DETAILED ACTION
Disposition of Claims
Claims 1-10 are pending.
Examiner’s Note
All paragraph numbers (¶) throughout this office action, unless otherwise noted, are from the US PGPub of this application US20250084131A1, Published 03/13/2025.
Applicant is encouraged to utilize the new web-based Automated Interview Request (AIR) tool for submitting interview requests; more information can be found at https://www.uspto.gov/patent/laws-and-regulations/interview-practice.
Optional Authorization to Initiate Electronic Communications
The authorization provided by Applicant’s representative to correspond with the Examiner via electronic mail (e-mail) is acknowledged and entered.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Should applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d) prior to declaration of an interference, a certified English translation of the foreign application must be submitted in reply to this action. 37 CFR 41.154(b) and 41.202(e).
Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). See e.g. Figs. 5, 8. Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Claim Rejections - 35 USC § 112(b); Second Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1 and dependent claims 2-10 thereof are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites, “a T-cell epitope polypeptide of foot and mouth disease virus (FMDV), the epitope polypeptide having an amino acid sequence represented by one of SEQ ID Nos: 1-11”. It is unclear whether the phrase “having an amino acid sequence represented by one of SEQ ID NOs: 1-11” limits the claimed polypeptide to a polypeptide whose complete amino acid sequence is one of SEQ ID NOs: 1-11 (e.g. a polypeptide that consists of any one of SEQ ID NOs: 1-11) or if the polypeptide encompasses a longer polypeptide which contains or comprises said sequence (e.g. a polypeptide that comprises any one of SEQ ID NOs: 1-11). The transitional phrase “having” does not, by itself, establish whether additional unrecited material is permitted, and its scope must be determined in view of the claim language and specification. However, the instant specification does not clearly define “having” or otherwise state whether additional amino acid residues may or may not be present in the claimed T-cell epitope polypeptide. Moreover, the specification separately refers to a “recombinant protein comprising a T-cell epitope polypeptide of FMDV” and to a “fusion protein of the epitope polypeptide,” while also stating that the T-cell epitope polypeptide may comprise an 80-100% homologous sequence polypeptide. These disclosures do not clearly resolve whether the polypeptide recited in claim 1 itself is limited to the amino acid sequence represented by the specific SEQ ID NOs: listed or may be a longer peptide of that sequence.
Since a skilled artisan would not be reasonably apprised as to the metes and bounds of the claimed invention, instant claim 1 is rejected on the grounds of being indefinite. Claims 2-10 are also rejected since they depend from claim 1, but do not remedy these deficiencies of claim 1.
Claim 4 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The use of “and/or” in between the “host cell” and “cell” of claim 4 is unclear, as the use of “and” appears to allow one interpretation of a “host cell” which further comprises another “cell”. It is suggested this claim be amended to use only “or” so that it is clear these are alternative limitations.
For at least these reasons, the metes and bounds of claim 4 are unclear.
Claim 6 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 6 is drawn to, at lines 2-3, “RNA or DNA of an antigenic polypeptide of FMDV”. As a polypeptide does not comprise RNA or DNA, it is unclear what is being claimed in this instance. It is assumed that the claim was meant to be drawn to “RNA or DNA encoding an antigenic polypeptide of FMDV”. Further, claim 6 further limits claim 5, and is drawn to “further comprising a recombinant protein comprising a T -cell epitope polypeptide of FMDV, RNA or DNA encoding an antigenic polypeptide of FMDV, or a vector for expression of the antigenic polypeptide by an attenuated virus or bacterium.” The antecedent basis is unclear, as it is unclear if this antigenic polypeptide of FMDV is an additional peptide that is separate from the one listed in claim 1, or if they are meant to be the same peptide. Finally, it is unclear if only the virus is intended to be attenuated, or both the virus and bacterium.
For at least these reasons, the metes and bounds of claim 6 are unclear.
Claim 7 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 7 at line 2 is drawn to “a construct comprising the T-cell epitope polypeptide of FMDV”. However, the previous usage of “construct” is a nucleotide construct that encodes the polypeptide of FMDV, so it is unclear if this was meant to read on that previously recited construct or refers to a construct, such as a viral vector, wherein the polypeptide is comprises/present within the virion itself.
