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Prosecution History Estoppel Does Not Bar Application of DOE for Patent Directed to DNA Encoding

09-1568
August 04, 2010

Decision icon Decision

Last Month at The Federal Circuit - September 2010

Judges: Bryson, Dyk (concurring-in-part, dissenting-in-part), Prost (author)

[Appealed from: D.D.C., Judge Kennedy]

In Intervet Inc. v. Merial Ltd., No. 09-1568 (Fed. Cir. Aug. 4, 2010), the Federal Circuit reversed the district court’s claim construction, vacated the SJ of noninfringement, and remanded for a finding of whether the accused device infringes under the Federal Circuit’s claim construction.

In a DJ action, Plaintiff Intervet Inc. (“Intervet”) denied infringing U.S. Patent No. 6,368,601 (“the ’601 patent”), owned by Defendants Merial Limited and Merial SAS (collectively “Merial”), directed to DNA constructs encoding a type of porcine circovirus.  The prefix “circo” refers to the circular genome of the virus.  A porcine circovirus is thus a virus having a circular genome that infects pigs. 

Merial filed the application resulting in the ’601 patent pertaining to the discovery of what it described as a previously unknown pathogenic type of porcine circovirus that the inventors dubbed “PCV-2.”  The ’601 patent categorizes previously known, nonpathogenic porcine circoviruses as belonging to “type I” or “PCV-1.”  The ’601 patent identifies a particular known DNA sequence isolated from pig kidney cells called PK/15 as being representative of type I.  The ’601 patent then identifies five isolated pathogenic porcine circovirus strains as being representative of type II.  The patentee placed the five representative strains on deposit with the PTO as part of the description of the invention. 

The ’601 patent disclosure goes on to analyze the sequenced PCV-2 strains in more detail, providing tables comparing the sizes and alignments of the strains.  The disclosure then identifies one of the sequenced strains, designated SEQ ID 4, as being further representative of the other strains, and identifies thirteen open reading frames (“ORFs”) for PCV-2 using that sequence.  The ’601 patent specification identified nine of the thirteen disclosed ORFs that are unique to PCV-2, and four that are present in both PCV-2 and PCV-1. 

“ORF” is a commonly used term in molecular genetics.  An ORF is a portion of a gene that contains a sequence of nucleotide bases that may be translated into a protein.  Identifying the ORFs of a gene sequence differentiates the portions of the sequence that may encode a protein from the portions that do not encode a protein.  It allows those skilled in the art to estimate the size and composition of potential amino acid sequences for the proteins encoded by the gene.  Merial’s patent claims are directed to certain vectors and other DNA molecules that contain portions of the PCV-2 gene sequence. 

Intervet is an animal healthcare company that manufactures vaccines for livestock.  Intervet developed a vaccine called “Porcine Circovirus Vaccine Type 2” that contained a porcine circovirus nucleotide sequence in a vector for treating a circovirus in pigs.  Merial alleged that Intervet’s vaccine used an infringing PCV-2 sequence.

The district court construed six disputed claim terms of the ’601 patent.  Among these constructions, the district court defined “porcine circovirus type II” as consisting of the five nucleotide sequences that Merial placed on deposit with the PTO.  The district court construed the term “ORFs 1-13” as the DNA sequences of the thirteen ORFs of SEQ ID 4 listed in the table under Example 13 of the ’601 patent.  Finally, the district court construed claim 32 in its entirety to refer (in part) to a construct comprising at least one DNA molecule that is unique to one of the five sequences on deposit with the PTO.

The district court entered SJ of noninfringement based on these claim constructions.  It was undisputed that Intervet’s vaccine contained a nucleotide sequence that was 99.7% homologous to one of the deposited sequences.  The accused product was therefore held to be outside the literal claim scope of PCV-2, which required strict identity to one of the five deposited sequences.  The district court also held that the doctrine of prosecution history estoppel precluded Merial from arguing that the accused sequence infringed under the DOE.

Merial appealed the district court’s claim construction for three of the terms, and, in the alternative, appealed the district court’s SJ of noninfringement based on the DOE.

The Federal Circuit first considered claim construction.  The district court found that the claim term “porcine circovirus type II” was limited to the five sequences that were deposited with the PTO as part of the description of the invention.  The Federal Circuit, however, found that the ’601 patent states that the five deposited strains and listed sequences are “representative of” a “type of porcine circovirus,” and do not constitute the entire scope of the invention.  The Court reminded that “[s]equences are representative of the scope of broader genus claims if they indicate that the patentee has invented species sufficient to constitute the genera.”  Slip op. at 9.  Accordingly, the Court construed the claim term “porcine circovirus type II” to be “a pathogenic pig virus having a circular genome that is at about 96% or more homologous with the four sequences disclosed in the present specification, and about 76% or less homologous with the PK/15 sequence.”  Id. at 10.

