Dairy flu may be colliding with seasonal flu in California

[RonO]

https://www.politico.com/news/2024/10/17/avian-flu-california-pandemic-threat-00184027

When the dairy infections had spread to around 9 states the CDC gave up
because they claimed that they could not figure out how states that did
not get cattle were being infected. My take is that they always
understood that dairy workers were taking the virus to other states, but
they never wanted to acknowledge that fact. They knew that the virus
only survived on equipment for around 24 hours, and on skin and clothing
for less than 30 minutes, so infected animals or people were the obvious
transmission vectors to poultry farms and other dairies that did not
exchange cattle. Dairy workers shedding live virus could obviously
infect cattle, and likely other people.

The CDC stopped trying to contain the spread of the dairy influenza,
refused to start contact tracing and testing, and decided to only
monitor the infection in 2 states (Texas and Michigan, later expanded to
Colorado and now California). They did not try to identify all the
infected herds in Texas and Michigan, they just "monitored" the states
response to the epidemic. They claimed to increase their human
surveillance across the nation with the hope of detecting when the virus
adapted to better infect humans and started to spread in the human
population. They claimed that if they detected the evolution to human
infection early enough that they could try to contain the infection and
prevent the next pandemic.

This article is worried about the mixing of seasonal flu with the dairy
flu. A lot of dairy workers are likely being infected, and if they get
infected with both the dairy and seasonal viruses at the same time you
can get recombinant virus that share portions of their genomes with the
two strains. The article notes that the swine flu of 2009 with a higher
mortality rate than usual was a combination of 4 influenza strains that
included swine, avian, and human adapted influenza virus. The main
worry about the dairy H5N1 is that the original Asian strain had a 50%
mortality of infected humans, but the North American H5N1 is a
recombinant with an American avian influenza strain (about half of it's
genome remains the same as the Asian H5N1) and has only exhibited mild
symptoms in infected humans. The fear is that a recombinant with a
human adapted influenza may make the H5N1 dairy virus more pathogenic.

There are over 17,500 dairy workers in California, but the CDC is only
sending 5,000 seasonal flu vaccination doses. Over 9% of the California
dairy herds have been infected so far, but that is a low count because
they are still finding more infected herds by contact tracing.

What they need to do is to collect eye and nasal samples from all the
dairy workers that are vaccinated to get a base line number for current
infection rates. I am assuming that they will be vaccinating infected
farms first. This will not detect those that have already been infected
and recovered, but should identify those still shedding live virus. If
they want to do a thorough study they would take blood samples and test
for antibodies against the California H5 gene product. It is already
known that this gene has 2 to 3 more amino acid substitutions relative
to the original dairy virus detected in March, so they would have to
make antibodies against the current H5 gene for their testing.

It should be noted that the Missouri case also had 2 amino acid
substitutions in the H5 gene that the CDC determined to reduce
neutralizing activity of the current H5 vaccine strain antibodies, so
they needed to make a synthetic H5 gene with those substitutions in it
to try to identify dairy virus antibodies in the Missouri patient
contacts that showed symptoms. This means that the H5 vaccine that the
CDC decided to stock pile as part of their "rapid" response to the next
pandemic is likely worthless. They really need to work harder at
containing the dairy infection and preventing the evolution of the virus
to better infect humans. If the virus is allowed to evolve in a
populated state with international airports like California there likely
is no "rapid" response that will prevent the next world wide pandemic.

I should probably note that they call recombinant influenza virus
"reassortment" virus because usually whole chromosomes are swapped
between virus strains. Influenza has 8 RNA chromosomes or "RNA segments".

Ron Okimoto

[RonO]

