Layers, or chickens raised to produce eggs, and turkeys live longer than broilers, or chickens raised for their meat. Therefore, they have a greater chance of contracting disease, Hundley said.
Already, the decreased egg supply has had ripple effects throughout the food industry. Last month, Panda Express said it was testing a new version of its fried rice that incorporates corn instead of the pricy protein. It also discontinued its hot and sour soup after its suppliers told the chain the egg shortage could last as long as two years. Another restaurant, Rita's, pulled its frozen custard made with eggs in favor of a soft-serve ice cream until it can get more eggs.
Read More Latest victim of the egg shortage: Fried rice
If bird flu were to reemerge in the Southeast this fall, several companies could be impacted, including poultry producers Sanderson Farms, Pilgrim's Pride and Tyson Foods, and egg producer Cal-Maine Foods.
According to its annual report, Cal-Maine Foods has a sizable presence in the South but does not have locations in two of the hardest hit states: Minnesota and Iowa. So far, a lift in egg prices has helped boost its earnings and share price, which has risen more than 40 percent year to date. But if bird flu gets closer to home for the company, this could change.
"The recent outbreak has, to this point, been a positive for the company, helping to raise industry pricing; however, its flocks could be infected in the future, adding risk to revenue and profit growth expectations," noted D.A. Davidson analysts in a late July note.