Re: H5N1 genotype D1.1

On 12/28/2024 8:10 AM, RonO wrote:

On 12/27/2024 6:04 PM, *Hemidactylus* wrote:

RonO <rokimoto557@gmail.com> wrote:

https://www.cidrap.umn.edu/avian-influenza-bird-flu/cdc-h5n1- mutations-severely-ill-patient-could-boost-spread-risk-remains
>
There has been a second severe case of H5N1 infection involving the D1.1
genotype thousands of miles from each other.  In British Columbia a
teenager was in critical condition with an H5N1 D1.1 infection.  The
virus had two mutations that made it more infective in humans and it was
a respiratory infection in that case.  The claim was that the two
mutations occurred in the infected individual and the mutant took over
to cause the severe infection.
>
Another H5N1 D1.1 infection has occurred in Louisiana, and that patient
also has mutations that account for the severity of the infection, that
are not found among local wild birds, and they claim that they likely
occurred within that individual.  Two such cases likely means that there
is either a human adapted variant already existing, or that these
mutations commonly occur, and the genotype D1.1 may already be a
respiratory infection, so the two mutations would already be replicating
in the tissue that they would better adapt the virus to infect.
>
The Dairy virus is genotype B3.13.  Half it's genome comes from two
other strains of influenza (one high path and one low path).  D1.1 is
also a reassorted virus, but I can't find where the genotype is defined.
  Both virus still retain the H5 and N1 genes of the Asian avian
influenza virus that had 50% mortality in infected humans, but some of
their genomes come from other virus strains.  The dairy virus human
infections are mostly limited to eye infections, so the virus may not be
replicating in respiratory tissue. B3.13 is only one mutation away from
becoming more infective in humans, but somehow that mutation hasn't yet
occurred in any infected human.  It may be that the mutation would not
have an advantage replicating in mammary glands and tear ducts.
>
The D1.1 genotype is likely replicating in tissue where the mutations
would be selected for and would take over the infection of the host.
>
The CDC is currently not differentiating the dairy infection from the
D1.1 infections, but they should track them separately.  Both D1.1
infected individuals are seriously ill, but the B3.13 infected
individuals only have mild symptoms, mostly eye irritation.
>
https://www.cdc.gov/bird-flu/situation-summary/index.html
>

You should post this stuff to Bluesky or elsewhere with a greater reach
than here.
>

Everything that I put up is already out on the web.  I do make my own comments about it.
 What is sad about this current fiasco is the suppression of the data, and interpretations are suppressed of what is put out.  I haven't seen an epidemiological analysis of the viral sequences since the first one put out early in the infection when only around 8 states had been identified to be infected.  They have all the sequences and should be updating the phylogeny and determining how the virus is spreading at least weekly, but that doesn't seem to be done.  That first study pretty clearly indicated that dairy workers were likely spreading the virus. New Mexico, Kansas, and South Dakota had not gotten cattle from Texas, but they had somehow been infected by Texas strains.  Kansas and South Dakota seemed to have been infected by the same viral lineage.  The CDC and USDA refused to establish worker testing and contact tracing.  As stupid as it may be contact tracing was only started in California and resulted in the identification of a large number of infected dairies indicating that all the other states had under estimated the infected dairies in their states because they refused to look for them.  The USDA finally started to assist California in contact tracing, and found so many infected herds that they claimed that they were going to start bulk milk tank testing in all infected states, but that never happened.  A month later the USDA claimed that they were going to start bulk milk tank testing in half a dozen states, and the list included some states that had not admitted to have infected herds, but it left out the states that should have been tested like Washington, Florida and Missouri that were known to have the dairy virus in their states, but had not admitted to having infected herds.
 The press seems to just parrot what the USDA and CDC put out.  I still can't understand why the October CDC article claiming that the virus could survive the most common form of pasteurization has not gotten more press coverage.  The CDC article recommended that the milk supply should be reevaluated (the FDA claim was that pasteurization killed the virus).   The FDA did respond immediately, but published a bogus protocol that was asking for volunteer processing plants.  Nothing has come out of the FDA in the last 2 months.  In order to test the milk supply adequately the FDA needed to go to processing plants that were accepting infected milk, evaluate the milk as it came in and after pasteurization.  They needed to evaluate the entire process to see if there were any weak points like start up, maintenence, and shift changes.  It only takes a few gallons of milk to not be processed correctly to account for the sick child in California and the Missouri patients that did not have contact with cattle, but did drink milk, and if the CDC was correct and viable infective virus is surviving the 72 degree C pasteurization, the method needs to be modified so that it does kill all the virus routinely.  99% effective is probably not effective enough.
 https://wwwnc.cdc.gov/eid/article/30/11/24-0772_article
 QUOTE:
Abstract
Highly pathogenic avian influenza A(H5N1) detected in dairy cows raises concerns about milk safety. The effects of pasteurization-like temperatures on influenza viruses in retail and unpasteurized milk revealed virus resilience under certain conditions. Although pasteurization contributes to viral inactivation, influenza A virus, regardless of strain, displayed remarkable stability in pasteurized milk.
END QUOTE:
 They found that infective virus survived 72 degree for 15 to 20 seconds, and survived as infective virus in refrigerated milk for 4 days (the extent of the trial, the virus likely survives for more than 4 days).
 I do not understand why this study is not cited in the cases of the California child and the two Missouri cases.  The FDA is still silent about their reevaluation of the milk supply that they claimed that they were starting in early Nov..  The FDA claimed to be responding, but the press never did.
 https://www.fda.gov/food/alerts-advisories-safety-information/ investigation-avian-influenza-h5n1-virus-dairy-cattle
 QUOTE:
10/3/2024 - Silo Study
Since the onset of the Highly Pathogenic Avian Influenza A H5N1 (H5N1) outbreak in dairy cattle earlier this year, researchers across the federal and state governments have been working to understand the prevalence of H5N1 in the U.S. milk supply. This week, states were invited to participate in a new study that will generate data to aid in the understanding of the prevalence of H5N1 in bulk raw cow’s milk received by dairy processing facilities across the nation. Dubbed “the silo study,” the information garnered from this research can help inform the national strategy to control the spread of the virus to other dairy cattle and avian flocks, and to identify any viral transformations.
END QUOTE:
 The FDA claims to have initiated the Silo study the day that the CDC released their Nov. newsletter (Oct. 3rd) containing the research article.  The CDC and FDA had obviously been in contact before the release of the CDC research article.  In early Nov. the FDA claimed that they were starting it, but it is now the end of December and nothing has come out of this effort.  If you read the research protocol you should understand that the study was designed to fail to adequately test the milk supply.  The processing plants that do not volunteer that likely do not have their plants up to specifications, and are more likely to have other issues like training and quality control, are the plants that you want to evaluate.  You do not want volunteer dairies, but you want the dairies sending in infected milk.  Dairies are supposed to take sick cows out of the milk supply.  You want the dairies that are not doing a good job of identifying sick cows, not the dairies that say it is OK to test their milk.
 Ron Okimoto

