I have been speaking with a PhD biochemist I know and he says that Idenix's patents broadly cover most of the PSI structures. The main question is who owns the core patent for nucleosides, not the metabolites. I dug around a little and indeed Idenix provisional applications date back to June 2002, over a year before Pharmasset patent in question. Since US is first to invent, it could come down to dated lab notebooks.
Idenix presumably has an upper hand because of the senior party designation. I've seen quotes stating the senior party wins in greater than 90% of these kind of cases. Not sure what Idenix gets though.
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Bank of America has published a research report on Idenix Pharmaceuticals (NASDAQ: IDIX) commenting on what to expect from settlement talks for the company.
In the report, Bank of America writes, "A document was recently posted providing an update on the patent interference between GILD and IDIX related to patent ‘572 covering GILD's HCV nuc GS-7977. The document notes that by law, parties within three months of a patent interference declaration must enter into settlement discussions; IDIX and GILD (B-1-9; US$50.62) have discussed the possibility of a settlement and plan additional discussions in June. Given the settlement discussions are court mandated, it is difficult to draw conclusions or assign probabilities on the outcome of such discussions. We currently assign $6/sh in our IDIX for potential royalties on future sales of GS-7977." Bank of America maintains its Buy rating and $15 price objective on Idenix Pharmaceuticals, which closed yesterday at $10.08.