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The losers—and winners—of the US avian flu outbreak

The bird flu epidemic is annihilating flocks, panicking food products investors and moving faster than the scientific community can chase it. But some businesses actually stand to benefit from what is turning into a disaster for so many.

Above: An apology to shoppers for egg shortages is posted in a New Jersey Wegmans grocery store.

As the worst outbreak of bird flu in U.S. history rages on, its ripple effects are spreading. More than 200 separate cases of H5 avian influenza have been confirmed by the U.S. Department of Agriculture since December, mainly farms in the Midwest, affecting upwards of 46 million chickens and turkeys. The overwhelming majority of exterminated birds are egg-laying hens.

"We certainly did not anticipate an outbreak this big, so we are going through unchartered waters now," said Maro Ibarburu, an associate scientist and business analyst at Iowa State University's Egg Industry Center.

'This is our moment'

Nevertheless, for all of bird flu's financial and emotional devastation, it has created some beneficiaries—though many of them are reluctant to be called that. (Tweet This)

Perhaps one of the largest is actually the country's top egg producer: Cal-Maine. The Jackson, Mississippi-based company's operations are in the South and Southwest, areas removed (at least for now) from the outbreak.

Amid soaring demand and record prices, the company's stock has jumped 50 percent in three months, and many analysts think it could go higher as the company's bottom line gets a boost. Stephens analyst Farha Aslam increased earnings estimates for the company this week, maintaining an overweight rating on the stock.

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In a recent note, Sidoti & Company analyst Francesco Pellegrino wrote: "We consider avian influenza a game-changer in the industry that may prove to be a catalyst that accelerates industry consolidation; we view a supply chain alignment opportunity for (Cal-Maine) to greatly enhance its higher margin, egg-breaking operation (3% of sales in F2014) as viable." He has a "buy" rating on the stock.

Amid shortages, some food manufacturers are turning to plant-based egg alternatives. Archer Daniels Midland says it has started to see an increase in customers wanting to discuss options, from meat additives to baked goods.

Hampton Creek Foods, a start-up that manufactures plant-based ingredient alternatives, has experienced a surge in demand as well. "We are set up all across with Sysco, with U.S. Foods, with UNFI," Hampton Creek chief executive Josh Tetrick recently told CNBC. "This is our moment."

Another winner: the Netherlands. This week, the USDA announced it will soon allow imports of some pasteurized egg products from the European country. The Netherlands once exported products to the United States, but chose to stop several years ago, according to the USDA. Last year, the country requested reinstatement.

'We’ve had to raise our retail price'

The fact that the outbreak is showing an at least temporary benefit for some industry players doesn't discount the fact that other firms are taking a hit.

In less than two months, nearly 12 percent of the country's "layer" hen population has been compromised. The so-called "breaker" market—eggs cracked open and made into processed product for food companies—has been hit the hardest, sending egg prices to record highs.

"The first impact we've seen is on the egg product side," said Brian Moscogiuri, an egg reporter at Urner Barry, a commodity market research firm and the industry go-to for egg prices. "Now the egg processors … are buying shell eggs once destined for the carton market."

The carton market is composed of "shell" eggs that haven't been cracked open and processed—the table eggs that ultimately land on store shelves and in consumers' refrigerators.

Read More Bird Flu Virus Spreading Across US

According to Urner Barry, the wholesale price of a dozen Midwest large shell eggs—an industry benchmark for this market–has surged 120 percent over the past six weeks. There have also been reports that suppliers have been refusing new contracts and limiting sales.

Retail egg prices tend to be "sticky," meaning grocery stores are slow to push higher wholesale prices out to customers. Even when they do, the fluctuations tend to be modest.

Yet supermarkets across the United States have begun alerting patrons that a national egg shortage is resulting in fewer cartons on shelves, adjustments in bakery offerings—and higher prices.

In the Midwest, where shortages are most acute, grocery store chain Lunds & Byerlys says egg availability at some locations is limited due to shortages in the Twin Cities market.

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Even in the Northeast, some chains have begun posting notices in their dairy and bakery departments. "Unfortunately we have had to raise our retail price for fresh eggs sold in dairy and bakery products made with eggs," said one sign in a Wegmans in New Jersey.

"We don't know why other restaurants haven't been affected by this shortage yet, but it sure has affected us.ion's" -Whataburger, San Antonio-based restaurant chain

Major food manufacturers have been feeling the pain, as well. Sysco, the nation's biggest food distributor, has warned that its supply of eggs and layer hens will be limited for nine to 18 months due to bird flu.

At Post Holdings, bird flu has wiped out 35 percent of the egg supply that had been contracted out through its Michael Foods division. Last month, Post declared a "force majeure event … the effect of which renders Michael Foods unable to fully perform under its existing supply agreements with customers." In a release, the company said it's evaluating the financial impact.

The epidemic has struck Cargill as well. Cargill Kitchen Solutions, which doesn't actually own any egg-laying hens, has confirmed that several of its supplier locations were affected.

Read MoreBurger chain cuts breakfast hours due to egg shortage

That's trickling out to restaurants. San Antonio, Texas-based fast food chain Whataburger is curbing breakfast hours to peak times at its 770-plus locations since its primary egg supplier went offline.

"We're just as bummed as our customers about having to temporarily change our breakfast hours, due to the national egg shortage caused by an avian flu outbreak," the company said in a release. "We don't know why other restaurants haven't been affected by this shortage yet, but it sure has affected us."

As cases escalate, that could always change. McDonald's confirmed that one of its suppliers was also affected, though contingency plans have prevented any disruption. Cargill is a supplier for McDonald's.

Starbucks, Denny's and IHOP owner Dine Equity say they have not been affected. Neither has Dunkin Brands, though the company acknowledged that "the entire industry will experience supply issues and product price fluctuations as the market responds to these unfortunate circumstances."