Further, the antecedent basis for all the alternative embodiments in the claim should be made clear with respect to the “T-cell epitope polypeptide” and it should be made clear if the “pharmaceutically acceptable auxiliary” applies to ALL alternative embodiments or only the last alternative embodiment. One suggestion is to rewrite the claim along the lines of the following:
“7. A pharmaceutical composition comprising:
(a) the T-cell epitope polypeptide of FMDV of claim 1;
(b) a construct encoding the T-cell epitope polypeptide of FMDV of claim 1;
(c) an isolated host cell comprising a construct encoding the T-cell epitope polypeptide of FMDV of claim 1; or
(d) the T-cell epitope polypeptide of FMDV of claim 1 and a pharmaceutically acceptable auxiliary.”
For at least these reasons, the metes and bounds of claim 7 are unclear.
Claim 8 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 8 is drawn to an antibody comprising the T-cell epitope polypeptide of FMDV of claim 1 and a nucleic acid molecule of an antigen-binding fragment of the antibody or a vector or host cell comprising the nucleic acid molecule. It is unclear what the metes and bounds of what is being claimed in this claim. For instance, it is unclear if the antibody binds to the T-cell epitope of the polypeptide of claim 1, if there is a random antibody of any shape, form, or fashion that is fused to the 18mer T cell epitope of claim 1. Further, the nucleic acid molecule references an “antigen-binding fragment of the antibody”, but the antigen target of said antibody has not been identified. The specification does not provide further clarity, as it appears as though the T cell epitopes are intended to induce stronger neutralizing antibodies in the vaccinated host (¶[0023]) and are not physically bound to an antibody. Further experiments appear to fuse a B cell epitope to four T cell epitopes (¶[0054]).
Additionally, the use of alternative language “or a vector or host cell comprising the nucleic acid molecule” renders the overall statutory subject matter and structure of the claim unclear. As presently written, the claim can reasonably be read as requiring the recited antibody itself to comprise, in addition to the T-cell epitope polypeptide, a nucleic acid molecule, a vector, or a host cell. Such a reading would encompass, for instance, an antibody comprising a host cell, which does not technically appear consistent with the ordinary structural relationship of these items. Alternatively, the claim may have been intended to separately claim an antibody, a nucleic acid, or a host cell comprising the nucleic acid or vector. However, the present claim language does not clearly establish these articles as separate alternatives. Therefore, from the wording of the claim and the guidance in the specification, it is unclear what is being claimed in instant claim 8.
For at least these reasons, the metes and bounds of claim 8 are unclear.
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art.
Claim 1 is drawn to a T-cell epitope polypeptide of foot and mouth disease virus (FMDV), the epitope polypeptide having an amino acid sequence represented by one of SEQ ID Nos: 1-11:
SEQ ID NO: 1: KGKPFNSKVIIATTNLYS;
SEQ ID NO: 2: PLQNVYQLVQEVIDRVEL;
SEQ ID NO: 3: VVMDDLGQNPDGKDFKYF;
SEQ ID NO: 4: YNQQTVVVMDDLGQNPDG;
SEQ ID NO: 5: GRTDSVWYCPPDPDHFDG;
SEQ ID NO: 6: RGKSGQGKSFLANVLAQA;
SEQ ID NO: 7: PDFNRLVSAFEELATGVK;
SEQ ID NO: 8: AIRTGLDEAKPWYKLIKL;
SEQ ID NO: 9: MSTKHGPDFNRLVSAFEE;
SEQ ID NO: 10: MLDGRTMTDSDYRVF; and
SEQ ID NO: 11: VLDEVIFSKHKGDTK.
Further limitations on the epitope polypeptide of claim 1 are that the T-cell polypeptide has an amino acid sequence represented by one of SEQ ID Nos: 3, 6 and 7 (claim 2);
Claim 3 is drawn to a construct comprising a nucleic acid molecule encoding the T-cell epitope polypeptide of FMDV of claim 1.
Claim 4 is drawn to an isolated host cell, comprising the construct of claim 3, or an isolated cell transformed or transfected by the construct.
