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The difference is the left hand portion. Sovaldi has an elaborate phosphoramidate group that is metabolized via a series of enzymes in the body to the triphosphate. It is not possible to directly administer the triphosphate as it rapidly hydrolyzes in the intestinal tract to the free alcohol species that cannot be phosphorylated in vivo to the active drug.The Pharmasset (now Gilead) patents involved in the dispute are the "Clark" patents which cover the active metabolite.Jeremy Clark; Modified fluorinated nucleoside analogues; US patent number 7,429,572; Filing date: Apr 21, 2004.Jeremy Clark; Modified fluorinated nucleoside analogues; US patent number 8,415,322; Date of Patent: April 9, 2013.Let's start with the Idenix litigation with Gilead, which began in 2012 and is still in progress.

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