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.cnn.com/2025/02/08/health/bird-flu-variant-nevada-human-case/index.html
This CNN article reviews the D1.1 results.  The CDC is still in denial of what this new genotype means in terms of the possible start of the next pandemic.  The D1.1 virus has already killed one person and left another in critical condition before recovery.  That the CDC is still claiming that the risk is minimal is crazy.  They know that a lot of dairy workers are likely getting infected by this new virus that work at the infected dairy farms, but they still refuse to implement dairy worker testing and treatment of infected workers.  This virus mutated into a form that would better infect humans in the two critical cases. This means that since the virus is a respiratory infection in those cases that the needed mutations to start the next pandemic were likely selected for in the infected tissues of those individuals.  It isn't likely that the required mutations just occurred and took over the infections of two individuals thousands of miles apart without positive selection for those mutations during the infection.
The CDC needs to minimize human infections with this virus.  The more humans infected the more chance that these mutations will happen again and be selected for again.  They were lucky enough to contain the infections in the two known cases, but that would not be guaranteed with migrant dairy workers reluctant to admit to being infected.
It turns out that some of the Poultry workers infected in Washington were infected by D1.1 virus and only had mild respiratory symptoms when they were detected (because they were tested due to the poultry flock infection).  The Nevada dairies did not report symptoms, and a respiratory infection would not be detected in the milk until the infection somehow spread to the mammary gland.  For the B3.13 genotype the infection is not respiratory, but it infects the eyes, and mammary glands of the cattle.  It also infects the gut, but nasal swabs are often negative for both humans and cattle.  The D1.1 genotype should be detectable by nasal swabs before it is detected in the milk.
They need to be testing cattle with respiratory symptoms at all Nevada dairies because the virus has already spread to, at least, 4 dairies. The infection may have spread from one dairy because the infected dairies have a mutation that improves the ability of the virus to replicate in mammals.  This mutation is not found among the wild birds in Nevada.  This likely means that this version of D1.1 has spread via the same transmission vectors as the B3.13 dairy virus.  Cattle and humans are taking this virus to other farms.  Just like all the other states most dairy workers work at more than one dairy farm and some of them also work at poultry farms.  It may be that the D1.1 virus came from an infected poultry farm via a dairy worker that worked at both the poultry farm and a dairy.  Infected people and cattle have been taking the 3.13 virus to other farms, and the same thing is likely occurring with the D1.1 genotype.
The USDA and CDC have been in denial of dairy worker transmission from the start of the dairy epidemic and that denial has to end, and dairy workers have to be subjected to contact tracing and testing in order to determine how the virus has spread among the Nevada dairies.  How did the same mutation get to all 4 dairies?  If they start contact tracing like they did in California they might find more Nevada herds infected.
They need to identify the infected herds as quickly as possible and get the workers tested and infected workers placed on anti-virals as quickly as possible to prevent the next pandemic.  They might also issue anti-virals to all the workers at the infected dairies working with the sick cows.  They know for an absolute fact that a significant percentage of the workers will get infected working with infected poultry and cattle.  They should be acting on that fact.
Ron Okimoto