https://www.statnews.com/2024/12/20/california-h5n1-bird-flu-emergency-declaration-avian-flu-spread-dairy-cattle/
I am not the only one that has been frustrated by the lies and stupidity of the CDC and USDA.  It turns out that the USDA had understood by July that workers were involved in spreading the virus, but no testing program nor quarantine was implemented.  That is sad, they relied on voluntary compliance with their "suggestions" that workers from infected farms should not go to other farms, but it was not enforced.  Not only that, but the USDA and CDC refused to do contact tracing to try to find all the infected herds until California started doing it in October.
The CDC and USDA are just in denial of worker infections, and refuse to acknowledge reality.
QUOTE:
Reports from Payne and others that cows are being infected despite diligent preventive measures indicate that there are multiple routes of transmission, some of which aren’t being accounted for in current mitigation measures, said Seema Lakdawala, an associate professor in the department of microbiology and immunology at Emory University School of Medicine. She bristles at the USDA’s theory that fomites carried on people’s clothing could play a significant role in spreading the disease.
“It’s just not an efficient transmission route for the virus to go from a porous surface like your clothes up into the mammary gland of a cow,” she said. More likely, when it comes to personnel, is that workers are contracting the virus themselves and spreading it to other animals, she said. On the farms she’s visited, Lakdawala has observed workers wearing the same pair of gloves for an entire day of milking, and rarely seen people wear eye or face protection. “They’re using the same rags to dry the cows and wipe their own faces so there’s a lot of potential contaminants happening right there.”
END QUOTE:
It has probably been known for decades that influenza only survives in infectious form on clothing and skin for less than 30 minutes, so the CDC and USDA have understood from the beginning that their claims about the spread on clothing were bogus.
As I noted in the previous post the first epidemiology phylogeny of the virus spread indicated that humans were spreading the virus to states that did not get cattle.  Interstate clothing and equipment transfer is very unlikely, so unlikely that it shouldn't even be considered when it obviously happened to multiple states.
How many months ago did I claim that about a 5% infection rate of dairy workers would explain the spread of the virus and infection of nearby poultry farms?  After they found out that around 10% of the dairy workers in Colorado and Michigan had likely been infected and that some of them did not show symptoms (early Nov.) the CDC was supposed to have started a testing program for workers, but nothing seems to have happened.
They understood that they needed to identify the infected and treat them with antivirals in order to reduce the chance that muations would occur in humans that would facilitate respiratory infections.  Identifying the infected would have also identified the ones spreading the virus to other dairies and poultry farms.  Every dairy worker working on an infected dairy farm should have been tested by now, and they should be routinely tested because it takes a couple months for the herds to clear the virus.  In California they are claiming that 56 of the original infected dairies from October are now virus free, but they continue to test them.
As the article claims bulk milk tank testing has limits.  The raw milk dairy that got infected initially tested negative by bulk milk tank testing.  It wasn't verified to have infected cattle until subsequent testing of the milk.
The stupid claims that they do not know how the virus is spreading between herds is stupid.  The reason that no one knows for certain is because everyone has failed to test the dairy workers and follow up on their contact tracing.  When they found infected dairies that shared workers by their contact tracing they should have tested those shared workers for the virus and antibodies, but that never happened.  When California found the first 20 infected farm workers they claimed that they were going to test more workers and their contacts, but that never happened.  California is admitting that they have only tested 130 workers out of the over 5,000 that they are monitoring.  That is a senseless tragedy.  Thousands of dairy workers should have been tested by now, and the CDC is still claiming +540 tested, and that includes the California tests.
The current count of California dairies is down to 984 total with 659 already infected.  Any additional steps is literally trying to close the barn door after the cows have run off.  Initial press reports claimed that there were 1200 to 1300 dairies in California, but now the claim is that there has been consolidation and they have fewer but larger daries.
It is apparent that this happened in every state that got infected and is happening in states like Washington and Florida that will not admit to having infected herds.  They tested all the dairies in Colorado and over half of them were found to be infected.  As I noted the virus has changed enough so that it can likely start reinfecting herds.  Texas reported a positive herd Dec. 13, and their last reported herd was Sept 12.  They need to do a phylogenetic analysis to determine where that virus came from.
Ron Okimoto