A close reading of the Merck and Schering-Plough first-quarter conference calls suggests that Merck is distancing itself from its joint-venture partner — who is, in any event, in a much worse position to weather the storm over their cholesterol-fighting pill Vytorin.

Vytorin, of course, is a combination of Merck’s generic statin Zocor and Schering’s newer cholesterol drug Zetia. It’s been in the news recently because the two companies appear to have sat for nearly two years on the results of a major clinical trial, since published, that suggested Vytorin was no better at reducing arterial plaque — and thus, presumably, at preventing heart attacks — than Zocor alone. Last year, Zetia and Vytorin racked up more than $5 billion in sales, although usage of both drugs has plunged since January, when the trial results first finally emerged.

Both companies are blaming market “confusion” for the drugs’ problems, but so far only Merck is willing to put a number on how much the confusion is costing it — $700 million in “equity income” from the joint venture for the full year. Schering, by contrast, has opted to try to bull through without giving specifics, although in a peculiarly dishonest way. In the company’s own conference call earlier today, Schering CEO Fred Hassan claimed that “we really have no model” for figuring out how much the Zetia/Vytorin sales drop will cost the company, although in a Form 8-K filed yesterday with the SEC, Schering acknowledged:

The Merck/Schering-Plough cholesterol joint venture developed potential scenarios about the 2008 equity income. Merck chose an estimate that is within the ranges established in those scenarios.

Schering’s disinclination to talk numbers is in keeping with its general practice, but probably also reflects the fact that it’s far more vulnerable to the Zetia/Vytorin losses then Merck. Exacerbating things is the fact that Merck also has another anti-cholesterol iron in the fire — an experimental drug called Cordaptive, a form of niacin coupled with another compound designed to reduce the hot-flash style flushing that niacin alone can cause. Cordaptive could be approved as early as next week, and if that happens, it will immediate emerge as a competitor to Zetia as a cholesterol-fighting drug that can be combined with statins like Zocor.

Cordaptive isn’t without its own critics, who call its anti-flushing component untested and its potential heart effects unknown. Schering VP for global pharmaceuticals Carrie Cox, meanwhile, tried to play it down as a niche product. Still, the two companies really don’t need any additional sources of tension, particularly given how two lower-level executives were caught referring to one another in Vytorin-related emails recently released by the House Energy and Commerce Committee:

(Hat tip to the blog Schearlings Got Plowed.)