Truvada isn’t going anywhere—it will remain the HIV backbone of choice for many years, IMO. The question is what third agent will be added to it?
As far as Atripla is concerned, GILD does not have a partnership with BMY in the usual biotech sense of the word. Rather, GILD purchases Sustiva from BMY at full cost and adds it to Truvada to make Atripla. If something better than Sustiva comes along, GILD will seek to combine it with Truvada.
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