Gilead Sciences (GILD 0.41%) rose nearly 14% on Monday on word that 100% of patients treated with its drug combo had undetectable levels of virus four weeks after treatment. While 100% is better than the 97% that Abbott Labs (ABT 0.40%) posted, it's still too early to call a winner.

Red apples to green apples
Within a clinical trial, the treatment arms are balanced so that the patient makeup is approximately equal. Everything from race of the patient to secondary conditions can affect the ability of drugs to rid the patient of the virus. Balancing the arms allows the drug candidate to be compared to the comparator arm (placebo or the current treatment paradigm).

Comparing results from two different clinical trials is dangerous. It's not quite apples to oranges, but it's hard to know if the two trials enrolled the same types of patients and how the potentially different makeup of the patients affected the results.

The only way to compare the two directly is in a head-to-head trial, but that'll only happen once they're on the market.

Sample size matters
Gilead only tested 25 patients with the combination of sofosbuvir, GS-5885, and ribavirin that produced the 100% result. If it had tested 26 patients and the one additional one failed, the cure rate would have been just 96%, and we'd be declaring Abbott the apparent winner.

Not all "cures" are created equal
Talk to a hepatologist and you won't hear them say the patient was cured of hepatitis. Instead, they use the term "sustained virological response," or SVR, which means that the virus level has dropped below detectable levels. There's no way to know if there truly isn't any virus remaining in the patient or if there's a small amount of virus waiting to pounce once the treatment has stopped.

Gilead presented SVR4 data, which measures the SVR after four weeks. Abbott used SVR12, which measured the level after 12 weeks. Generally very few patients rebound between week four and week 12 post-treatment, but it would only take one to knock Gilead down a rung in the race to the top.

Winner, winner, chicken dinner
While it's hard to declare a winner based on these phase 2 data, it's clear that Abbott isn't going to walk away with the prize, so the jump today in Gilead is warranted if you assume the hepatitis C drug market is as large as investors hope it is (debatable, especially for a disease where treatment can be put off, but we'll leave that for another article).

No matter what the size of the market is, as we approach 100% cure rates, it's clear that side effects and convenience -- how many pills a patient has to take a day and for how long -- will become an increasingly important factor in whether Vertex Pharmaceuticals (VRTX 1.36%), Idenix Pharmaceuticals (NASDAQ: IDIX), Achillion Pharmaceuticals (ACHN), and the rest of the trailing companies are able to compete with the front runners.