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 with traverse of Group I (claims 1-13 and 19) and the species of mutant ApxAIA , ApxAIIA, and ApxAIIIA proteins corresponding to SEQ ID NOs: 4-6 in the reply filed on 9 Sep 2025 is acknowledged. The traversal is on the ground(s) that the Xu reference describes synthetic constructs containing fragments of the Apx toxins, but the inventors allegedly provide for the first time a single microorganism that expresses all three of ApxIA, ApxIIA and ApxIIIA proteins, not just short fragments of these proteins.
This is not found persuasive because applicant is arguing a feature (presence of the nucleic acids in a single bacteria) that is not part of the shared technical feature (nucleic acids encoding the genes, note that claim 20 only claims a vector and does not include a bacteria). The specification admits that “a series of constructs each expressing individual ApxA toxins” (i.e. set of vectors) was known in the art at the time of filing [0083].
Also, this is not found persuasive because applicant is arguing a feature (the presence of the full length Apx sequence) that is not claimed. Claim 1 does not require that the full length of the protein be present in the bacteria, and this is made explicit in dependent claim 4 and other dependent claims that claim includes “fragment[s] thereof”. Also applicant’s statement that the synthetic construct “bear[s] minimal resemblance to any of the wildtype ApxA toxins” is disputed in view of Xu’s choice to use the names ApxIA, ApxIIA and ApxIIIA for the fragments (as cited in the Restriction, showing that one of ordinary skill in the art considers them ApxIA, ApxIIA and ApxIIIA proteins) and the evidence that these proteins are able to generate protective immunity by sharing the same antigenic structure as the wild-type proteins (see Xu abstract).
Finally, the argument is also not found persuasive because it does not argue the other grounds for lack of unity, which is that the claims present 3 different products and 4 different methods of using the products, contrary to the requirements of 37 CFR 1.475(b).
The requirement is still deemed proper and is therefore made FINAL.
Upon further search and consideration, the species election is expanded to ApxIA proteins with substitutions or deletions at both K560 and K686, ApxIIA proteins with substitutions or deletions at both K557 and N687, and ApxIIIA proteins with substitutions or deletions at both K571 and K702, and claim 6 is rejoined. SEQ ID NO: 4 was not disclosed in the art at the time of filing. The corresponding wild-type sequence SEQ ID NO: 1 was also not used in a reference at the time of filing, and there is not enough of a motivation to choose this particular ApxIA protein sequence over other more widely-used ApxIA protein sequences and to specifically make an alanine substitution over the other potential options.
Also, upon further search and consideration, the requirement for an election between the inventions of live vaccines and inactivated vaccines (Groups 1-2) are withdrawn and claim 14 is rejoined.
In view of the above noted withdrawal of the restriction requirement, applicant is advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application. Once a restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Claim Status
The amended claim set filed 26 Sep 2023 is acknowledged. Claims 1-20 are currently pending. Of those, claims 3, 5-6, 8, 10-12, and 15-20 are currently amended, and no claims are new. Claims 15-18, and 20 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. Applicant timely traversed the restriction (election) requirement in the reply filed on 9 Sep 2025. No claims are cancelled. Claims 1-14, and 19 will be examined on the merits herein.
Priority
Applicant’s priority claim to foreign application GB2011902.0 (filed 30 July 2020) and PCT/IB2021/000549 (filed 30 July 2021) is acknowledged. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. The effective filing date for the claims under examination is 20 July 2020.
Information Disclosure Statement
The information disclosure statement filed 27 Jan 2023 fails to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. Specifically, foreign patent document #5 was not submitted. Accordingly, the information disclosure statement has been considered by the examiner, except for the struck-through reference. A signed copy of the statement is attached with this action.
Specification
References to the specification in this action will use the paragraph numbers from the Pre-Grant Publication US-20230322870-A1 (PTO-892) in order to ensure the record remains clear even if a new specification is filed with different page and line numbers.
Claim Interpretation
Regarding the sequences and species election, SEQ ID NO: 4 is SEQ ID NO: 1 comprising K560A (the K at position 560 is replaced with an A) and K686A mutations, SEQ ID NO: 5 is SEQ ID NO: 2 comprising K557A and N687A mutations, and SEQ ID NO: 6 is SEQ ID NO: 3 with K571A and K702A mutations.
