Bird Flu in Dairy Cows: Timeline, Part I (March – April 2024)

Note: many of these websites were updated as more information was released. The original content as referenced here can be found as captured by secondary sources as events unfolded, such as here.

March 25, 2024: USDA reports that samples of unpasteurized milk from sick cows at two dairy farms in Kansas and one in Texas, as well as an oropharyngeal (upper throat) swab from another Texas dairy, have tested positive for highly pathogenic avian influenza. Anecdotal reports indicate that, as it had generally been assumed that cattle could not be infected with an influenza A virus, cattle were not tested following initial signs of illness for several weeks.

March 25, 2024 — After the USDA reported that cattle had tested positive for H5N1, the National Milk Producers Federation issues a joint statement of dairy organizations, stating that:

“USDA confirmed that there is no threat to human health and milk and dairy products remain safe to consume. Pasteurization (high heat treatment) kills harmful microbes and pathogens in milk, including the influenza virus.”

• • “routine testing and well-established protocols for U.S. dairy will continue to ensure that only safe milk enters the food supply. . . . milk from sick cows must be collected separately and is not allowed to enter the food supply chain. This means affected dairy cows are segregated, as is normal practice with any animal health concern, and their milk does not enter the food supply.”

In its April 2024 Newsletter, the American Association of Bovine Practitioners made reference to the “emerging disease” in certain dairy farms, noting that:

• • “An emerging disease continues to spread in dairy cattle in the central and southwest portions of the U.S. AABP has provided member communications throughout this process and has created a landing page where all resources will be placed during this disease event.”

• • “As veterinarians, it is critical that we remain informed. . . . When discussing this disease event, avoid propagating rumors and help others to understand the science and the known facts. If you have potentially affected herds, encourage your clients to submit the appropriate diagnostic samples.”

April 1, 2024: CDC reports a human H5N1 case in Texas. The human case, as stated in a news release titled “Highly Pathogenic Avian Influenza A (H5N1) Virus Infection Reported in a Person in the U.S”, was associated with the cattle outbreaks. The person was a farmworker who had contact with infected cattle. The case was mild with conjunctivitis (eye redness) as the only symptom.

April 2, 2024: USDA confirms H5N1 in a dairy herd in Idaho, bringing the list of confirmed infected cattle herds to 11: Texas (7) Kansas (2), Michigan (1), New Mexico (1), Idaho (1). It is also reported that several cats in the same area as some of the Texas farms had tested positive for H5N1, the samples being collected in late March.

April 2, 2024: CDC publishes a “Technical Update: Summary Analysis of Genetic Sequences of Highly Pathogenic Avian Influenza A(H5N1) Viruses in Texas”, in which the human H5N1 case is analyzed. In its update, CDC noted that:

• • The human virus “contains the PB2 E627K mutation, known to be associated with viral adaptation to mammalian hosts.”

• • The HA gene “lacks amino acid changes that improve recognition of mammalian receptors or fusion of the viral membrane[.]”

• • The human virus is “very closely related” to certain pre-pandemic strain candidate vaccine viruses available for manufacturers.

• • Analysis of the NA gene “showed that it did not have any known or suspected markers of reduced susceptibility to this class of antivirals [NA inhibitors], which includes oseltamivir.”

• • Overall investigation indicates that “this case represents a single zoonotic event and while the HA lacked changes likely to enhance transmission to mammals, it did acquire substitutions in PB2 likely to enhance replication in mammals, which illustrates that we have to remain vigilant and continue to characterize zoonotic viruses.”

April 2, 2024: APHIS issues updated recommendations for PPE to be used by people who work with or around cattle. APHIS also recommended “minimizing the movement of cattle as much as possible” but did not implement quarantine measures.

April 4, 2024: USDA creates new Avian Flu in Livestock online interface.