Post by RonO
https://www.politico.com/news/2024/10/17/avian-flu-california-pandemic-
threat-00184027
When the dairy infections had spread to around 9 states the CDC gave up
because they claimed that they could not figure out how states that did
not get cattle were being infected.  My take is that they always
understood that dairy workers were taking the virus to other states, but
they never wanted to acknowledge that fact.  They knew that the virus
only survived on equipment for around 24 hours, and on skin and clothing
for less than 30 minutes, so infected animals or people were the obvious
transmission vectors to poultry farms and other dairies that did not
exchange cattle.  Dairy workers shedding live virus could obviously
infect cattle, and likely other people.
The CDC stopped trying to contain the spread of the dairy influenza,
refused to start contact tracing and testing, and decided to only
monitor the infection in 2 states (Texas and Michigan, later expanded to
Colorado and now California).  They did not try to identify all the
infected herds in Texas and Michigan, they just "monitored" the states
response to the epidemic.  They claimed to increase their human
surveillance across the nation with the hope of detecting when the virus
adapted to better infect humans and started to spread in the human
population.  They claimed that if they detected the evolution to human
infection early enough that they could try to contain the infection and
prevent the next pandemic.
This article is worried about the mixing of seasonal flu with the dairy
flu.  A lot of dairy workers are likely being infected, and if they get
infected with both the dairy and seasonal viruses at the same time you
can get recombinant virus that share portions of their genomes with the
two strains.  The article notes that the swine flu of 2009 with a higher
mortality rate than usual was a combination of 4 influenza strains that
included swine, avian, and human adapted influenza virus.  The main
worry about the dairy H5N1 is that the original Asian strain had a 50%
mortality of infected humans, but the North American H5N1 is a
recombinant with an American avian influenza strain (about half of it's
genome remains the same as the Asian H5N1) and has only exhibited mild
symptoms in infected humans.  The fear is that a recombinant with a
human adapted influenza may make the H5N1 dairy virus more pathogenic.
There are over 17,500 dairy workers in California, but the CDC is only
sending 5,000 seasonal flu vaccination doses.  Over 9% of the California
dairy herds have been infected so far, but that is a low count because
they are still finding more infected herds by contact tracing.
What they need to do is to collect eye and nasal samples from all the
dairy workers that are vaccinated to get a base line number for current
infection rates.  I am assuming that they will be vaccinating infected
farms first.  This will not detect those that have already been infected
and recovered, but should identify those still shedding live virus.  If
they want to do a thorough study they would take blood samples and test
for antibodies against the California H5 gene product.  It is already
known that this gene has 2 to 3 more amino acid substitutions relative
to the original dairy virus detected in March, so they would have to
make antibodies against the current H5 gene for their testing.
It should be noted that the Missouri case also had 2 amino acid
substitutions in the H5 gene that the CDC determined to reduce
neutralizing activity of the current H5 vaccine strain antibodies, so
they needed to make a synthetic H5 gene with those substitutions in it
to try to identify dairy virus antibodies in the Missouri patient
contacts that showed symptoms.  This means that the H5 vaccine that the
CDC decided to stock pile as part of their "rapid" response to the next
pandemic is likely worthless.  They really need to work harder at
containing the dairy infection and preventing the evolution of the virus
to better infect humans.  If the virus is allowed to evolve in a
populated state with international airports like California there likely
is no "rapid" response that will prevent the next world wide pandemic.
I should probably note that they call recombinant influenza virus
"reassortment" virus because usually whole chromosomes are swapped
between virus strains.  Influenza has 8 RNA chromosomes or "RNA segments".
Ron Okimoto

https://www.latimes.com/environment/story/2024-10-22/how-did-h5n1-bird-flu-get-into-california-dairy-farms

This LA Times article has some variant information about the California
infection. You may have to subscribe to see the article.

The article claims that there are "roughly 1,300 dairy farms" and not
the "more than 1,100" quoted by all the other articles so far. the 1.7
million dairy cattle stays the same.

The article has speculation that the virus came from Idaho and the claim
by California officials is that the virus is most similar in sequence to
Idaho and not Colorado as was first reported. No one can verify this
very well because the USDA puts out the sequence, but only gives the
date of the sequencing, and does not give the location that the sample
was collected (the dairy virus samples are all listed as being collected
in the USA).

Apparently the most likely incident is when a California dairy farm sold
some cows to an Idaho farm, but the Idaho farm did not like the cows so
they sent them back. This occurred in late July or early August. This
sounds like there has not been enough time to infect so many herds. It
likely takes the infection a couple weeks to establish in a herd before
it can be taken to another herd by cattle or workers. This infection
story is likely why they first believed that they had limited the
infection to half a dozen farms in late August, but they were very
wrong, and it looks like around a hundred herds were already infected.
An alternative is that the infection of dairy workers shedding virus is
much higher than everyone thinks, and is the reason that California was
able to detect so many infected herds so rapidly by contact tracing.
Previous work with H5N1 avian influenza among poultry workers before the
start of the dairy epidemic found that some asymptomatic poultry workers
that had worked with infected birds did have H5 antibodies indicating
infection, but they did not produce neutralizing antibody levels. All
the workers need is a mild infection and be shedding virus from, likely,
their eyes to infect the cattle that they are handling.

Once a sequence analysis is done where the samples are properly labeled
they can likely determine how the infection spread through the
California dairy herds as they did with Texas, but did not bother to do
for the other states. If they think that they know the first farm
infected the sequence analysis can confirm that because the virus
evolves very rapidly.

Ron Okimoto