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USDA- APHIS Response to Bovine Influenza Outbreaks


USDA-APHIS has responded aggressively with a detailed, preliminary epidemiologic investigation of the expanding incidence rate of bovine influenza-H5N1 outbreaks among dairy cattle in Michigan with spillover to egg production complexes.  At the outset, the Agency is to be complemented by deploying highly qualified personnel from the Strategy and Policy and the Field Operations units to Michigan together with participation and support by the National Veterinary Services Laboratories. The team of seven APHIS veterinarians with collectively ten post graduate degrees or board certifications was assisted by a colleague at the Colorado State University College of Veterinary Medicine and with resources and support from the Michigan State Veterinarian.


Bovine influenza-H5N1 virus characterized as genotype B3.13 was diagnosed during late March in a dairy herd in Texas.  Subsequent genomic assay suggests that the infection was circulating in dairy herds since late December 2023. Clinically the disease in cows presents as an acute decline in milk production, anorexia and depression in habitus. 


Cattle shipped from the index farm were received by a herd in Michigan on March 8th.    Clinical signs were detected on March 20th. This was followed by an episode of high mortality in an in-line egg production complex near Saranac, MI. confirmed as HPAI on April 2nd.  Whole genome sequencing of virus isolates from the Michigan dairy and poultry operations were identified as Eurasian lineage goose/Guangdong, clade, genotype B3.13 with homology among isolates from both the dairy herd and layer complexes.


The USDA team published their preliminary findings on June 9th and circulated the manuscript in the form of a report that encapsulated epidemiologic findings including recommendations for prevention*.  The report comprised observations made on 15 dairy herds and 8 poultry flocks covering the period March 29th through May 16th.


The principal epidemiologic findings included: -

  • Almost a third of dairies employed workers who owned livestock or poultry at their personal residences.
  • There was extensive commonality of employment among dairy herd workers.  Twenty percent of those employed and 7 percent of their family members worked with dairy herds other than their principal location.
  • Of considerable significance to interspecies transmission, seven percent of workers on the affected dairies also worked on poultry farms and 13 percent of workers on affected dairy farms had family members working on poultry complexes.
  • With respect to the dairy operations, 62 percent used shared vehicles to transport live cattle but only 12 percent of responders recorded decontamination after delivery.
  •  All dairy farms had regular visits by veterinarians, consultants and contract haulers with evident direct contact among herds.  Almost half of the dairy herds used a contractor to dispose of dead animals with a history of removal within 30 days of the emergence of clinical signs in 40 percent of the affected herds.
  • As with all dairy operations, milk haulers visited operations at least daily.


The epidemiologic evaluation based on a questionnaire requiring participation of up to two hours by a responsible reporter and follow-up investigations and an environmental sampling form the basis of the publication.


The major conclusions of relevance to the outbreak included: -

  • Introduction of the virus into Michigan herds by infected but apparently asymptomatic cattle originating in Texas.
  • Evident inter-herd and inter-flock dissemination of H5N1 by movement of personnel, lactating cows and vehicles, without appropriate operational biosecurity.
  • HPAI H5N1 genotype B3.13 was detected in pigeons, a starling, cats, raccoons, opossums and foxes at five of the dairy farms surveyed and on one participating poultry farm.  The question arises as to whether the free-living resident passerine birds introduced the infection by viral shedding or whether they became infected by contact with a contaminated environment.  Cats are highly susceptible to infection and demonstrate clinical signs and death. They may be involved as a ptential link between wild birds and cattle.  Cats could also have become infected by consuming discarded raw milk from infected cows.
  • Movement of personnel and their families among dairy and poultry farms was considered to be significant in the context of the extension from the initial cases in dairy herds to the catastrophic loss involving 4.8 million hens among six farms under common ownership.  It is understood that workers were not required to disrobe and shower before donning company-provided outer clothing.  The investigation confirmed that at least 20 employees of three poultry flocks worked weekend shifts at two dairy farms.  The report also confirmed that shared housing could have contributed to dissemination of infection in the case of three poultry farms and two dairy herds.


Recommendations to prevent infection included: -

  • Maintaining closed herds although 9 out of 15 farms that were evaluated did not receive animals within 30 days of their respective outbreaks.
  • Surveillance of both individual animals by PCR assay of respiratory swabs and pooled samples of milk is now mandated before interstate movement of lactating cows.  Clearly, this is inadequate since heifers could transmit infection and individual states should be required to impose a similar restriction on intra-state movement.  Recommendations in the Secure Milk Supply Enhanced Biosecurity Plan should be followed. 
  • The Michigan Department of Agriculture and Rural Development issued a Determination of Extraordinary Emergency-HPAI Risk Reduction Response Order on May 1st requiring adherence to acceptable operational biosecurity.  It is noted that procedures to limit transmission of infection require structural biosecurity including facilities to decontaminate personnel vehicles and equipment which, if absent, invalidates operational biosecurity.
  • It is a longstanding practice within the poultry industry to require personnel to avoid visiting other poultry farms or maintaining poultry at their homes.  The industry has, however, not considered swine or dairy operations as a possible source of infection.  Even in the absence of a prohibition of contact with other farms, introduction onto egg production complexes may have been avoided by decontamination of personnel using available showers.
  • Since the early April outbreak in the Michigan egg production complex, virtually all poultry producers have amended their personnel requirements to include a ban on working on any other livestock operation with some companies extending this restriction to family members.  Since declarations are voluntary and impossible to verify, disrobing, showering and donning company-provided outer clothing and PPE is considered to be an essential preventive measure.



The report prepared and published by USDA-APHIS illustrates how a field investigation with appropriate laboratory support can be implemented within a short period, given resources but more important with motivation and direction by senior administrators. Since the onset of the current epornitic in 2022, APHIS has functioned to diagnose outbreaks of avian influenza and to depopulate flocks. The APHIS concentration has been an attempt to eradicate a seasonally and regionally endemic infection introduced and disseminated by migratory waterfowl that constitute reservoirs and shedders. The Agency has neglected epidemiologic studies that could have contributed to recommendations for prevention. Only two superficial and flawed reports were belatedly published, based on telephone-administered surveys one year after the 2022 outbreaks in diverse egg production and turkey grow-out farms respectively. Information including the critical determination of whether HPAI can be transmitted, albeit it over short distances, by the aerogenous route would have been helpful along with other recommendations based on logical assumptions and more structured and focused investigations. 


The rapid response by APHIS, with real-time recommendations relating to H5N1 outbreaks in Michigan demonstrate that the Agency is capable of responding to a disease emergency.  Why was a similar approach not adopted in 2022 following the emergence of HPAI collectively responsible for subsequent depopulation of close to 90 million commercial poultry? Does APHIS operate according to the Animal Farm ethos of Four legs good-two legs bad? There is a lot that the poultry industry needed to know 50 million or so birds ago!


*Nguyen, T-Q., et al.  2024 Highly Pathogenic Avian Influenza (H5N1)-Michigan Dairy Herd and Poultry Flock Summary