April 5, 2024: CDC issues a Health Alert Network update on the H5N1 case in a Texas farmworker. According to the HAN statement:

• • “A farm worker on a commercial dairy farm in Texas developed conjunctivitis on approximately March 27, 2024, and subsequently tested positive for HPAI A(H5N1) virus infection. HPAI A(H5N1) viruses have been reported in the area’s dairy cattle and wild birds. There have been no previous reports of the spread of HPAI viruses from cows to humans.”

• • “CDC has sequenced the influenza virus genome identified in a specimen collected from the patient and compared it with HPAI A(H5N1) sequences from cattle, wild birds, and poultry. While minor changes were identified in the virus sequence from the patient specimen compared to the viral sequences from cattle, both cattle and human sequences lack changes that would make them better adapted to infect mammals.”

• • “In addition, there were no markers known to be associated with influenza antiviral drug resistance found in the virus sequences from the patient’s specimen, and the virus is closely related to two existing HPAI A(H5N1) candidate vaccine viruses that are already available to manufacturers, and which could be used to make vaccine if needed. The current risk these viruses pose to the public remains low.”

April 8, 2024: The American Association of Bovine Practitioners (AABP) issues an open letter in which it advocates for referring to the disease not as bird flu or H5N1 but as “bovine influenza A.” This rebranding is not adopted by the scientific community.

April 10, 2024: H5N1 is confirmed in a dairy herd in North Carolina.

April 11, 2024: H5N1 is confirmed in a dairy herd in South Dakota, bringing the county to 24 herds across 8 states.

April 12, 2024: It is reported that links between Texas cattle and herds in other states are established.

• • In Michigan, three more dairy herds test positive for the virus.

• • In North Carolina, officials confirm that cattle infected with the virus are linked with dairy cattle from Texas. State officials from Idaho, Michigan, and Ohio confirmed the same.

• • However, officials in New Mexico noted that cattle herds infected with H5N1 were not linked to cattle shipped from Texas.

April 16, 2024: USDA releases a FAQ titled “Detection of Highly Pathogenic Avian Influenza (H5N1) in Dairy Herds: Frequently Asked Questions”. This 5 page document provides an overview of the situation and some useful tidbits, without much elaboration. Key points include:

• • “Based on the information and research available to us at this time, a milk recall is not necessary. Because products are pasteurized before entering the market, at this time there is no concern about the safety of the commercial milk supply[.]”

• • “At this point, we are not aware of impact on milk supply or consumer prices.”

• • “genomic sequencing of viruses isolated from cattle indicates there is no change to this virus that would make it more transmissible to or between humans, and the CDC considers risk to the public to be low at this time.”

• • “Yes [cow-to-cow transmission is a factor in the spread], although it is unclear exactly how virus is being moved around. We know that the virus is shed in milk at high concentrations. . .”

• • “we have not found significant concentration of virus in respiratory related samples, which indicates to us that respiratory transmission is not a primary means of transmission.”

• • As to wild birds on the Texas farms, “three species have been identified among these cases: pigeons, blackbirds, and grackles.”

• • No detections in commercial beef herds have been reported.

April 16, 2024: A pre-print study from researchers at Iowa State University, titled “Highly Pathogenic Avian Influenza A (H5N1) clade 2.3.4.4b Virus detected in dairy cattle”, is released. The study examined the genetic sequences of the virus from some of the cattle in Texas:

• • All H5N1 samples obtained from the Texas cows as well as samples from two dead cats in the area contained certain mutations “which may increase binding affinity to the human-type receptor.” (These were mutations in the HA gene: 137A, 158N, 160A.)

• • All samples also contained “other mutations that “may increase the viral virulence in mammals.” (These were mutations in the M1 gene: 30D, 43M, 215A; and mutations in the NS1 gene: 42S, 103F, 106M.)

• • The well-recognized PB2-E627K mutation was not present (but it was present in the human farmworker case).

• • “no critical site mutations associated with increased influenza antiviral resistance have been identified[.”