Claim 5 is drawn to a composition comprising the T-cell epitope polypeptide of FMDV of claim 1 and a pharmaceutically acceptable vector or auxiliary.
Further limitations on the composition of claim 5 are wherein the composition is further comprising a recombinant protein comprising a T-cell epitope polypeptide of FMDV, RNA or DNA encoding an antigenic polypeptide of FMDV, or a vector for expression of the antigenic polypeptide by an attenuated virus or bacterium (claim 6).
Claim 7 is drawn to a pharmaceutical composition comprising:
(a) the T-cell epitope polypeptide of FMDV of claim 1;
(b) a construct encoding the T-cell epitope polypeptide of FMDV of claim 1;
(c) an isolated host cell comprising a construct encoding the T-cell epitope polypeptide of FMDV of claim 1; or
(d) the T-cell epitope polypeptide of FMDV of claim 1 and a pharmaceutically acceptable auxiliary.
Claim 8 is drawn to an antibody comprising the T-cell epitope polypeptide of FMDV of claim 1 and a nucleic acid molecule of an antigen-binding fragment of the antibody or a vector or host cell comprising the nucleic acid molecule.
Claim 9 is drawn to an immune composition comprising the T-cell epitope polypeptide of FMDV of claim 1 and an adjuvant.
Further limitations on the immune composition of claim 9 are wherein the composition is in the form of a vaccine, a detection reagent, or a biological diagnostic reagent (claim 10).
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.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claim 4 is rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101). It is suggested that claim 4 be amended to read on “An isolated host cell” in order to overcome this rejection.
Claims 1-7 are rejected under 35 U.S.C. 101 because the claimed invention is directed to foot-and-mouth disease virus (FMDV) proteins, nucleic acids, and virions without significantly more.
The claims recite a T-cell epitope polypeptide of FMDV having an amino acid sequence selected from SEQ ID NOs: 1-11. One of those embodiments is SEQ ID NO: 3, which is 100% identical to a naturally occurring sequence found in a FMDV polyprotein as evidenced by the teachings of Knowles et. al. (Knowles NJ, et. al. Polyprotein [Foot-and-mouth disease virus SAT 2]. GenBank: XMD96914.1. 01/12/2025.) SEQ ID NO: 3 is VVMDDLGQNPDGKDFKYF. Claim 2 expressly limits one of the alternatives of the T-cell epitope as SEQ ID NO: 3. Claims 3-4 are drawn to nucleic acid encoding said polypeptide and a host cell comprising said peptide, while claim 5-7 are drawn to a composition comprising said peptide and a pharmaceutically acceptable vector or auxiliary, wherein said composition may further comprise an additional RNA or DNA of an antigenic polypeptide of FMDV.
This judicial exception is not integrated into a practical application because, under Step 2A, Prong One, SEQ ID NO: 3 is a nature-based product that lacks markedly different characteristics from its naturally occurring counterpart. The amino acid sequence of SEQ ID NO: 3 occurs at 100% sequence identity as a contiguous portion of a naturally occurring FMDV polyprotein. The claims do not require any amino acid substitution, chemical modification, conjugation, altered terminus, or other structural modification that distinguishes the recited amino acid sequence from the corresponding naturally occurring FMDV sequence. Further, characterizing the sequence as a “T-cell epitope” does not impart a markedly different characteristic because recognition of the sequence by FMDV-responsive T cells is an innate property of the naturally occurring viral sequence rather than a characteristic produced by human intervention. Claim 3 encompasses a nucleic acid molecule which encodes said peptide, which reads on naturally-occurring viral nucleic acid sequences, and similarly does not require any structural or sequential change to the nucleic acid to impart a marked difference over the naturally occurring viral nucleic acid. Claim 4 recites a host cell which comprises the construct of claim 3, which, under broadest reasonable interpretation, reads on a host cell within a host subject that is naturally infected with the FMDV. Claims 5-7 recite compositions which comprise the epitope, the nucleic acid encoding said epitope, or a vector or construct encoding said epitope. The claim does not require any specific pharmaceutical reagent that structurally or functionally changes any of these elements, such as an adjuvant. The compositions do not require a specific dosage of any component, the use of a heterologous vector or construct to encode the nucleic acid, or require any other structural change to distinguish it from its naturally occurring counterpart. Therefore, claims 1-7, under broadest reasonable interpretation, all read upon naturally occurring products.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because, under Step 2A, Prong Two, the claims do not recite any additional elements that integrate the identified product-of-nature exceptions into a practical application. As discussed supra, the limitations in the instant claims do not require any structural or functional limitation to the components or compositions that require a structural or functional distinction from the naturally-occurring counterparts. Considered individually and as ordered combinations, these limitations do not impose a meaningful limit that integrates the product-of-nature exceptions into a practical application.
