October 30 - Reflections on the Day the Earth Moved for H5N1

Pigs are now in the picture, a new genotype adds caseload and complexity, and USDA is finally moving towards national bulk tank surveillance to assess dairy herd status

Sometimes events come together at a point in time when we later look back and say, “that was the day we finally conceded that this is serious”. October 30, 2024, may well be that day:

1. The first natural infection of a domestic pig with H5N1 was reported on an Oregon mixed species farm which also reported an H5N1 HPAI outbreak in 70 poultry: Federal and State Veterinary Agencies Share Update on HPAI Detections in Oregon Backyard Farm, Including First H5N1 Detections in Swine | Animal and Plant Health Inspection Service

2. California reported 2 new infected broiler flocks (with rumors of more to come), making a total of 7 confirmed U.S. commercial and back yard flocks and several more reported in southern Canadian poultry flocks: Confirmations of Highly Pathogenic Avian Influenza in Commercial and Backyard Flocks | Animal and Plant Health Inspection Service

3. Utah reported that 8 dairy herds in Cache County were bulk tank positive for H5N1, tested as a result of a B3.13-infected layer flock. Utah is the 15th state with confirmed infections in the U.S.: Avian Influenza Confirmed in Utah Dairies

4. Washington State Department of Health reported its 9th H5N1 human case in Washington depopulation responders: Avian Influenza | Washington State Department of Health

5. California reported another 5 B3.13-infected dairy herds with the count as of yesterday standing at 193 (of approximately 400 nationally confirmed infected herds): CDFA - AHFSS - AHB - H5N1 Bird Flu Virus in Livestock

6. USDA issued a press release announcing a new H5N1 surveillance initiative: USDA Builds on Actions to Protect Livestock and Public Health from H5N1 Avian Influenza | Animal and Plant Health Inspection Service

That is a lot of news to digest in one day, with each item worthy of further comments. However, the pig infection is especially significant and as usual, Helen Branswell of STAT dug up some additional crucial information directly from Dr. Ryan Scholz, the Oregon State Veterinarian: H5N1 bird flu found in pig, raising concern about potential human risk

H5N1 bird flu virus has been found in a pig on a farm in Oregon, the first time the virus has been seen in a pig in the United States, the U.S. Department of Agriculture reported Wednesday. A second pig may also have been infected, Oregon authorities later revealed.

The pig confirmed to have been infected was one of five on a farm in Crook County in south-central Oregon that was experiencing an H5N1 outbreak in poultry. The pig did not display signs of illness but was euthanized and necropsied — the animal equivalent of an autopsy. Tissue testing showed the pig “had virus throughout their body,” said Ryan Scholz, Oregon’s state veterinarian. 

…The USDA said in its statement that it has generated a genetic sequence of virus from poultry on the farm, but it did not indicate what the sequencing revealed. Scholz said Oregon’s Department of Agriculture had been informed that this version of H5N1 was from wild birds. “It is not associated with the dairy strain that we’ve been seeing in other states,” he said.

First, this information would indicate that infection was systemic, not just a positive nasal swab from environmental contamination. Results are apparently still pending on a second potentially infected pig, later referred to as a “tea cup” pig (pot-bellied pig)

Second, this strain is not B3.13, but rather a “wild bird strain”. The current strain found in the Washington human and poultry detections is labelled a H5N1 2.3.4.4b D1.1 genotype; that may well be the strain involved here given its presence in migrating birds this fall. NVSL still needs to share the sequence information to confirm the exact genotype of the virus involved. I’ll write more broadly about the implications of the swine finding this weekend as I learn more and reflect upon it.

In the meantime, the last item may be the most significant of all: USDA Builds on Actions to Protect Livestock and Public Health from H5N1 Avian Influenza | Animal and Plant Health Inspection Service

Although it’s tough to glean from an initial read of the press release, a Reuters interview with Secretary Tom Vilsack much more explicitly announced that USDA is “leading” a phased national bulk tank H5N1 surveillance program: Exclusive: US to begin bulk milk testing for bird flu after push from industry | Reuters

…The agency in early November will begin sampling milk in states where dairy cattle have contracted bird flu, including testing specific farms as needed to track the virus' spread, Vilsack said in an interview.

USDA will then begin testing in states that have not identified the virus in dairy cows, he said.

This is a huge policy change for USDA, essentially moving to mandatory bulk tank testing. The USDA announcement states:

USDA is working closely with state and private veterinary groups, which include practitioners who will play a vital role in carrying out this effort. USDA plans to first sample milk in bulk at the regional level, with additional testing at the farm level if necessary, until herds in an area are determined to be free of the virus.  USDA will continue to work with state and private veterinarians on the final details of implementation and will share guidance documents soon. 

This wording indicates to me that initial efforts may be aimed at testing pooled milk samples at the processing plant level to screen for regions where the virus is likely to be found. By starting in historically infected areas (e.g. TX, MI, IA, MN, SD, etc.) USDA and SAHO’s can get some idea of whether infection remains in herds or areas previously diagnosed. It will also allow the process to be utilized in known infected areas before venturing into areas not previously diagnosed as positive.

If a processing plant sample is positive, then the SAHO(s) of state(s) representing the dairies contributing to the composite sample will be involved in permitting testing of individual herd bulk samples for H5N1. At that point it would become a state-led herd-based disease response, as is the case now.

Bulk sampling is fast and relatively cheap, with samples already collected for other purposes. This whole initiative could be in place by the end of the year across the United States if not legally challenged or delayed by unforeseen issues.

At some point the number of new herds infected will become a meaningless statistic. Herd reinfections or ongoing infections will become a metric for measurement, as will herd and state status (positive or negative, based on bulk testing results).

As always, we cannot forget the zoonotic implications of H5N1. Worker protection and monitoring in positive herds will remain critical, and ongoing genomic data transparency will remain critical for monitoring change in this virus, first for human risk, but also for updating of vaccines for animal protection.

Take a deep breath! Much of the “what if” has now happened and can’t be undone. It’s time to move forward with the many tools we have! Turning points can be liberating…

John