Re: D1.1 genotype H5N1

On 2/9/2025 11:53 AM, RonO wrote:

https://www.aphis.usda.gov/sites/default/files/dairy-cattle-hpai-tech- brief.pdf
 The USDA has released their sequence results for the D1.1 genotype H5N1 influenza that has infected dairy cattle in Nevada.
 Genotype D1.1 is a reassorted virus (recombinant between multiple viral strains).  It is derived from the Asian H5N1, but has recombined with North American influenza virus.  It continues to have the H5N1 antigen designation, but the N1 gene comes from a North American virus.  Only the HA, PB1, M and NS segments (chromosomes or genes) come from the Asian H5N1 virus.  This likely means that the currently available H5N1 vaccine that they have stockpiled will be ineffective against this virus.
 The antigen designations are pretty worthless in describing antibody binding ability.  They have maintained the designations for decades and even though they are antigen type designations that are still used to describe the virus the sequences of the various genotypes and clades within subtypes can be so different that they do not have to have antibody crossreactivity.  The H5 just indicates that it is the same lineage, descended from, the first H5 designated antigen sequence of the HA gene.  The Missouri patient infected with the dairy virus had enough mutations in the H5 gene to decrease antibody binding by around 100 fold and they needed to make a synthetic H5 sequence with those amino acid substitutions in it to test for H5 antibodies in the patients blood, and still 2 out of the 3 antibody tests failed when they knew that the patient had been infected.
 They really do need to start making up a vaccine for the D1.1 genotype because 2 patients infected that were in critical condition (one died) both had developed the mutations needed to make the virus more infective to humans.  I would likely make sure that their viral sequences where in the vaccine.
 It turns out that they are finding a change that allows the D1.1 virus to more efficiently replicate in mammals among the dairy herds in Nevada.  This mutation in the PB2 gene has not been found in wild strains of the virus.  It turns out that poultry workers infected with H5N1 in Washington were infected with D1.1 and had respiratory symptoms, but, had only mild symptoms.  This means that the dairies could be being infected by infected poultry farms due to shared workers between farms, and would indicate how it has spread in Nevada if there wasn't an exchange of cattle.  Like the B3.13 genotype the D1.1 may use dairy workers as a vector for transmission to other farms.
 They do need to start testing all the dairy workers, and get them treated as quickly as possible.  They need to keep the mutations that put the two patients into critical condition from occurring again.  They already know that the mutations have occurred twice.
 Ron Okimoto
 

https://www.cidrap.umn.edu/nevada-reports-h5n1-dairy-worker-usda-fleshes-out-d11-sequencing-affected-herds
The first Dairy worker had been detected as being infected with H5N1. They do not note the genotype, but the Nevada dairies are infected with the D1.1 virus.  The worker's eyes were infected like with genotype B3.13.
They do need to start testing all dairy workers at all farms known to be infected with the D1.1 virus, but they are not doing that.  They even knew that the cattle were not showing symptoms until after the virus was detected in their milk.  There is no reason to not test all the dairy workers when they already know that 1/4 of those positive for H5 antibodies did not show symptoms (2 out of 8 from a "random" sample with respect to whether they showed symptoms or not).  They need to get the infected workers on anti virals as quickly as possible.
This makes it more likely that infected dairy workers helped take the virus to other farms.  If they do not restrict dairy worker movements they will end up like California with nearly all their dairies infected.   They obviously cannot just restrict cattle movements.
Ron Okimoto