Under Step 2B, the claims likewise do not recite additional elements sufficient to amount to significantly more than the identified judicial exceptions. The recited characterization of the natural peptide as a T cell epitope merely describes an inherent property of the naturally occurring sequence. The broadly recited nucleic acid, host cell, pharmaceutical vector or auxiliary, and naturally occurring viral RNA or DNA do not require any inventive structural or functional relationship with the product-of-nature limitations. In particular, merely combining a naturally occurring peptide with a pharmaceutically acceptable auxiliary, without requiring any marked change in the characteristics of either component, does not provide an inventive concept beyond the nature-based products themselves.
Accordingly, claims 1-7 encompass nature-based products that lack markedly different characteristics from their naturally occurring counterparts. One suggestion is to incorporate structural limitations into the claims to distinguish the components from their naturally occurring counterparts, such as the use of heterologous tags, fusion proteins, detectable markers, or reagents which markedly change the natural product (e.g. adjuvants.) Applicant is additionally free to persuasively argue that the claims are drawn to patent-eligible subject matter.
Claim Rejections - 35 USC § 112(a); First Paragraph
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 3-4 and 7 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for isolated constructs or isolated host cells/isolated cells , does not reasonably provide enablement for non-isolated constructs, host cells, or cells in all contexts. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
The claim is directed broadly to “a construct, comprising a nucleic acid” and “a host cell” or “cell” without limitation as to form, environment, or method of use. As such, the claim encompasses the nucleic acid in a wide range of contexts, including incorporation into vectors, plasmids, artificial chromosomes (e.g. bacterial or yeast artificial chromosomes (BACs or YACs)), cosmids, prokaryotic and eukaryotic cells, and organismal systems (e.g. Bacteria and Archaea, Eukaryotes (including vertebrate and invertebrate animals, plants, and fungi), and viruses). Likewise, the “host cell” and “cell” can be incorporated into a wide range of contexts, such as prokaryotic and eukaryotic cells and organismal systems (e.g. Bacteria and Archaea, Eukaryotes (including vertebrate and invertebrate animals, plants, and fungi)).
The specification does not provide guidance sufficient to enable the use of the claimed nucleic acid or host cell across this full scope, including in complex biological systems where expression, stability, and functionality may vary depending on the host environment and delivery method.
Accordingly, undue experimentation would be required to determine how to make and use the claimed nucleic acid and host cell across the full scope of the claim. It is suggested that the claim be amended to read upon “an isolated construct, comprising a nucleic acid”, “an isolated host cell” , and “an isolated cell transformed…” [emphasis added] in order to overcome this rejection.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1, 3-7, and 9-10 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bellinzoni et. al. (US20190142926A1; Pub. 05/16/2019; hereafter “Bellinzoni”.)
The Prior Art
Bellinzoni teaches Peptide_L1, which is SEQ ID NO: 45, and is 100% identical in length and sequence to instant SEQ ID NO: 11 (Table 1; instant claim 1). Bellinzoni teaches FMDV epitopes include, but not limited to, the peptides described in Table 1, and one would recognize that the FMDV peptides encompass the Table 1 peptides as well as their variants, homologous sequences and/or functional analogues (¶[0071]). Bellinzoni teaches recombinant expression vectors and plasmids which express the FMDV peptides in eukaryotic cells (¶[0046]; instant claims 3-4). Bellinzoni teaches pharmaceutical combinations or formulations for inducing one or more immune responses and/or for enhancing effectiveness of vaccination in the host, wherein said formulations comprise carriers, emulsifiers, or molecular adjuvants (entire document; see abstract; ¶[0019]; instant claims 5-7, 9-10).
