According to a recent report, this year’s Avian Flu outbreak has cost the state of Iowa, the country’s largest egg producer, $1.2 billion in sales, lost wages and losses for farmers. Minnesota and Nebraska also suffered heavy losses.

In all, about 200 farms in 15 states were affected by this year’s outbreak, costing U.S. egg and poultry exporters more than $380 million, said the Poultry & Egg Export Council, as reported by Associated Press.

The outbreak was no picnic for the birds, either. In Iowa, 30 million hens and 1.5 million turkeys were euthanized because of the H5N2 virus. As the Guardian reported:

When avian flu infects a single bird on a chicken farm, the whole population has to be destroyed in order to stop the spread. In Iowa, for example, where an egg farm holds anywhere from 70,000 to 5 million birds, infection means slaughtering an unimaginable number of animals.

Minnesota and Nebraska also suffered heavy losses this year. Nationwide, the flu killed about 50 million birds.

Avian Flu brings with it a measure of human suffering, too, as poultry workers find themselves jobless. It also creates a hardship for consumers, who pay skyrocketing prices for eggs. According to one report, egg prices in the Midwest are breaking all-time highs, thanks to this year’s outbreak.

To hear the media and the U.S. Department of Agriculture (USDA) tell it, the solution to Avian Flu is to stockpile vaccines. That notion rattles broiler meat exporters, who say other countries won’t buy their vaccinated meat. (This year’s flu outbreak affected egg-producers; broiler producers were largely spared).

Talk of vaccines isn’t exactly music to the ears of consumers, either. They want fewer, not more, vaccines used on factory farms.

Is there another way to deal with Avian Flu? Yes, says Reginaldo Haslett-Marroquin, COO of the Main Street Project, a large-scale organic regenerative poultry project under way in Minnesota, Mexico and Guatamala. Haslett-Marroquin argues that we should focus more on prevention, and less on a cure. That means replacing today’s poultry factory farms with an alternative organic, regenerative model.

It turns out that we haven’t been asking the right question, which is: Which came first? The diseased chicken? Or the chicken disease?

Identifying the culprit, or culprits

Typically, wild migrating birds are blamed for infecting poultry flocks with H5N2. Human “biosecurity errors” are suspects, too, as are wind and ventilation systems, according to a report in Fortune magazine. Still, the USDA admits that the problem is likely more complex than that. Truth be told, the agency can’t pinpoint, at least with any reasonable certainty, “one factor or group of factors in a statistically significant way at this time” responsible for the latest outbreak.

Industrial poultry farms engage in elaborate biosecurity measures to prevent contamination of their flocks. According to the Center for Disease Research and Policy:

The egg industry’s huge “layer operations”—the sort that house millions of birds in one place—are designed to protect birds from contamination, says Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota at the University of Minnesota. The animals’ environment is tightly controlled, and workers who enter the henhouse follow special hygiene protocols; often, they must shower in and out, change clothes and wear special boots. But when a virus pierces such defenses, or when defenses lapse, having all of one’s eggs in one basket (so to speak) can make the impact more devastating.

Yet all those special clothes, extra showers and “special hygiene protocols” didn’t protect farmers and their flocks this year. Some argue that it was because of lapses in the industry’s biosecurity audit program—only 43 percent of farms were actually audited.

Whether it’s a failure of the protocols themselves, or the failure of poultry farm operators and workers to adhere to the protocols, it’s hard to reconcile descriptions of near-sterile cleanliness standards with the reality of factory farms—where millions of birds are crammed into filthy, unnatural and highly stressful conditions, deprived of the ability to nest, roost, flap their wings or even see the light of day.

As demand grows, so grow the factory farms

According to the United Egg Producers, there are about 181 egg-producing companies in the U.S., with flocks of 75,000 hens or more. These companies represent about 99 percent of all the layers in the U.S.

Egg-producing factory farms are inhumane. They are also big polluters of the environment. And they’re not a healthy place for people to work, either.

And as it turns out, industrial poultry farms aren’t a healthy place for birds, no matter how many times workers shower and change their clothes, or engage in other  “biosecurity protocols.”

And that, says Haslett-Marroquin, is why the birds on industrial poultry farms, who live in misery, under stress, deprived of a normal diet, in a controlled, rather than natural environment, are more vulnerable to disease.

All viruses or bacteria that make animals sick need an entry point. Confinement animal production is based on the complete manipulation of the animal’s life cycle outside of its natural environment.  No natural environment = no naturally developed defenses which result from exposure to such natural conditions and a lifetime of interactions with these conditions. These characteristics define the intricate environmental control systems that must be installed in confinement operations in order to keep ALL bacteria, viruses, dust particles, temperature, humidity, and especially natural behaviors that the bird wants to manifest, under control. The result, is an animal that is VERY vulnerable to a natural environment and a quick entry point for such aggressive viruses such as the bird flu.

According to Haslett-Marroquin, it’s impossible to achieve completely sterile conditions outside of a laboratory. Viruses eventually will find their way into CAFO (Confined Animal Feeding Operations, the industry name for “Factory Farms). Without a doubt, he says, animals raised in factory farm conditions will never develop resistance that can be converted into a natural disease control strategy going forward.

Dr Michael Greger, director of public health and animal agriculture for the Humane Society of the United States, told the Guardian that commercial poultry farms “are designed like a disease incubator,” thanks to dark, moist and crowded conditions. Sunshine and warm temperatures, on the other hand, are effective at killing the virus.

The Guardian also cited genetics as another contributor to the weakened immune systems of birds raised on factory farms.

On top of that, the genetic makeup of birds found in factory farms is often less diverse than those raised in backyard flocks. Due to the industry’s reliance on homogenous breeding techniques, commercially raised broilers are all pretty much genetically identical. Broilers and turkeys are artificially selected and bred to produce birds that grow quickly – at a rate 300% faster than those birds raised in 1960, according to the ASPCA–and produce as much breast protein as possible, to the point where the birds have a hard time standing upright.

Avian Flu isn’t going away anytime soon, says the USDA. But Haslett-Marroquin is probably less concerned about a potential outbreak than his factory farm neighbors in Minnesota. His regenerative design system presents a greater challenge for viruses to find an entry point. But if they do, he says, he’ll use that as an opportunity to continue research and development of avian flu-resistant strains of birds that have already been produced in Mexico and throughout Latin America.

As regenerative systems improve, we have seen significant improvements in the quality of plants and their resistance to diseases and pests that normally affect them, and we have seen healthy egg layers and meat birds (with the exception of industrial cornish broiler breeds) for over 6 years. We have no hesitation in concluding that these overall environmental conditions enhance the birds’ ability to fight diseases—a phenomenon that has proven true for humans and other species as well.

While the operators of poultry factory farms finish cleaning up the carnage and wring their hands in anticipation of another Avian Flu outbreak, and while the USDA stockpiles vaccines they’re not even sure will work, maybe it’s time to ask: What’s the real problem? Avian Flu? Or factory farms?

Katherine Paul is associate director for the Organic Consumers Association.

Tagwongo Obomsawin is a writer and researcher for the Organic Consumers Association.