The JPMorgan Healthcare Conference just finished up in San Francisco and was arguably the most important event of the entire year for the health care sector. This is one of the rarest opportunities for biotechnology, pharmaceutical, and medical device companies to open up about where they've been and where they're headed, so it pays to take notice.

With dozens of companies presenting each day last week, it was veritably impossible to review each and every one. That doesn't mean, however, that there weren't other companies squarely in my sights.

Hepatitis-C-focused biotech Idenix Pharmaceuticals (NASDAQ: IDIX) may be small from a market-cap perspective, but I've been closely monitoring it following the mid-summer clinical hold put on IDX-184 and IDX-19368 by the FDA. I was curious what, if anything, Idenix would have to say about these clinical holds, and what else might be coming down the pipeline in 2013. 

As expected, CEO Ron Renaud did his best to distance Idenix from its reliance on IDX-184 and IDX-19368 as being pillars of his company's success. Although both of Idenix's drugs share the same activity metabolism, 2'-methyl G, that was found in Bristol-Myers Squibb's BMS-986094, which contributed to the death of a patient in trials, further echocardiograms and studies have revealed no cardiovascular complications on its end. According to Renaud, following a brief meeting with the FDA, Idenix expects to get a response regarding the hold from the FDA later this quarter.

One of the biggest eye-openers in Renaud's presentation came early when he declared IDX-719 to be its lead compound. This was a marked and clean shift from further de-emphasizing its clinical holds.

Furthermore, Idenix was open about the possibility of combining its drugs with existing antivirals or other developing compounds. This is important for a number of reasons. First, last year saw a clean break between Novarits and Idenix's previous collaborative partnerships, which allows Idenix to control the destiny of its own pipeline. Second, it brings in the possibility that bigger partners with struggling hepatitis-C programs (ahem, Bristol) could consider partnering up their developing compounds with Idenix's extensive hep-C library of drug hopefuls and may wind up shouldering some or all of the cost of development.

As laid out by Renaud, Idenix's big development goals this year will be to initiate a 12-week all-oral phase 2 combination study with IDX-719 and its newly developed uridine nucleotide prodrugs; file possibly up to three new investigational new drug, or IND, applications over the next 12 to 18 months for its uridine nucleotide prodrugs; and act on its nucleotide program (IDX-184 & IDX-19368) once it hears back from the FDA.

Renaud also glossed over Idenix's ongoing spat with Gilead Sciences (GILD -0.09%) over which company owns the rights to certain hep-C patents. Renaud's comments seem to suggest a resolution and appeal to this case may not come around for two more years.

Ultimately, this is going to come down to whether there's any room left for Idenix in the hepatitis-C market – especially if it falls too far behind its competitors. We already have two interferon-based hep-C treatments in Vertex Pharmaceuticals' (VRTX -0.94%) Incivek and Merck's Victrelis on the market, and Gilead's Sofosbuvir has cruised through clinical trials and seems like a lock for FDA approval in the first half of 2013. Similarly, AbbVie's (ABBV -0.76%) hepatitis-C drug combination eliminated the virus in 99% of all patients tested back in October. Some of Idenix's other competitors, like Achillion Pharmaceuticals (ACHN), are developing non-nucleotide based inhibitors which have received less of a discerning eye from the FDA.

In short, the market for hepatitis-C products is huge, but the clinical hold and rapidly advancing competition is a big strain on a company unlikely to get a drug to market any time before late 2014 or 2015 at the earliest. I'd still suggest staying away from Idenix as an investment and would watch its developing pipeline from a distance.