DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election of Group I (claims 1-4) in the reply filed on 10 February 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). Claims 5-13 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 10 February 2026. Thus, claims 1-4 will be examined on the merits herein.
Priority
The instant application is a 371 of application PCT/US2021/065668 (filed 30 December 2021) and claims priority to U.S. Provisional application 63/132,006 (filed 30 December 2020). Therefore, the effective filing date of instant claims 1-4 is 30 December 2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4 August 2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-2 and 4 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural product without significantly more.
Claim 1 recites, “A composition comprising: (a) a recombinant Surface Attachment Protein 1 (Sap1) polypeptide having the amino acid sequence of SEQ ID NO:1, (b) a recombinant Surface Attachment Protein 2 (Sap2) polypeptide having the amino acid sequence of SEQ ID NO:10, or (c) a combination of (a) and (b), wherein the recombinant Sap1 polypeptide and/or recombinant Sap2 polypeptide is tagged and/or in admixture with an adjuvant.” The limitation is drawn to a natural product because the scope of Sap1 and Sap2 proteins encompassed by the claim includes proteins which are naturally produced by Burkholderia species, as is described in para. 24 and 27 and Figs. 9-10 of the instant specification. In Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 591-94, 106 USPQ2d 1972, 1979-81 (2013; herein “Myriad”), the Supreme Court made clear that not all changes in characteristics will rise to the level of a marked difference, e.g., the incidental changes resulting from isolation of a gene sequence are not enough to make the isolated gene markedly different. In this case, incidental changes in the sequence of a protein obtained from an isolated bacterium without genetic engineering of the protein are not enough to make the claimed protein markedly different. While the claim recites “recombinant” Sap1 and/or Sap2 polypeptides, the specification does not teach that any genetic modifications are made to the natural polypeptides encompassed by SEQ ID NOs: 1 and 10; thus, the “recombinant” Sap1 and/or Sap2 polypeptides are not markedly different from the naturally occurring Sap1 and/or Sap2.
Regarding the limitation “wherein the recombinant Sap1 polypeptide and/or recombinant Sap2 polypeptide is tagged and/or in admixture with an adjuvant”, it is known in the art that bacterial lipopolysaccharide (LPS) may be used as an adjuvant, as is taught by Arenas (Abstract and pg. 530, left col., para. 3). Morici (US2014/0004178) teaches that Burkholderia produces LPS (para. 88) and that it stimulates the immune response in a B. pseudomallei OMV vaccine (para. 165), i.e., is used as an adjuvant. Thus, the claimed composition comprising Sap1 and/or Sap2 in an admixture with an adjuvant is not markedly different from a naturally occurring Burkholderia expressing Sap1 and/or Sap2 and LPS, because the broadest reasonable interpretation of claim 1 encompasses, for example, cultures of Burkholderia and mixtures of lysed Burkholderia, both of which would comprise Sap1 and or Sap2 and LPS expressed by naturally occurring Burkholderia cells.
Claim 2 recites, “wherein the Sap2 polypeptide further comprises a signal peptide.” The limitation is drawn to a natural product because Sap2 proteins contain a native signal sequence, as is described in para. 28 and 101 of the instant specification. Because the scope of the limitation encompasses signal sequences naturally produced by Burkholderia and naturally part of the Sap2 protein, the Sap2 polypeptide further comprising a signal peptide is not markedly different from the natural Sap2 polypeptide containing a signal peptide.
