The reliance on eggs to produce vaccines is potentially problematic because of the risk of a pandemic, the possibility of a shortage of eggs and limitations on what types of vaccine viruses can be grown in eggs, the CDC has acknowledged.
In light of that, the federal government in 2009 provided $147 million in funding to Connecticut-based Protein Sciences Corp. to help it develop a vaccine that is produced with recombinant DNA technology instead of eggs.
"They really wanted to have a backup," Manon Cox, CEO of Protein Sciences, told CNBC.
The Food and Drug Administration approved the company's vaccine, known as Flublok, in 2013 for people age 18 and over. So far it is the only flu vaccine that does not rely on eggs to be made.
"It is the wave of the future," said Cox, who noted that other vaccines are based on a technology that is more than 70 years old.
In an unusual move in June, the FDA granted Flublok regulatory exclusivity, which means that no other similar flu vaccine can win product approval from the agency before January 2025.
Still, Flublok's market share is relatively tiny.
The company hopes to ship 1.2 million doses for this season starting next week, Cox said. That's less than 1 percent of the overall flu vaccine market in the U.S.
But Cox says the company hopes to increase sales by appealing to customers and health providers who would be attracted by the presence of more active ingredients in the vaccine, and the lack of ingredients such as egg protein, mercury or antibiotics.
"We sell it as the pure choice," she said.
Protein Sciences is also hoping that the results of a clinical trial it released in late June will make Flublok a more attractive option for health providers, Cox said. The study of about 9,000 people age 50 and older, showed that 31 percent more people were protected from the flu by quadrivalent Flublok than by a traditional egg-based quadrivalent vaccine.
(CORRECTION: This year, GlaxoSmithKline will ship between 32 million and 38 million doses of quadrivalent vaccine. An earlier story misstated the amount.)