-charts high, making it easy to see how one cow’s infection soon becomes a herd’s problem."

- "Taylor noted another worry: H5N1, which is notorious for its ability to evolve, is being given a huge opportunity to adapt to bovine hosts. “The concern is if it becomes effective as a respiratory pathogen in cattle, it’s more likely to become effective as a respiratory pathogen in humans,” he said."

- "Sifford noted that cows in a herd without symptoms tested positive after cattle were moved into it from another herd whose remaining animals then went on to develop symptoms. The positive cows in the second herd haven’t developed symptoms, she said. “We are just getting underway with those studies to give us an idea of the opportunity for viremia either ahead of or after clinical signs,” she said. “So we should have more information about that in the coming weeks.”

One such study will be taking place in the high-containment laboratories at Kansas State University’s Center of Excellence for Emerging and Zoonotic Animal Diseases. Director Jürgen Richt said his group already has the necessary approvals and hopes to begin the research in mid-May."

- "Some uninfected cows will be housed with the infected animals to see whether they contract the virus, Richt said."

- "As to whether infected cows that have no symptoms are shedding virus in their milk, the evidence of viral traces in commercially purchased milk brings that question to the forefront. Farmers are supposed to discard milk from infected cows, which reportedly looks odd — yellowish and unusually thick. But PCR testing of commercially sold pasteurized milk has shown a substantial portion of samples were positive for RNA from H5N1, indicating the presence of either viral fragments or dead viruses. (The FDA said last week about one in five samples purchased in a cross-country survey tested positive.) So either some farmers aren’t following the recommendation, or some milk isn’t noticeably altered, or some cows that aren’t known to be sick are shedding the virus in their milk."

- "Kuiken is a bit pessimistic about whether, once the virus has found its way into a herd, transmission can be stopped: “You can’t not milk. And you probably can’t milk so well as to prevent cow-to-cow spread. I don’t think you can do it.” "

- "The CDC recommends that people working with or around cattle suspected or confirmed to be infected with H5N1 wear gloves, disposable fluid-resistant coveralls, vented safety goggles or a face shield, and an N95 respirator."

I would like to add to this that the CDC has recommendations for backyard flock owners since 2022 and I have yet to hear of anyone following it, even after bird flu has been found in their area. Recommendations, such as an N95, safety goggles and head to toe PPE, are pointless if no one follows them, or knows about them to begin with.

https://www.cdc.gov/flu/avianflu/h5/backyardflockowners.htm

- "Kuiken said the setup of many milking parlors is almost tailor-made to put workers in contact with viruses being shed in milk. That’s because there is typically a well — think of the area under the hoist in the garage where your car gets repaired — where workers are located while cows are being milked.

“So the milk worker is standing in a depressed area, and therefore his eyes are about at knee level — a little bit higher, maybe — with the cow. So very good for being inoculated, for eye infection,” he said."

- "Cook is also concerned about the possibility that the high pressure hoses that are used to spray down the parlors after milking may be aerosolizing virus that has fallen to the floor, making it easier for cows — and humans —to breathe in. He and other colleagues at the University of Wisconsin have begun deploying air monitoring devices into the milking parlors of affected farms to investigate the extent to which they can find genetic evidence of the virus in the air."

- "Farmers, who mostly haven’t been willing to have their cows tested, haven’t been keen to have their workers tested either."

Look, I know a lot of people are mad at the CDC about this, but, they can't raid farms and force people to test for a virus. I would sincerely like everyone who is calling for this to think it all the way through.

- "The World Health Organization appears to be concerned about the possibility of undetected human cases. Maria Van Kerkhove, acting head of the department of epidemic and pandemic preparedness, told STAT she’d like to see, among other things, studies looking for antibodies to H5N1 in the blood of farm workers and people who’ve been in contact with farm workers, to determine if there have been unreported cases and possibly even spread from those individuals to others."

People who don't want the CDC to test their workers for an active infection are really going to love the idea of the WHO coming in and testing their blood, right?