April 18, 2024: WHO weighs in on the H5N1 outbreak in U.S. cattle, which invites concerns about how the virus continues to spread to novel species, including humans:

• • Past outbreaks of H5N1 in humans, primarily infected through contact with animals, have led to “extraordinarily high” mortality rates, as noted by Chief Scientist Jeremy Farrar’.

• • Dr. Farrar’s statements were widely reported in the news (but with almost no context to understand where the remarks originated from), specifically his statement that: “This remains I think an enormous concern.”

• • Farrar outlined the concern shared by many in the scientific community that, as the virus continues to infect different species of birds, “and then increasingly mammals, that virus now evolves and develops the ability to infect humans and then critically the ability to go from human to human.” The spillover to cattle is another example of the virus infecting a new mammalian species, at which time “you’re getting closer to humans.”

April 22, 2024: USDA uploads 239 genetic sequences of H5N1 clade 2.3.4.4b to the NIH National Library of Medicine. This is newsworthy as the typical practice is to publish genetic sequences of influenza viruses on the GISAID interface (“Global Initiative on Sharing Avian Influenza Data”). However, USDA noted that “ in the interest of public transparency and ensuring the scientific community has access to this information as quickly as possible to encourage disease research and development to benefit the U.S. dairy industry,” the sequences were also uploaded to the NIH library. USDA had faced pressure in the preceding days to release more information and data on the ongoing H5N1 outbreak in dairy cattle.

April 23, 2024: USDA confirms a dairy herd in Idaho tested positive for H5N1, raising the number of herds affected to 33.

April 23, 2024: It is reported that samples of commercial pasteurized milk from grocery stores test positive for fragments of H5N1 virus.

• • The USDA stressed that viral fragments are not live virus and “do not represent actual virus that may be a risk to consumers.”

• • Dr. Andrew Bowman of the College of Veterinary Medicine at Ohio State University, who operates a lab as part of the NIH network for the Centers for Excellence in Influenza Research and Response, tested commercial milk samples for H5N1 and reported the results. Dr. Bowman relayed how he and a graduate student took a road trip and purchased 150 gallons of milk from various locations in the Midwest. This included over a dozen products purchased in Columbus, Ohio.

• • Of those 150 mink samples, 58 showed the presence of viral RNA. This is an indicator that the H5N1 virus was in the milk at some point but was “likely inactivated” through pasteurization.

• • Dr. Bowman noted that the milk samples that tested positive were from different states in the Midwest, and by tracking the milk production codes on the containers, it shows that the milk came from 10 different states.

• • Dr. Bowman found “no evidence of viable virus” in the milk samples and clarified that viral RNA fragments are not live virus, but what they do show is that the outbreak amongst dairy cattle is more widespread than is being reported.

• • Samples that tested positive are sent to Richard Webby’s department at St. Jude’s Children’s Research Hospital, where they will attempt to grow cultures in order to determine if any infectious virus was present. In an interview, Dr. Webby relayed how he purchased a gallon of milk in Memphis, TN, with the intent to use it as a negative control, which ultimately tested positive for viral RNA as well. Dr. Webby stated he was not concerned about the safety of the milk itself, but that it represented a larger presence of the virus than what is being reported.

April 24, 2024: USDA updates its FAQ document on its website.

April 24, 2024: The FDA, on its webpage “Updates on Highly Pathogenic Avian Influenza (HPAI)” reports that:

• • “During the course of the outbreak, the FDA has been evaluating milk from affected animals, in the processing system, and on the shelves. We are completing a large representative national sample, to better understand the extent of these findings.”

• • “Data from previous studies . . . show that pasteurization is very likely to effectively inactivate heat-sensitive viruses, like H5N1, in milk from cows and other species. [D]ata shows thermal inactivation of HPAI (H5N1) has been successful during the pasteurization process for eggs, which occurs at lower temperatures than what is used for milk.”

• • “Work is underway to test samples of milk in systems that represent current industry practices using the range of temperature and time combinations that are used in pasteurization processes. Additional analysis is underway of milk on store shelves across the country in addition to work to evaluate any potential differentiation for various types of dairy products (e.g., whole milk, cream).”

