Experts are closely watching reproductive flocks of chickens and turkeys, some of which have also been infected, but not nearly to the same extent as layer hens. If more young birds are taken out of the system, that could create a shortage in the second half of the year as farmers struggle to repopulate their flocks.
Broiler chicken, the largest segment of the country's $48 billion-per-year poultry market, has been largely unaffected by this bout of bird flu. Comprising 68 percent of the overall poultry market, broilers—chickens raised for meat—were an 8.5-billion-bird business in the U.S. last year.
Industry experts say broilers have been insulated for two reasons: location, since the top producers are in the Southeast; and tight biosecurity, since the industry already had strict protective measures in place.
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But even broilers aren't immune to the effects of the flu. As cases mount, some countries have imposed bans or restrictions on poultry imports from the United States, including two of the industry's biggest trade partners, China and Mexico. That's weighing on demand for chicken, particularly the leg quarters, or dark meat, which is predominantly what's shipped overseas.
On a recent earnings call, Tyson Foods executives stressed that the chicken processor's supply has not been affected, since the broiler industry has remained largely untouched by the outbreak. Still, it's feeling the ripple effects as top export markets enact bans or restrictions due to bird flu.
"At this point, the primary impact on our business is not from bird health concerns, but rather from the loss of export markets for certain states and the resulting excess leg quarters [dark meat chicken] in the domestic market," the company said. "We've positioned ourselves well over the past several years by reducing our dependency on export leg quarters which now represent only a smaller percentage of our total portfolio."
It's something the entire food industry is watching closely–whether they've been affected yet or not. Panera Bread chief executive Ron Shaich told CNBC that the fast casual chain has not experienced issues with its turkey supply, but that "if there is a serious problem with the bird flu it could cause serious problems for all of us in the restaurant industry—and for consumers."