The Comptroller's refusal of the SPC application relied heavily on Takeda Chemical Industries Ltd's SPC Applications (No.3)  RPC 1,  EWHC 649 (Pat), where the Patents Court upheld a refusal of SPC applications on lansoprazole in combination with other named antibiotics. The judge held in Takeda that the patent did not protect the combination, but only the lansoprazole element of the combination.
The Comptroller in Gilead indicated that the specification of the patent should at least provide a clear pointer to the specific combination product. Kitchen J rejected this test, holding at para.33 that a clear test applicable to a product comprising a combination of active ingredients
"is to identify the active ingredients of the product which are relevant to a consideration of whether the product falls within the scope of a claim of the basic patent. It is those ingredients, and only those ingredients, which can be said to be protected within the meaning of the Regulation. So, in the case of a product consisting of a combination of ingredients A and B and a basic patent which claims A, it is only A which brings the combination within the scope of the monopoly. Hence it is A which is protected and not the combination of A and B. ... The product comprises two active ingredients... It falls within the scope of claims 1 and 25 only because of the presence of (one of those compounds). Hence, on the Takeda test, claims 1 and 25 do not protect the product within the meaning of the Regulation. However, claim 27 is directed to a composition comprising (the first compound) together with a carrier and optionally other active ingredients. The product falls within this claim too and it does so, in so far as the claim is directed to a combination, as result of the presence of both (compounds)."The Comptroller has been granted leave to appeal.
Thanks to Helen Jones (Gill, Jennings & Every -- who acted the for appellant, instructing Charlotte May, 8 New Square) for supplying this information.