Regarding claim 1, the protein names ApxIA, ApxIIA, and ApxIIIA are each interpreted as including fragments named after the proteins, based on dependent claims such as claim 4 that explicitly claim that the proteins may be fragments.
Regarding claims 5, 8-11, 13, and 19, each claim recites “preferable” limitations. Per MPEP 2111.04: “Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed, or by claim language that does not limit a claim to a particular structure.” As the preferable limitations are optional, they are given no weight.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2 and 9-11 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Regarding claim 2, the claim recites “the nucleic acid sequences of (a), (b) and/or (c) are: (i) comprised within the genome of the microorganism; or (ii) comprised extra-chromosomally.”. This includes all possible options within the same claim because the nucleic acids must either be in the genome/chromosome or they must be outside of it. So each of (i-ii) independently limits claim 1, but the combination of both in the same claim does not further limit claim 1.
Regarding claims 9-11, each claim recites a limitation on “the A. pleuropneumoniae strain”. However, these limitations have antecedent basis in the optional limitation of claim 8 “preferably an Actinobacillus pleuropneumoniae strain”. As the optional limitation does not limit claim 8, the further limitations of the optional limitation in claims 9-11 also do not limit claim 8. In the interest of compact prosecution, features in these claims will be pointed out if they are present in the art.
Claim Rejections - 35 USC § 112(b)
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 5 and 19 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 5 recites the limitation "each amino acid not susceptible to acylation" in (a). There is insufficient antecedent basis for this limitation in the claim. The term “an amino acid not susceptible to acylation” was defined in claim 4, but claim 5 was amended so it does not depend from claim 4.
Regarding claim 19, the claim recites “An expression system comprising a microorganism of claim 1 further comprising at least one additional nucleic acid which encodes one or more additional swine pathogen antigen, wherein preferably the at least one additional nucleic acid is comprised within the genome of the microorganism”, but one of ordinary skill in the art would not be able to determine what is claimed in an “expression system” other than the microorganism itself (note that “comprises” includes other, undisclosed elements). See MPEP 2173.05(a): “The meaning of every term used in a claim should be apparent from the prior art or from the specification and drawings at the time the application is filed. Claim language may not be "ambiguous, vague, incoherent, opaque, or otherwise unclear in describing and defining the claimed invention." In re Packard, 751 F.3d 1307, 1311, 110 USPQ2d 1785, 1787 (Fed. Cir. 2014).” The specification does not define the term “expression system”. The section beginning [0180] discusses expression systems states “The microorganisms, nucleic acids and/or vectors of the invention may be used as a means to express one or more additional antigen from a swine pathogen. Thus, the invention provides an expression system for antigens from other swine pathogens.” Therefore, the specification does not provide guidance on what is claimed in an expression system other than the microorganism and the nucleic acids and/or vectors that are within the microorganism. The art also does not provide guidance as “expression system” is not a term with a well-known, unambiguous definition in the art at the time of filing. Neither the specification nor the art define the term, so one of ordinary skill in the art would not be able to determine what components, other than the microorganism itself, are included in claim 19.
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 1-10, 12-14, and 19 are rejected under 35 U.S.C. 103 as being unpatentable over MacInnes et al. (US-6019984-A, filed 1996, published 2000; hereafter MacInnes; PTO-892) in view of Hur and Lee (2013; hereafter Hur; PTO-892), Segers et al. (US-6770275-B1, filed 1997 and published 2004; hereafter Segers; PTO-892), and Oh and Yoo (2017; hereafter Oh; PTO-892).
Regarding claims 1, 12, and 19, MacInnes teaches “a bacterial preparation comprising one or more isolated and purified strain of a microorganism which produces one or more RTX toxins, and which strain has at least one RTX toxin which is substantially cell-associated” (quote from col. 3 ln. 15-19, see also claims 1 and 5), and teaches that the RTX toxins can be produced by selecting strains that produce one or more RTX toxins or by using gene transfer techniques to create the strain (col. 3 ln. 43-52, col. 9 ln. 10-15), and teaches that the bacteria can be modified to include other genes including other toxins that would increase the immunogenicity of the bacterial preparation or induce a response against other antigens (col. 9 ln. 17-19, col. 11 ln. 7-11).
