A Concerned Scientist @BE@qoto.org

@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?

@PacificNic

Someone has to care enough to test, first, then someone has to design the test, test in real life conditions, certify it, etc.

Seems like this paper designed the test from what I understood under the "H5 assay design" section.

@PacificNic

If this paper is to be believed, and I have no reason not to, I was wrong to go along with what I read previously on this. Also, why there was no paper that I could find on testing for H5 in wastewater.

https://www.medrxiv.org/content/10.1101/2024.04.26.24306409v1.full.pdf+html

Wastewater plants appear to test for H1, H3, N1 and N2, but not H5.

@JMMaok

Legitimate question!

As pointed out by @HelenBranswell there's an early release of a paper from Iowa State with scientific details of the early part of this cattle H5N1 outbreak. To be quite honest, there's a lot in there that I can't really intelligently talk about as it's just out of my scientific comfort zone, but, I'm sure people who are more knowledgable will spring up to discuss it somewhere out there.

Some things I found interesting:

- From the cats in Texas that died "In total, >50% of the cats at that dairy became ill and died."

They were being fed milk from sick cows.

- "The HA sequences from the milk samples had 99.94% nucleotide identities with HA sequences from the cat tissues, resulting in a distinct subcluster comprising all 4 HA sequences, which clustered together with other H5N1 viruses belonging to clade 2.3.4.4b"

- "This case series differs from most previous reports of IAV infection in bovids, which indicated cattle were inapparently infected or resistant to infection (9). We describe an H5N1 strain of IAV in dairy cattle that resulted in apparent systemic illness, reduced milk production, and abundant virus shedding in milk. The magnitude of this finding is further emphasized by the high death rate (≈50%) of cats on farm premises that were fed raw colostrum and milk from affected cows; clinical disease and lesions developed that were consistent with previous reports of H5N1 infection in cats presumably derived from consuming infected wild birds (10–12). Although exposure to and consumption of dead wild birds cannot be completely ruled out for the cats described in this report, the known consumption of unpasteurized milk and colostrum from infected cows and the high amount of virus nucleic acid within the milk make milk and colostrum consumption a likely route of exposure. Therefore, our findings suggest cross-species mammal-to-mammal transmission of HPAI H5N1 virus and raise new concerns regarding the potential for virus spread within mammal populations."

- "Clinical IAV infection in cattle has been infrequently reported in the published literature. The first report occurred in Japan in 1949, where a short course of disease with pyrexia, anorexia, nasal discharge, pneumonia, and decreased lactation developed in cattle (17). In 1997, a similar condition occurred in dairy cows in southwest England leading to a sporadic drop in milk production (18), and IAV seroconversion was later associated with reduced milk yield and respiratory disease (19–21)."

- "An IAV-associated drop in milk production in dairy cattle appears to have occurred during >4 distinct periods and within 3 widely separated geographic areas: 1949 in Japan (17), 1997–1998 and 2005–2006 in Europe (19,21), and 2024 in the United States (this report). The sporadic occurrence of clinical disease in dairy cattle worldwide might be the result of changes in subclinical infection rates and the presence or absence of sufficient baseline IAV antibodies in cattle to prevent infection. Milk IgG, lactoferrin, and conglutinin have also been suggested as host factors that might reduce susceptibility of bovids to IAV infection (9). Contemporary estimates of the seroprevalence of IAV antibodies in US cattle are not well described in the published literature. One retrospective serologic survey in the United States in the late 1990s showed 27% of serum samples had positive antibody titers and 31% had low-positive titers for IAV H1 subtype-specific antigen in cattle with no evidence of clinical infections (24). Antibody titers for H5 subtype-specific antigen have not been reported in US cattle."

- "The genomic sequencing and subsequent analysis of clinical samples from both bovine and feline sources provided considerable insights. The HA and NA sequences derived from both bovine milk and cat tissue samples from different Texas farms had a notable degree of similarity. Those findings strongly suggest a shared origin for the viruses detected in the dairy cattle and cat tissues. Further research, case series investigations, and surveillance data are needed to better understand and inform measures to curtail the clinical effects, shedding, and spread of HPAI viruses among mammals. Although pasteurization of commercial milk mitigates risks for transmission to humans, a 2019 US consumer study showed that 4.4% of adults consumed raw milk >1 time during the previous year (29)"

(Is anyone monitoring these people, specifically?)

