Why hasn't the bird flu pandemic started?

[RonO]

https://www.science.org/content/article/why-hasn-t-bird-flu-pandemic-started

The science news article is talking about the H5N1. They know that they
are talking about a recombinant (reassorted) virus, but choose to just
refer to it by the H5 designation of 2.3.4.4b. That is the H5
designation of the virus that had high mortality in the humans that it
infected in Europe and Asia, but the current dairy virus is genotype
B3.13 that is a reassorted virus that has half it's genome from two
other avian influenza. One of which I have learned was a low pathogenic
avian virus. There are low path and high path avian influenza strains
and the high path viruses like the dairy variant require flocks to be
depopulated, but low path virus are survivable. The dairy variant
produces minor symptoms in humans at this time, and does not have the
same mortality rate as the Asian virus.

https://pmc.ncbi.nlm.nih.gov/articles/PMC11271078/

The dairy variant is pretty distantly related to the original 2.3.4.4b
H5 sequence. You can get an idea of how different the virus is from
Figure 1 of the above link. Figure 1 is based on RNA sequence of the H5
gene, so around 2/3rds of those changes might change the amino acid
sequence. I do not know when they start calling a clade something other
than H5. It looks like as long as you can trace the lineage back to the
original H5 designation, that is what it is characterized as even though
the antigenicisty of the protein has changed. They had to make a
synthetic H5 gene with the two amino acid substitutions that the
Missouri patient had because the H5 antigens that they had to screen for
antibodies circulating in the patients blood were not effectively bound
by those antibodies. They had to create a new H5 sequence that would be
neutralized by the patient's antibodies, and even then only one assay
was positive. Two of the antibody assays failed. This probably means
that the H5 vaccine that the CDC stockpiled is probably going to be
worthless once the virus does switch to human infection.

The Science news article does identify the genotype of the virus that
infected the Canadian teenager (genotype D1.1) that is a different
reassorted virus, and it looks like it does cause severe symptoms
because the teen was in critical condition when diagnosed. We seem to
be lucky that the dairy virus has such mild symptoms in humans.

No one knows how bad things will get if the virus does adapt to humans,
but we should not want to find out. That is why the CDC's and USDA's
response has been so pathetically lame. The news article notes that
recent research indicates that just a single amino acid change will
allow the dairy virus to better infect humans. We have been extremely
lucky that, that has not happened. It may be that the current sequence
is selected for to effectively infect dairy cattle, and the human
facilitating mutation would be more likely to occur and amplify in
humans. That is even more reason to identify all the infected herds and
protect the dairy workers.

Ron Okimoto

[*Hemidactylus*]

Post by RonO
https://www.science.org/content/article/why-hasn-t-bird-flu-pandemic-started
The science news article is talking about the H5N1. They know that they
are talking about a recombinant (reassorted) virus, but choose to just
refer to it by the H5 designation of 2.3.4.4b. That is the H5
designation of the virus that had high mortality in the humans that it
infected in Europe and Asia, but the current dairy virus is genotype
B3.13 that is a reassorted virus that has half it's genome from two
other avian influenza. One of which I have learned was a low pathogenic
avian virus. There are low path and high path avian influenza strains
and the high path viruses like the dairy variant require flocks to be
depopulated, but low path virus are survivable. The dairy variant
produces minor symptoms in humans at this time, and does not have the
same mortality rate as the Asian virus.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11271078/
The dairy variant is pretty distantly related to the original 2.3.4.4b
H5 sequence. You can get an idea of how different the virus is from
Figure 1 of the above link. Figure 1 is based on RNA sequence of the H5
gene, so around 2/3rds of those changes might change the amino acid
sequence. I do not know when they start calling a clade something other
than H5. It looks like as long as you can trace the lineage back to the
original H5 designation, that is what it is characterized as even though
the antigenicisty of the protein has changed. They had to make a
synthetic H5 gene with the two amino acid substitutions that the
Missouri patient had because the H5 antigens that they had to screen for
antibodies circulating in the patients blood were not effectively bound
by those antibodies. They had to create a new H5 sequence that would be
neutralized by the patient's antibodies, and even then only one assay
was positive. Two of the antibody assays failed. This probably means
that the H5 vaccine that the CDC stockpiled is probably going to be
worthless once the virus does switch to human infection.
The Science news article does identify the genotype of the virus that
infected the Canadian teenager (genotype D1.1) that is a different
reassorted virus, and it looks like it does cause severe symptoms
because the teen was in critical condition when diagnosed. We seem to
be lucky that the dairy virus has such mild symptoms in humans.
No one knows how bad things will get if the virus does adapt to humans,
but we should not want to find out. That is why the CDC's and USDA's
response has been so pathetically lame. The news article notes that
recent research indicates that just a single amino acid change will
allow the dairy virus to better infect humans. We have been extremely
lucky that, that has not happened. It may be that the current sequence
is selected for to effectively infect dairy cattle, and the human
facilitating mutation would be more likely to occur and amplify in
humans. That is even more reason to identify all the infected herds and
protect the dairy workers.

