In Ex parte Smith, Appeal No. 2016-007565 (PTAB, May 16, 2016), the Board reversed the examiner’s s . 101 and 103 rejections of a claim to a modified flavivirus envelop (E) protein comprising a mutated envelop protein, where the unmodified E-To domain comprises a central glycine amino acid and 15 recited points of mutation, “wherein the mutation selectively inhibits the replication of a flavivirus comprising the modified E protein in mammalian cells relative to insect cells.”

For some reason known only to the prosecution history, the examiner rejected this claim on the basis that is was directed to a natural product (and the SPE did not intervene) because “it reads on a fragment of the naturally occurring protein and that the fragment does not appear to be structurally different from the full-length sequence except through cleavage of a peptide bond” and the claim “reads on a product that is not markedly different from a naturally occurring product and is, therefore, directed to patent ineligible subject matter.”

Facially, these rejections make no sense. Appellants argued that the claim recites specific internal deletions and the mutation selectively inhibits the replication of the virus in mammalian cells relative to insect cells. The Board could see this as clearly as you can, even from my truncated summary of the claim, and ruled that the Examiner “has failed to establish a prima facie case that the claims are directed to non-statutory subject matter. The Examiner has pointed to nothing in the record…that shows that a protein with the specific deletions recited in the claims exists in nature.”

Interestingly, the Board did not refer to the PTO requirement that the mutated protein have markedly different characteristics from its closest flavivirus E protein counterpart existent in nature (although such characteristics are recited in the claim). The Board apparently felt that the structural differences between the claimed mutant flavivirus and the native ones were so great that the Step 2A analysis of the Mayo/Alice rule (“not a natural product”) rendered the relative properties irrelevant to its decision. Does “markedly different” = “inventive concept?” (The claims were found to be unobvious as not close structurally to other mutants in the prior art.) So, does an unobvious structural modification of a natural product yield a patent eligible compound per se? Apparently.

But a nagging question lingers. Why was this rejection maintained by the Examiner? Worse yet, how did these rejections survive an interview or a pre-appeal conference (if there was one)? The Examiner appears to be trying to shoehorn this case into the Myriad “line” but doesn’t come close. Either the resolution of the natural products question is even more complicated that it first appeared in the PTO Guidance, or the necessary Examiner training has not occurred. As the Captain said in Cool Hand Luke after hitting convict Paul Newman and rolling him down a hill, “What we’ve got here is a failure to communicate.”

This article was originally published on Patents4Life.com.

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