- "Ingestion of feed contaminated with feces from wild birds infected with HPAI virus is presumed to be the most likely initial source of infection in the dairy farms. Although the exact source of the virus is unknown, migratory birds (Anseriformes and Charadriiformes) are likely sources because the Texas panhandle region lies in the Central Flyway, and those birds are the main natural reservoir for avian influenza viruses (30)"

- "The mode of transmission among infected cattle is also unknown; however, horizontal transmission has been suggested because disease developed in resident cattle herds in Michigan, Idaho, and Ohio farms that received infected cattle from the affected regions, and those cattle tested positive for HPAI H5N1 (33)"

- "In conclusion, we showed that dairy cattle are susceptible to infection with HPAI H5N1 virus and can shed virus in milk and, therefore, might potentially transmit infection to other mammals via unpasteurized milk. A reduction in milk production and vague systemic illness were the most commonly reported clinical signs in affected cows, but neurologic signs and death rapidly developed in affected domestic cats. HPAI virus infection should be considered in dairy cattle when an unexpected and unexplained abrupt drop in feed intake and milk production occurs and for cats when rapid onset of neurologic signs and blindness develop. The recurring nature of global HPAI H5N1 virus outbreaks and detection of spillover events in a broad host range is concerning and suggests increasing virus adaptation in mammals. Surveillance of HPAI viruses in domestic production animals, including cattle, is needed to elucidate influenza virus evolution and ecology and prevent cross-species transmission."

https://wwwnc.cdc.gov/eid/article/30/7/24-0508_article

@datum

I had read what I think you're referring to as "CFRs are always overestimated at the beginning of an outbreak and here's an example" but on second read I might have misread it.

On a quick search I couldn't find that graph, specifically, and even 2020 and 2021 estimates were lower than that.

https://www.cebm.net/covid-19/global-covid-19-case-fatality-rates/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8451339/

I see some prominent people on Mastodon discussing the amazing speed at which bird flu has evolved from birds to mammals. Let's debunk.

"The first description of avian influenza (bird flu) dates to 1878 in northern Italy, when it was described as a contagious disease of poultry associated with high mortality, referred to as “fowl plague.” At the turn of the 20th century, it was determined that “fowl plague” was caused by a virus; however, it was not until 1955 that the virus was shown to be a type A influenza virus."

https://www.cdc.gov/flu/avianflu/timeline/avian-timeline-background.htm

Even just mammal to mammal spread was first scientifically documented 20 years ago.

https://wwwnc.cdc.gov/eid/article/10/12/04-0759_article

Just because you learned about something recently, it doesn't mean it just happened.

Separately, from a US-centric point of view, which is the view I think many people are taking this from, bird flu was first found in North America in 2021.

I have my suspicions about why mammal spread has been far more wide-spread in the last few years, but, I'm not sharing them as "fact" and I only wish others would do the same.

Another interesting article from @HelenBranswell at StatNews today on the subject.

https://www.statnews.com/2024/04/29/bird-flu-raw-milk-h5n1-risk-us-cattle/

One, don't drink raw milk, and be wary of cheeses that use raw milk. I once had a roommate who was a head cheese maker, and knowing the process there I'm a little less worried about cheeses, but, I'm a big fan of the precautionary principle.

“Expect the unexpected. That’s the situation we deal with here.”

I think this was an interesting portion:

"But H5N1 has more tricks up its sleeve than seasonal flu viruses do; it can infect organs other than the lungs. Kuiken noted that the virus has been seen to move into the liver, the central nervous system and the brain, among other tissues. He saw the latter when he experimentally infected cats in the mid-2000s. Similar results were seen when baby goats were infected with the virus on a Minnesota farm in March. Ten of the kids died; necropsies on five of them showed virus in the brains and other organs.

Many of the animal species infected in the wild have been reported to sustain damage outside of the respiratory tract. It’s believed these animals — bears, raccoons, seals, foxes, and a raft of other mammals — became infected by eating sick or dead wild birds or poultry infected with the virus.

“So many, many species, they get a brain infection and brain disease, not a pulmonary disease,” Kuiken said. “In some cases the disease is missed because people are expecting pneumonia. If the animal is found dead, they don’t see the neurologic signs, and they forget to test the brain.”

Human infection with flu occurs when people breathe viruses emitted by others into their upper respiratory tracts. But the shared real estate of the top of the respiratory and gastric tracts make it impossible to rule out the possibility that ingestion of food or drink that contained high levels of viable H5N1 virus could trigger infection, scientists said.

Krammer said there are several mechanisms that could come into play. “You could get infection of cells in the upper respiratory tract that could go down and cause lower respiratory tract infection. There could be a route where it’s really going to the olfactory bulb,” he said, going from there to the brain. “And there’s the other option that it really makes it through the stomach … and then you start an infection from the mid gut.”

Krammer said he thought that last option was unlikely; he thinks stomach acids would inactivate the virus. But Kuiken doesn’t believe that’s necessarily true, referring to his study of H5N1 in cats. Milk acts as a buffer, he said. “It’s the perfect fluid for [virus] reaching the intestine in an infectious state.”

Maria Van Kerkhove, acting head of the WHO’s department of epidemic and pandemic preparedness, pointed to another outbreak, involving another virus and another animal species — the MERS coronavirus, which spreads to people from camels — as an example of where ingestion of virus-laced milk may have triggered infection of a respiratory disease. Some cases of MERS were traced to the drinking of raw camel’s milk, Van Kerkhove said, though she noted it wasn’t generally possible to tease out whether it was the drinking of the milk or the act of milking that led to the infections. (Influenza viruses and coronaviruses belong to different families.)"