Can H5 go pandemic? Hilleman didn’t think so. Of course if he was right we
will be getting hit by an H2 pandemic next year according to Offit’s
*Vaccinated*. Wouldn’t that be ironic?

[RonO]

Post by *Hemidactylus*

Post by RonO
https://www.science.org/content/article/why-hasn-t-bird-flu-pandemic-started
The science news article is talking about the H5N1. They know that they
are talking about a recombinant (reassorted) virus, but choose to just
refer to it by the H5 designation of 2.3.4.4b. That is the H5
designation of the virus that had high mortality in the humans that it
infected in Europe and Asia, but the current dairy virus is genotype
B3.13 that is a reassorted virus that has half it's genome from two
other avian influenza. One of which I have learned was a low pathogenic
avian virus. There are low path and high path avian influenza strains
and the high path viruses like the dairy variant require flocks to be
depopulated, but low path virus are survivable. The dairy variant
produces minor symptoms in humans at this time, and does not have the
same mortality rate as the Asian virus.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11271078/
The dairy variant is pretty distantly related to the original 2.3.4.4b
H5 sequence. You can get an idea of how different the virus is from
Figure 1 of the above link. Figure 1 is based on RNA sequence of the H5
gene, so around 2/3rds of those changes might change the amino acid
sequence. I do not know when they start calling a clade something other
than H5. It looks like as long as you can trace the lineage back to the
original H5 designation, that is what it is characterized as even though
the antigenicisty of the protein has changed. They had to make a
synthetic H5 gene with the two amino acid substitutions that the
Missouri patient had because the H5 antigens that they had to screen for
antibodies circulating in the patients blood were not effectively bound
by those antibodies. They had to create a new H5 sequence that would be
neutralized by the patient's antibodies, and even then only one assay
was positive. Two of the antibody assays failed. This probably means
that the H5 vaccine that the CDC stockpiled is probably going to be
worthless once the virus does switch to human infection.
The Science news article does identify the genotype of the virus that
infected the Canadian teenager (genotype D1.1) that is a different
reassorted virus, and it looks like it does cause severe symptoms
because the teen was in critical condition when diagnosed. We seem to
be lucky that the dairy virus has such mild symptoms in humans.
No one knows how bad things will get if the virus does adapt to humans,
but we should not want to find out. That is why the CDC's and USDA's
response has been so pathetically lame. The news article notes that
recent research indicates that just a single amino acid change will
allow the dairy virus to better infect humans. We have been extremely
lucky that, that has not happened. It may be that the current sequence
is selected for to effectively infect dairy cattle, and the human
facilitating mutation would be more likely to occur and amplify in
humans. That is even more reason to identify all the infected herds and
protect the dairy workers.

Can H5 go pandemic? Hilleman didn’t think so. Of course if he was right we
will be getting hit by an H2 pandemic next year according to Offit’s
*Vaccinated*. Wouldn’t that be ironic?

There has been the belief that there is a low possibility that H5N1
could turn into a human pandemic virus.

The H5 avian influenza has been causing serious illness in humans that
it infected since the first such cases were identified in 1995, but the
virus has not mutated to better infect humans in all this time. The CDC
used to claim that 2 mutations are needed to change the viral receptor
binding to the receptor most common in humans, but these changes also
change the avian receptor binding properties and the virus would no
longer be able to infect birds. These two mutations have obviously been
selected against as the virus propagated for all of these years in birds.

This just means that as long as the virus propagates mostly in birds
that it is unlikely to become a human pandemic virus, but since Oct 2023
(current estimate for the start of the dairy epidemic) the virus has
been propagating in dairy cattle where these two mutations could
facilitate infection in mammals. Just last week research was published
that a single mutation would change the virus to better infect humans.
The mutations have likely not been selected for because the virus
probably requires the current sequence to keep infecting the tissues
that it is infecting in cattle and humans. The issue is that the more
virus produced the more likely that the needed mutations will occur and
are more likely to infect the respiratory tissues where such mutations
would multiply and become an issue.

The Canadian case where the infected teen exhibited severe symptoms and
was in critical condition when diagnosed it turned out that he had
somehow been infected by the H5N1 virus, and that the facilitating
mutations occurred during his infection and blew up into a full blown
severe case of influenza. The virus that patient was shedding could
become a pandemic virus. Some of the virus in that patient retained the
avian receptor affinity and some had mutated to better infect mammals.
Just an unlucky break for that teenager. Such unlucky breaks are more
likely to occur in infected dairy workers.

The dairy virus does not seem to be as pathogenic as the Asian H5N1, so
when it makes the jump to humans, I do not know how severe any
"pandemic" would be, but it is something that we really do not want to
find out by experiencing it. That is why the diddle farting around that
the USDA and the CDC have been doing is such a stupid thing to do.

Ron Okimoto