Claim 4 recites, “A kit for diagnosing a Burkholderia infection comprising a recombinant Surface Attachment Protein immobilized on a substrate, comprising: (a) a recombinant Surface Attachment Protein 1 (Sap1) polypeptide having the amino acid sequence of SEQ ID NO:1, (b) a recombinant Surface Attachment Protein 2 (Sap2) polypeptide having the amino acid sequence of SEQ ID NO:10, or (c) a combination of (a) and (b).” The limitation “immobilized on a substrate” is drawn to a natural product because the broadest reasonable interpretation of “substrate” encompasses substrates on which the protein(s) can naturally be found, such as the Burkholderia cell membrane, as evidenced by para. 99 and 101 of the instant specification, which teaches that Sap1 and Sap2 are naturally membrane-bound (i.e., substrate-bound) proteins. Thus, the broadest reasonable interpretation of claim 4 encompasses, for example, whole cell Burkholderia or compositions comprising outer membrane vesicles produced from Burkholderia cell membranes (see, e.g., Morici, Abstract). Because the scope of the claim encompasses the natural phenomenon of Sap1 and/or Sap2 polypeptides bound to a Burkholderia cell membrane, the structure of a Sap1 and/or Sap2 immobilized on a substrate is not markedly different from the natural membrane-bound Sap1 and/or Sap2. While the claim recites “recombinant” Sap1 and/or Sap2 polypeptides, the specification does not teach that any genetic modifications are made to the natural polypeptides encompassed by SEQ ID NOs: 1 and 10; thus, the “recombinant” Sap1 and/or Sap2 polypeptides are not markedly different from the naturally occurring Sap1 and/or Sap2.
This judicial exception is not integrated into a practical application because claims 1-2 and 4 do not recite additional elements that integrate the judicial exception into a practical application.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because claims 1-2 and 4 do not require additional elements other than the natural product(s).
Therefore, claims 1-2 and 4 do not qualify as eligible subject matter. See MPEP 2106.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-4 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Morici (US 2014/0004178 A1; cited in IDS) as evidenced by Hayden et al. (2012, “Burkholderia pseudomallei 1026b chromosome 2, complete sequence”; herein “Hayden”).
Regarding claims 1, Morici teaches a vaccine comprising B. pseudomallei outer membrane vesicles (OMVs) (para. 245) and an adjuvant (para. 249 and 275). Morici teaches that the OMVs are naturally derived from B. pseudomallei 1026b (para. 171) and comprise the protein BPSS1860 (Table 3), which comprises an amino acid sequence identical to the instant SEQ ID NO: 10 (see Figure 1 for alignment below), as is evidenced by Hayden (pg. 2).
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Figure 1: Alignment of instant SEQ ID NO: 10 (Qy) with Hayden’s B. pseudomallei 1026b protein (Db).
Regarding claim 2, the full sequence of BLSS1860 contains an amino acid sequence identical to instant SEQ ID NO: 96 (see Figure 2 for alignment below), as is evidenced by Hayden (pg. 2). This SEQ ID NO: 96 is identified as a signal peptide by the instant specification (para. 101). While both Morici and Hayden are silent on the function of this peptide sequence, the function of a “signal peptide” is inherent to its structure; thus, because the structure is present in the amino acid sequence taught by Hayden, it is presumed that the structure has the function of a signal peptide. See MPEP 2112.01(I): “Where the claimed and prior art products are identical or substantially identical in structure or composition,… a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). ‘When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not.’ In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).”
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Figure 2: Alignment of instant SEQ ID NO: 96 (Qy) and residues 1-20 of Hayden’s BPSS1860 protein (Db).
Regarding claim 3, Morici teaches a method comprising administering the OMV vaccine comprising an adjuvant to mice (para. 247), which conferred significant protection against challenge with B pseudomallei (para. 248-249), i.e., immunized the mice against a Burkholderia infection.
Regarding claim 4, Morici teaches that BPSS1860 is an outer membrane/extracellular protein (Table 3), i.e., it is immobilized to the outer membrane, which may act as a substrate. With respect to the limitation in the preamble of claims 4, please note that MPEP 2111.02(II) states "a preamble generally is not limiting when the claim body describes a structurally complete invention such that deletion of the preamble phrase does not affect the structure or steps of the claimed invention." In the instant case, claim 4 is drawn to a product, and the preamble does not affect the structure of the product. The preamble in this case recites a statement of purpose or use, and therefore must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY M MORGAN whose telephone number is (703)756-5388. The examiner can normally be reached M-F 9-5 ET.
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/BAILEY M MORGAN/Examiner, Art Unit 1645
/DANIEL E KOLKER/Supervisory Patent Examiner, Art Unit 1645