• • FDA restates its position regarding the Grade “A” milk program and the Pasteurized Milk Ordinance (PMO), which is meant to ensure milk from sick cows does not enter the food supply.

April 24, 2024: USDA issues a press release, titled “USDA Actions to Protect Livestock Health From Highly Pathogenic H5N1 Avian Influenza,” in which the USDA announces there will be mandatory testing for Influenza A before interstate movement of dairy cattle, effective April 29, 2024. USDA issued a Federal Order to that effect. USDA further noted:

• • “USDA has identified spread between cows within the same herd, spread from cows to poultry, spread between dairies associated with cattle movements, and cows without clinical signs that have tested positive.”

• • “On April 16, APHIS microbiologists identified a shift in an H5N1 sample from a cow in Kansas that could indicate that the virus has an adaptation to mammals. [CDC] conducted further analysis of the specimen sequence, which did not change their overall risk assessment for the general public, because the substitution has been seen previously in other mammalian infections and does not impact viral transmission.”

• • “APHIS’ National Veterinary Services Laboratories found H5N1 in a lung tissue sample from an asymptomatic cull dairy cow that originated from an affected herd and did not enter the food supply.”

April 25, 2024: FDA reports initial results from the nationwide representative commercial milk sampling study for H5N1 in pasteurized, commercial milk:

• • “the initial results show about 1 in 5 of the retail samples tested are quantitative polymerase chain reaction (qPCR)-positive for HPAI viral fragments, with a greater proportion of positive results coming from milk in areas with infected herds.”

• • FDA cautions that “qPCR-positive results do not necessarily represent actual virus that may be a risk to consumers. Additional testing is required to determine whether intact pathogen is still present and if it remains infectious, which would help inform a determination of whether there is any risk of illness associated with consuming the product.”

• • “To date, the retail milk studies have shown no results that would change our assessment that the commercial milk supply is safe.”

• • On that same day, an online symposium hosted by the Association of State and Territorial Health Officials was held in which the FDA discussed the initial results.

April 26, 2024: CDC issues an updated Technical Report on H5N1 Viruses, adding infections in baby goats and dairy cattle to the growing list of mammalian infections, and adding the recent human H5N1 in a Texas farm worker. Key points of the updated analysis include:

• • The H5N1 viruses from wild birds, poultry, and mammals including cattle, “have a high degree of genetic identity with each other and no significant mammalian adaptive substitutions, insertions, or deletions have been identified.”

• • Genetic sequencing of some of the viruses from mammals, including humans, has shown genetic changes “that allow more efficient replication in the lower respiratory tract or extrapulmonary tissues”. These mutations are “associated with mammalian adaptation during infection” but have not been associated “with enhanced transmissibility of the virus to humans.”

• • CDC maintains that the overall threat of H5N1 clade 2.3.4.4b to public health is low, but “additional sporadic zoonotic infections are anticipated among people with exposures to infected sick or dead poultry, wild birds, or other infected animals.”

• • Although the threat to the public is low, “the widespread geographic prevalence of infected birds and poultry raises the potential for exposures and infections of humans and other mammals that could result in viral evolution or reassortment events which might change the current risk assessment.” Continued vigilance is critical.

April 26, 2024: H5N1 dairy cattle infection is reported in Colorado, making it the 9th state to report cattle infections.

April 26, 2024: The WHO along with WOAH and FAO issue a joint assessment on H5N1 clade 2.3.4.4b in cattle:

April 27, 2024: CDC reports 4 more cats tested positive for H5N1, bringing the total to 7 cats infected associated with the ongoing cattle outbreaks. All cats were said to have suffered “neurologic symptoms, rapid decline, and death.” Of the new cases, 3 of them were at farms in New Mexico, and 1 of them was at a farm in Ohio.

Stay tuned for the next installment in this timeline of the H5N1 outbreak in U.S. dairy cattle.