For at least these reasons, Bellinzoni teaches the limitations of instant claims 1, 3-7, and 9-10, and anticipates the invention encompassed by said claims.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-7 and 9-10 are rejected under 35 U.S.C. 103 as being unpatentable over Bogoch et. al. (US20090017052A1, Pub. 01/18/2008; hereafter “Bogoch”) in view of Liao et. al. (Liao YC, et. al. PLoS One. 2013 Dec 17;8(12):e84443.; hereafter “Liao”), in further view of Gutierrez et. al. (Gutiérrez AH, et. al. PLoS One. 2016 Jul 13;11(7):e0159237.; hereafter “Gutierrez”) and Collen et. al. (Collen T, et. al. Vet Immunol Immunopathol. 2002 Sep 10;87(3-4):235-8.; hereafter “Collen”).
The Prior Art
Bogoch teaches amino acid sequences of foot-and-mouth disease virus (FMDV) and teaches identification of shorter peptide sequences within known FMDV sequences for immunogenic, vaccine, diagnostic, therapeutic, and predictive purposes (entire document; see abstract; ¶[0069][0089-0090][0144][0123]; reference claims 71-72). Bogoch teaches that a replikin sequence may contain about 7 to about 50 amino acids and teaches the in silico identification of shorter peptide sequences from larger pathogen-derived amino acid sequences (¶[0005][0155][0197][0211][0249][0285-0286]). Bogoch teaches the analysis of publicly available FMDV amino acid sequences and identifies shorter FMDV-derived peptide sequences as preferred sequences for immunogenic compositions and vaccines (¶[0283-0305]). Bogoch teaches SEQ ID NO: 131, which comprises the complete amino acid sequence of instant SEQ ID NO: 1 at 100% identity (See ABSS sequence alignment .rapbm files for alignments against 12-010-027 sequences). Bogoch additionally teaches SEQ ID NO: 168, which comprises the complete amino acid sequence of instant SEQ ID NO: 6 at 100% identity. Bogoch also teaches SEQ ID NOs: 1556, 157, 285, 539, and 566, which comprise instant SEQ ID NO: 3 at 100% identity.
Bogoch teaches nucleic acid sequences which encode the peptides (¶[0192][0197-0199][0205][0286]; reference claim 32; instant claim 3). Bogoch teaches isolating the peptide from cells or tissues (¶[0197]; instant claim 4). Bogoch teaches immunogenic compositions comprising the peptides and wherein said compositions further comprise a pharmaceutically acceptable carrier (¶[0090]; instant claims 5, 7), wherein the immunogenic compositions may be vaccines that comprise a plurality of sequences from the same virus and additionally may comprise adjuvants (¶[0235]; instant claims 6, 9-10).
While Bogoch teaches shorter peptides of FMDV, and teaches shorter peptides which comprise instantly claimed sequences, such as SEQ ID NOs: 1 and 6, and teaches the sequences may be from about 7 to about 50 amino acids in length, the sequences of Bogoch are not exactly 18 amino acids in length and specifically comprise T-cell epitopes. However, arriving at such a length would be obvious to a skilled artisan whilst identifying T-cell epitopes, given the teachings of Liao, Gutierrez, and Collen.
Liao teaches an integrated bioinformatics approach specifically directed to identifying T-cell epitopes of swine viruses, including FMDV (entire document; see abstract.) Liao teaches that screening large panels of overlapping peptides spanning an entire viral polyprotein was known to facilitate detection of CTL epitopes but was costly and cumbersome, and provides a computational approach for identifying potential T-cell epitopes from known viral sequences (abstract). In particular, Liao teaches retrieving FMDV coding sequences, predicting proteasomal cleavage sites using NetChop, generating shorter linear peptides, and predicting peptide binding to swine leukocyte antigen (SLA) using NetMHCpan (p. 2, “Materials and Methods: Sequence collection and peptide analysis.”) Liao further teaches genome-wise scanning of FMDV sequences to identify conserved potential CTL epitopes for use in peptide vaccine design (abstract; p. 2, rt. Col., ¶1). Liao specifically identifies the sequence IIATTNLY within FMDV 2C protein as a predicted CTL epitope having complete conservation in the FMDV sequences evaluated and predicted binding to SLA-1*0601 (Table 1). The Liao peptide is completely contained within instant SEQ ID NO: 1. Liao therefore provides a specific teaching directing one of ordinary skill in the art to the same FMDV 2C sequence region encompassed by instant SEQ ID NO: 1 and teaches that a sequence within the claimed 18 amino acid peptide constitutes a candidate porcine T cell epitope.