 

“Merial is not . . . estopped from arguing that a pathogenic porcine viral sequence with over 99% nucleotide homology with one of the five representative strains is equivalent to that strain.  Such a draconian preclusion would be beyond a fair interpretation of what was surrendered.”  Slip op. at 18 (footnote omitted).

The Federal Circuit next turned to the district court’s claim construction of “ORFs 1-13,” which defined the claim scope as consisting of the DNA sequence of the thirteen ORFs enumerated in Example 13 of the ’601 patent specification as those ORFs apply to SEQ ID 4.  The Court found that, although the district court was correct that the disclosed ORFs define the claim term, it erred in confining the scope of the term to the precise limits of the representative ORFs listed in Example 13 and the exact DNA sequence of SEQ ID 4.  The Court concluded that the term “ORFs 1-13” is properly construed as “lengths of translatable DNA between pairs of start and stop codons, corresponding to the 13 ORFs identified in the patent specification.”  Id. at 12.

Turning next to the construction of claim 32, the Court found no error in the district court’s construction, “an isolated DNA molecule that includes, but is not necessarily limited to, a DNA sequence which codes for an immunodominant region of a protein, wherein the sequence is from the genome of a PCV-2 circovirus, and not from the genome of a PCV-1 circovirus.”  Id. at 13.  The Court, however, agreed with Merial that the district court erred in explaining during its infringement analysis that the part of the claim construction specifying that the sequence be “from” the genome of a PCV-2 circovirus, etc., excluded sequences that were physically derived from a non-PCV-2 source.  The Federal Circuit focused its analysis on the term “specific to” in claim 32, since it appeared that this term determined whether the sequence was unique to and derived from PCV-2. 

Intervet argued that the term “specific to” is a specialized term of art in immunology that typically refers to one structure’s proclivity for binding to another structure.  The Court found, however, that a specialized definition of this term did not make sense in the context of claim 32 because the claimed epitope was not described as binding to porcine circoviruses; it was described as located within a porcine circovirus.  The Court concluded that, to the extent that the district court’s application of its claim construction required that the encoded epitope be unique to PCV-2 among all possible antigens, it was erroneous.

Accordingly, the Federal Circuit reversed the district court’s claim construction of the terms “porcine circovirus type II” and “ORFs 1-13,” clarified the proper interpretation of the construction of the term “specific to PCV-2 and not specific to PCV-1,” and remanded the question of infringement for a determination consistent with the revised claim constructions.

Finally, the Court considered the DOE.  The district court found that prosecution history estoppel precluded Merial from invoking the DOE.  Merial was estopped from arguing that the accused PCV strain was equivalent to the claimed “porcine circovirus type II.”  The Federal Circuit disagreed, finding that the purpose of the claim amendment at issue was to narrow the claimed universe of ORFs down to those of PCV-2, and that the amendment bore only a tangential relation to the question of which DNA sequences were and were not properly characterized as PCV-2.  The Court concluded that, while Merial was estopped from arguing that ORFs of pathogenic circoviruses found in other organisms were equivalent to ORFs of PCV-2 and from arguing that ORFs of a pathogenic strain of PCV-1 were equivalent to ORFs of PCV-2, Merial was not estopped from arguing that a pathogenic porcine viral sequence with over 99% nucleotide homology with one of the five representative strains was equivalent to that strain. 

Judge Dyk wrote separately, concurring-in-part and dissenting-in-part.  Judge Dyk agreed with the majority’s construction of claim 32 of the ’601 patent but disagreed with its construction of the other two claim terms.  Judge Dyk noted that, under the majority’s claim construction of all terms, claim 32 covered DNA sequences that were not in fact isolated by the inventor and were distinct from the five isolated strains disclosed in the ’601 patent, raising issues of patentable subject matter under 35 U.S.C. § 101.  Claim 32 encompassed “[a]n isolated DNA molecule comprising a nucleotide sequence encoding an epitope which is specific to PCV-2 and not specific to PCV-1.”  Applying the majority’s constructions of “PCV-2” and “specific to PCV-2 and not specific to PCV-1,” in Judge Dyk’s view, raised the question of whether the isolated DNA molecule, separate from any applications associated with the isolated nucleotide sequence (e.g., the production of a vaccine), was patentable subject matter.  It was unclear to Judge Dyk that an “isolated” DNA sequence was qualitatively different from a product occurring in nature such that it would pass the test laid out in Diamond v. Chakrabarty, 447 U.S. 303, 309 (1980), and Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 130 (1948).

Judge Dyk also disagreed with the majority with respect to its construction of “ORFs 1-13” and agreed with the district court that the phrase must be limited to the specific DNA sequences defined as ORFs
1-13 in the ’601 patent based on the intrinsic evidence.  Under the district court’s construction, in Judge Dyk’s view, claim 9 of the ’601 patent was not literally infringed or infringed under the DOE.

Summary authored by Joyce Craig, Esq.