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The road to success can be a bumpy one for clinical-stage vaccine developers. Novavax (NVAX 15.33%) shareholders can attest to that, while Inovio Pharmaceuticals (INO -2.21%) investors hope to enjoy a smoother ride. So far in 2016, Novavax has lost around 80% of its market cap. Inovio's shares have jumped over 20% year to date. But which of these stocks is the better pick for investors now?

The case for Inovio

There are three primary reasons to buy Inovio. The one that has received the most attention lately is Inovio's experimental Zika vaccine. Inovio can legitimately claim to have the pole position in the race to develop a vaccine for the Zika virus.

In February, Inovio announced robust antibody and killer T cell responses in mice treated with its Zika vaccine. That was followed up in May when the company reported similar positive results in monkeys. Based on the success of these pre-clinical studies, the Food and Drug Administration gave the green light to Inovio and South Korean partner GeneOne Life Science to move forward with clinical testing in humans. Inovio expects to announce interim results from the phase 1 study before the end of 2016.

Another reason for investors to like Inovio is its lead candidate, VGX-3100. The cervical dysplasia vaccine should begin phase 3 testing in the near future. Inovio said in August that it had worked out a plan to proceed with regulators in the U.S. and Europe. 

Then there's the rest of the pipeline. Although every candidate Inovio has outside of VGX-3100 is only in early-stage testing, the pipeline appears to be pretty full for a small biotech. INO-3112, a combination of VGX-3100 and DNA-based immune activator encoded for IL-12, showed enough potential to attract the attention (and money) of AstraZeneca. The immunotherapy is in two phase 1 studies, one focusing on cervical cancer and the other on head and neck cancer. 

 Inovio's pipeline includes three other potential cancer vaccines, but it's the anti-viral vaccine area that the company has really been busy. Not counting the Zika vaccine, Inovio has eight clinical studies in progress for vaccines to treat viruses such as Ebola, HIV, and MERS. Fortunately for the company's financial position, most of these studies have collaborators to help fund research.

Speaking of finances, Inovio reported cash, cash equivalents, and short-term investments of $134.5 million as of the end of June. That should be enough to at least carry the company until the second half of 2017.

The case for Novavax

There's good and bad news for investors thinking about buying Novavax stock. First, the bad news. Novavax's lead candidate, its RSV F vaccine, failed in a phase 3 study in older adults. The announcement of the clinical trial results in September caused Novavax's stock to drop like a brick.

What's the good news? Now that the share price is much lower, Novavax might be able to make a comeback. No results have been reported yet from its other late-stage study of RSV F vaccine in infants. The RSV F vaccine is also in a phase 1 study for children six months through five years old.

Novavax still hasn't given up hope for its vaccine in treating the larger market for older adults. The company is analyzing the results from the unsuccessful phase 3 study to see if it can figure out what happened. Gregory Glenn, president of research and development, said that the company "continue[s] to believe that there is a path forward for our RSV vaccine."

If the RSV F vaccine doesn't prove to be effective, Novavax does have a few more candidates in its pipeline. Two influenza vaccines are in phase 2 clinical studies. Novavax also reported positive results last year from a phase 1 study of its Ebola vaccine in combination with the company's Matrix-M adjuvant. 

Novavax reported $366.4 million in cash and cash equivalents and marketable securities at the end of June. The company says that amount will fund operations and ongoing development at least through the middle of 2017. 

Better buy

I think there's a clear winner between these two stocks: Inovio. If Novavax finds a way to successfully move forward with its RSV F vaccine, the stock would undoubtedly soar. However, the odds against that happening appear to be steep.

Inovio, on the other hand, has plenty of momentum. I wouldn't underestimate the risks associated with buying the stock, though. Inovio could run into the same kinds of problems with its candidates that Novavax did. Right now, however, my view is that Inovio is more likely to reward investors over the long run.