On Sunday, April 21st, USDA-APHIS released 239 genetic sequences relating to H5N1 isolates. The data was released to the National Library of Medicine database as raw sequence data (FASTQ files). The sequences lacked essential supporting information that can be used by molecular epidemiologists to ascertain the sources of the isolates and how they have evolved over time.
An alternative database, the Global Initiative on Sharing All Influenza Data (GISAID), was established by scientists under the guidance of the World Health Organization to monitor the emergence of both human and animal influenza strains. The objective was to identify viruses with zoonotic and pandemic potential. Information posted to GISAID contains consensus sequences that have been refined and are devoid of contamination and errors. These sequences are supported by the origin of the sample, species and the location and time of collection. The data posted by USDA identifies ‘time’ as 2024 and ‘location’ as USA.
In late 2019, scientists and regulatory officials worldwide condemned China for reluctance to release sequences and detailed information on SARS-CoV-19 and their subsequent removal of molecular biological information from data sets that they maintained. Are we not in a similar situation? Is this due to institutional ignorance since deliberate obfuscation could never be contemplated by a U.S. agency! Why was USDA-APHIS or ARS holding 239 sequences when the H5N1 HPAI epornitic has persisted since 2022?
Notwithstanding the paucity of data released, molecular epidemiologists were able to draw some conclusions. Dr. Michael Worobey, at the University of Arizona, was able to determine that the most recent common ancestor of the H5N1 isolates from dairy cows was introduced into herds during mid- to late December 2023. This has profound epidemiologic implications suggesting widespread infection, notwithstanding the apparently low morbidity rate in infected herds. The larger question relates to the extent of H5N1virus in U.S. dairy herds given that asymptomatic cows have yielded positive nasal swabs. The revelation that PCR assays on commercial milk have yielded viral RNA, but not live replicating virus in 58 out of 150 samples from ten states is not unexpected and suggests widespread infection. Epidemiologists affiliated to GISAID are eager to access curated sequences to continue studies and to determine the potential for emergence of a human pandemic strain.
On the positive side, only one individual working with dairy cows who demonstrated conjunctivitis has yielded H5N1 virus, but with no evidence of human-to-human transmission. Preliminary studies confirmed that the H5N1 virus isolated from the dairy farm in Texas was similar to the virus isolated from a dairy farm in Michigan that received animals from the index case. The virus isolated from the extensive outbreak in laying hens in Michigan and implicated in a preliminary field investigation of the source of infection conformed to a common cluster. Enigmatically, the genetic sequence from the human case on the Texas dairy farm was sufficiently different from the similar wild bird, cat, cow and chicken sequences suggesting a different origin of infection. Evidently the worker did not contract infection from contact with cows on the index dairy herd in Texas. Dr. Tom Peacock, affiliated with the U.K. Pirbright Institute, noted, “The virus is basically too distant a cousin to be connected directly to the outbreak which either means it is either from a second spillover or that there was an early bifurcation of the cattle sequences.”
Susceptibility of mammals to the avian strain of H5N1 has been known since mid-2023 given isolation from scavenging mammalian species in North America including skunks, raccoons, pumas, coyotes and bears. Emergence of the infection in farmed mink in Spain and in marine mammals was clearly associated with animal-to-animal transmission.
Under the aeg
is of the Pan-American Health Organization, scientists in Latin America have made available sequences from marine mammals and migratory birds. They have organized meetings to review findings and to consider contingency plans in the event of an emergence of a zoonitic strain of H5N1.
EGG-NEWS has previously criticized USDA-APHIS for their pedestrian approach to HPAI , comprising a repetitive sequence of diagnosis, depopulation and decontamination. Failure to assign adequate resources to field and molecular biology and an apparent reluctance to aggressively investigate and publish on the epidemiology of avian influenza represents a grievous and ultimately costly omission. The egg-production and turkey segments of the poultry industry have experienced an ongoing epornitic extending over two years and involving depopulation of over 70 million commercial birds. This has been costly to the public sector, to producers and ultimately consumers.
This criticism is now extended to a lack of transparency with respect to releases on the molecular epidemiology of HPAI and publication of annotated sequences. Dr. Rick Bright who led the Biomedical Advance Research and Development Authority from 2016 to 2020 stated, “It’s so critical that the U.S. Government should be as transparent as they can right now and share sequences and all of the data so the world can look at it and make their own risk assessment and start making their own vaccines if they need to.” Bright continued, “What would we say if this particular virus did get out of control? Would we look back on these last two or three months and say I wish we would have done something else? We must share all these sequences so the world can get ready.”
Dr. Worobey noted, “There is a whole community of colleagues around the world who have a lot of experience with influenza and often can see things or conduct analyses that might show something that others have missed.” In the unfortunate event that a zoonotic strain emerges from the current circulating H5N1 in free-living avian and mammalian species or in commercial flocks and herds, administrators at USDA-APHIS will have a lot on their collective conscience. This is attributed to their unconscionable lack of transparency and their inactivity in failing to aggressively investigate the epidemiology of HPAI. The U.S. poultry and dairy industries, consumers, and ultimately taxpayers deserve better.