The most highly-consumed animal protein in the U.S. is poultry, primarily chicken, with a 2021 per-capita consumption of 68 lbs. per person. In 2022, the commercial poultry industry contributed an estimated $77 billion to the U.S. farm economy, providing hundreds of thousands of jobs and comparatively low-cost animal protein to hundreds of millions of Americans.

These figures highlight a significant economic incentive for maximizing poultry farm productivity. Almost all poultry in the U.S., and increasingly globally, is produced in concentrated animal feeding operations or CAFOs, which consist of thousands of birds raised in close proximity to one another. In fact, 99% of broilers (chickens sold for meat) in the U.S. are raised in CAFOs—a practice found in most mid- and high-income countries. With the ever-increasing global demand for animal-based protein leading to greater reliance on CAFOs, and poultry being the most-consumed meat globally, biosecurity of this resource is essential. Yet, several biosecurity risks accompany this massive scale and close proximity of production, many of which happen to be microbial in nature (i.e., antimicrobial resistance and zoonotic infectious disease outbreaks).

We now recognize that several of the deadliest human pandemics of the 20th and 21st century were zoonotic in origin, including HIV, SARS-COV-1 and 2 and Influenza A 2009. Today, the global poultry supply is under constant threat from highly pathogenic influenza A or HPAI. In 2024, the spillover of a novel, highly pathogenic influenza A virus (HPAI) H5N1 clade 2.3.4.4b in cows and humans captured global headlines—begging the question: from a food biosecurity standpoint, what is our current understanding of this threat and what is being done to contain it?

Understanding Biosecurity

Biosecurity risks necessitate complex national systems to ensure food supply safety (that the food that is produced in CAFOs is both safe to consume and that the people who raise and process the animals will be safe from acquiring zoonotic infections) and  security (that the animals will be safe from predation and disease so that this component of the food supply chain will be available at a price that people can afford).

In the U.S., the U.S. Department of Agriculture (USDA) and their corresponding state entities have an essential role in maintaining food biosecurity. Globally, the United Nations Food and Agriculture Organization (FAO) plays a similar role. Understanding pathogen transmission dynamics is an essential part of risk assessment, and, when it comes to avian influenza, flyways are key.

Avian Flu and Flyways

Migratory, aquatic birds are the major reservoir and an important vector for influenza A viruses. In the Western Hemisphere, these birds migrate from Northern Canada and Alaska to the Caribbean, Central America and as far south as southern Chile. Migrations occur twice a year, from north to south in late-August to early-November, and from south to north between early-March to mid-June, with birds migrating to breeding grounds and for food.

There are 4 major flyways over the U.S., and phylogenetic analysis of avian influenza A viruses in migratory birds traveling on North American flyways shows that viral clades tend to be transmitted along flyways rather than across them, meaning that a particular clade of avian influenza is not likely to cross from 1 flyway to another.

It is well established that migrating birds are the key vector for HPAI H5N1 clade 2.3.4.4b. Each year, millions of migrating birds on the Atlantic flyway use North Carolina, which produces, 10% of broilers and 13% of turkeys raised in the U.S., as a waystation. During the 2022 spring migration, when the HPAI H5N1 novel clade was first recognized, there was a death toll of approximately half a million broilers (less than 0.5% of production) and 100,000 turkeys (approximately 3%) in North Carolina. These outbreaks occurred in the North Carolina coastal plain region, which is along the Atlantic flyway. As of this writing, 2 additional outbreaks occurred in this same region with the loss of 50,000 turkeys.

Although devastating for the individual farmer, the economic loss was modest compared to the loss along other flyways in the U.S., where total losses to avian flu stand at close to 100 million birds (over 97 million poultry have died or been euthanized as a preventive measure, since H5N1 was identified in 2022). The reason why commercial poultry along Atlantic Skyway are relatively spared while poultry have been lost at higher rates along other flyways is unclear.

Biosecurity Mitigation of Avian Flu in CAFOs

When considering biosecurity measures, the knowledge that migrating birds are an important source of disease and poultry located along flyways are particularly vulnerable to exposure, along with an understanding of the epidemiology of HPAI is crucial. The interaction of wild birds with commercial poultry, the burden and disposal of animal waste, HPAI persistence in the environment and the potential for transmission to other animals and humans are all important factors in the equation.

HPAI is highly virulent, causing disseminated infection in poultry with death within 48 hours. The virus can be found in high concentrations in bird feces and body secretions, with transmission mainly occurring by the fecal-oral route or by direct contact. Given the proximity of poultry in CAFOs, the rapid transmission of HPAI is not surprising, and control of infection becomes difficult, if not impossible once a farm has been affected.

Therefore, biosecurity measures are 2-fold and involve preventing disease outbreaks in CAFOS in the first place, as well as mitigating the economic damage and spread to other CAFOs, other species and humans when an outbreak does occur.

Prevention

Preventing infections with HPAI in a poultry CAFO is complicated by the difficulty of segregating broiler and turkey flocks from migrating wild birds. Although poultry are most often in large enclosures, these pens are open to the air, and migrating birds roosting near local bodies of water increase the risk of HPAI exposure to poultry via contaminated secretions or feces.