Gutierrez further teaches the use of immunoinformatics to identify class I and II T cell epitopes from known swine viral protein sequences based on predicted binding to SLA alleles (entire document; see abstract.) Gutierrez teaches for SLA Class II epitopes, identification of shorter predicted SLA-binding cores can be done using EpiAssembler to construct conserved and immunogenic SLA-DRB1-restricted peptide sequences having lengths of 16-25 amino acids and contained predicted 9-amino acid SLA class II binding frames (p. 3, “Conservation analysis” and “T cell epitope prediction” to p. 4, “Construction of immunogenic consensus sequences”). Gutierrez therefore teaches that, when a shorter T cell/SLA-binding region has been identified within a known viral sequence, it was conventional to select additional flanking amino acids from the known viral protein to produce a longer T cell epitope peptide within a range that expressly encompasses an 18-amino acid peptide.
Collen further teaches experimental mapping of viral CD4+ T-cell epitopes using overlapping synthetic 18 amino acid peptides corresponding to known viral protein sequences (entire document; see abstract.) Collen teaches screening overlapping 18-mer peptides to identify regions containing CD4+ T-cell determinants and subsequently using shorter overlapping and terminally truncated peptides to define minimal stimulatory sequences (Table 1; pp. 236-7, “3. Fine specificity of CD4+ T cell response to E2 and NS3” and “4. Identification of minimal stimulatory sequences”). Collen therefore establishes that an 18-amino acid peptide was a conventional peptide length for identifying MHC class II/CD4+ T cell epitopes within known viral protein sequences.
Accordingly, selection of an 18-mer sequence of SEQ ID NO: 1 or SEQ ID NO: 6 from the FMDV sequences taught by Bogoch would have amounted to no more than application of known T cell epitope identification and peptide mapping techniques, such as those taught by Gutierrez, Collen, and Liao, to a known FMDV sequence, with the amino acid sequence itself already being present, at least with SEQ ID NO: 1, contiguously over the prior art. Therefore, the subject matter of instant claims 1 and 2 would have been obvious over Bogoch in view of Liao, Gutierrez, and Collen.
It would have been obvious to one of ordinary skill in the art to modify the FMDV-derived polypeptides taught by Bogoch in order to identify and select shorter 18mer T cell epitope polypeptides contained within the known FMDV sequences, thereby obtaining FMDV peptides useful for eliciting or evaluating T cell immune responses. One would have been motivated to do so, given the suggestion by Liao that known FMDV protein sequences could be computationally analyzed to identify conserved SLA-binding T cell epitopes for use as peptide antigens. There would have been a reasonable expectation of success, given the knowledge that predicted SLA-binding cores within known viral proteins could be incorporated into longer 16-25 amino acid T cell epitope peptides, as taught by Gutierrez, and also give the knowledge that overlapping 18mer peptides derived from known viral protein sequences were conventionally used to identify CD4+ T cell determinants, as taught by Collen. Thus, the invention was prima facie obvious to one of ordinary skill at the time the invention was made.
Conclusion
No claims are allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure and is listed below.
US20150306203A1. Teaches FMDV T helper epitope cluster peptides derived from FMDV proteins of approximately 10-70 amino acids. Not utilized as rejection would be redundant to those set forth supra.
US20190134183A1. Teaches FMDV proteins, peptides, fragments, and epitopes capable of eliciting cellular and humoral immune responses in pigs and other animals. Not utilized as rejection would be redundant to those set forth supra.
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/RACHEL B GILL/
Primary Examiner, Art Unit 1671
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