Poultry are not routinely vaccinated against HPAI strains, likely for economic reasons, but promising studies in China showed that an H5-H7 bivalent vaccine reduces infections of H7N9 virus by 93% in broilers. Whether vaccination to prevent HPAI infections in poultry would be effective and could be economically justified remains an open question.

However, vaccination of humans who work in poultry houses, along with controlled access to these facilities, can help prevent spillover events and cross-species transmission. Staff should change clothing, especially footwear, before entering the CAFOs, so they will not bring the virus in on clothing from the local environment. Facilities should require strict handwashing practices on entry and departure of the CAFO and provide workers with N-95 masks to help prevent transmission. Additionally, poultry house workers should be vaccinated against human strains of influenza, so they will not infect the birds with human strains. It is well recognized that pandemic influenza A H1N1 (2009) was a reassortment event with human, porcine and avian RNA sequences all being present in this virus.

Mitigation

If HPAI is detected within a CAFO—typically by the presence of clinical disease, which is identified through the sudden death of poultry—mitigation steps, need to be taken. The major strategy that CAFOs employ is culling (selective killing) of all animals in the house where the outbreak is occurring. Further all poultry within 3 km of the infected CAFO should be closely monitored for illness and additional culling may be performed as needed.

Disposal and burial of culled animals is a tedious process that should be approached carefully to prevent continued viral spread from the infected bodies. Culled animals should be buried in 3-meter-deep pits, the size of which is dependent on the number of animals culled. The carcasses, along with bedding, feed, eggs and protective clothing, should be covered with calcium dioxide (lime) then covered with a foot of soil, another layer of calcium dioxide and finally another foot of soil.

Decontamination of infected surfaces is another vital, multi-pronged biosecurity step when HPAI is detected within a CAFO. Studies have shown that avian influenza virus can survive for days to up to 5 weeks in infected poultry houses. The highly pathogenic and resilient nature of this virus necessitates the following disinfection and cleaning steps: 

1. Disinfect any surface with which infected animals come in contact, bedding or feed, with USDA approved disinfectant and let stand (untouched) for 1 day.
2. After primary disinfection, clean all surfaces with soapy, hot water or steam and apply another round of disinfectant. Let stand for 1 week.
3. Repeat a second round of cleaning and disinfection and let stand for 3 weeks.

Making sure that the people involved in the execution of the above mitigation steps (i.e., culling, burial and disinfection), as well as any equipment they use to carry out these procedures, do not “carry” the virus from the CAFO is critical. Therefore, proper disposal of PPE, handwashing/hygiene and disinfection of equipment are also important steps in mitigation.

Mitigation is extremely costly. A 2014 HPAI poultry outbreak in the upper Midwest along the Mississippi flyway resulted in the death of 50 million poultry with a cost of $3.3 billion, due to lost production and mitigation costs. It also resulted in a doubling of egg prices during a 9-month period in 2015. Costs of the current HPAI outbreak, with a loss of 97 million poultry, and its impact on egg production, is currently unknown but likely to be substantially higher to producers, which will ultimately result in increased cost and reduced supplies for consumers.

Could Avian Flu Cause the Next Pandemic?

The most feared human pathogens are those that are highly virulent and easily spread. A highly virulent and transmissible strain of influenza virus is one that the medical, public health and microbiology communities dread. Between 2020 and June 2024, another highly virulent and transmissible virus, SARS-CoV-2, caused close to 1.2 million deaths in the U.S. Only HIV has caused more pandemic related deaths in the U.S. during the modern medicine era. With avian flu causing untold hundreds of millions of deaths in birds, is this likely to be the next cause of a human pandemic? Three things make this unlikely:

1. Although avian influenza H and N types have caused disease in humans over the past 3 decades with very high mortality rates (often reaching over 50%), almost all cases are in individuals who have had direct contact with sick birds. There is no conclusive evidence of person-to-person transmission. Furthermore, there have been only a few thousand human cases reported in those 3 decades. At this time, it appears avian influenza types that infect birds lack fitness in humans, although the ability of the influenza virus to adapt and become more fit in new hosts is of concern.
2. To date, there are several anti-viral agents available to treat influenza; that was not the case for SARS-CoV-2, HIV or even the influenza virus when they were first detected in humans. This means that, today, we are better prepared to combat HPAI and help prevent it from spreading than we were in the past.
3. The development of mRNA vaccines to protect against SARS-CoV-2 provides a template for rapidly developing a safe and effective vaccine against avian flu variants.

Nevertheless, HPAI strains will continue to be a biosecurity concern for the food industry, particularly poultry, and the cost of existing mitigation strategies, from both an economic standpoint, as well as the loss of animal life, necessitate the development of novel biosecurity approaches to combat disease.

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Avian-origin influenza A virus (H5N1) has been circulating globally since 2020, but its discovery in dairy cattle in 2024 was a first. Want to learn more about where this particular clade of HPAI came from and how it jumped to cows? Check out our next article.