MacInnes teaches that the three RTX toxins in A. pleuropneumoniae are ApxIA, ApxIIA, and ApxIIIA (col. 1 ln. 48-55), but “No A. pleuropneumoniae strains have been identified which produce all three toxins” (col. 1 ln. 60-61). MacInnes teaches that “RTX toxins are also generally characterized by the organization of their operon. The operon generally consists of the following four genes: an activator gene (designated "C"), a structural toxin gene (designated "A"), and two secretion genes (designated "BD").” (col. 6 ln. 26-30).
MacInnes also teaches bacterial preparations comprising all three RTX proteins by teaching that one could use two or more isolated and purified strains of A. pleuropneumoniae which collectively have ApxI, ApxII and ApxIII which are substantially cell-associated (col. 3 ln. 31-34). MacInnes teaches that the toxins can be produced in a “cell associated” manner by several methods, such as treating with a substance that interferes with toxin secretion (col. 10 ln. 22-26) or by making genetic changes to the bacteria such as inactivation or deletion of the B and/or D transport genes (col. 10 ln. 63- col. 11 ln. 5).
Regarding claim 2, the Apx toxins that are naturally present are located at the normal chromosomal locus, and MacInnes teaches plasmid vectors can be used for genetic manipulation (col. 11 ln. 58-61).
Regarding claims 3-7, MacInnes teaches the sequences of ApxIA, ApxIIA, and ApxIIIA in Figures 1 and 2. Alignments against instant SEQ ID NOs: 1-3 are shown below in Alignments 1-3. The proteins all are at least 90% homologous to SEQ ID NOs: 1-3.
Regarding claims 8-9, MacInnes teaches that the bacteria can be A. pleuropneumoniae serotype 1 (col. 8 ln. 43-57) and teaches the use of this serotype in the Examples (col. 16 ln. 16).
Regarding claim 10, the inactivation of deletion to the B and/or D transport genes modifies an additional gene.
Regarding claims 12-14, the bacteria can be used as vaccines, either by being inactivated or in a live attenuated form (col. 13 ln. 54-59, col. 14 ln. 7-24). The vaccine may have an immunologically acceptable carrier or diluent and may comprise adjuvants (col. 14 ln. 65 – col. 15 ln. 10).
Regarding claim 19, the A. pleuropneumoniae attenuated strain further comprises the rest of the genome which encodes additional A. pleuropneumoniae antigens. For example, MacInnes teaches that outer membrane proteins (OMPs) are known in the art as protective antigens for a vaccine (col. 2 ln. 45-48).
MacInnes does not explicitly teach a single microorganism comprising all three Apx toxins, as in claim 1 and dependent claims. MacInnes does not teach inactive ApxIA, ApxIIA, and ApxIIIA with common antigenic cross-reactivity with wild-type proteins, as in claim 3, or specifically with the sequences of SEQ ID NOs: 1-3, as in claim 7. MacInnes does not teach making substitutions or deletions to ApxIA at K560 and K686, ApxIIA at K557 and N687, or ApxIIIA at K571 and K702, as in claims 4-6.
Regarding claim 1, Hur teaches “the Actinobacillus pleuropneumoniae antigens ApxIA, ApxIIA, ApxIIIA and OmpA were expressed in an attenuated strain of Salmonella (ΔlonΔcpxRΔasd)” (Abstract). Specifically, teach gene was inserted into a plasmid and separately electroporated into the attenuated strain (pg. 88 col. 1 par. 4), and mice were immunized using “approximately 1×105 CFU/ml in 10 μl of an equal-volume mixture of the four constructs” (pg. 88 col. 1 par. 4). Regarding claim 2, the genes are on a plasmid (i.e. extra-chromosomal). Regarding claim 3, the genes are wild-type ApxIA, ApxIIA, and ApxIIIA because no mutations are disclosed. Regarding claims 12-13, the bacteria in the vaccine are necessarily present in a carrier or diluent in order to be in a liquid form (note the use of μl as a measurement), and the OmpA expressing strain can be considered an adjuvant. The use of colony-forming units (CFU) as a unit of measurement requires that the vaccine is live because dead bacteria do not form colonies. Regarding claim 19, OmpA is an additional swine pathogen antigen (pg. 87 col. 1 par. 2).
Regarding claims 1-3, Segers confirms that the toxin gene (A) requires an activator gene (C) for activation (col. 2 ln. 21-30) and teaches that live attenuated vaccines have advantages over non-live vaccine types because the live vaccine is self-replicating so it can be administered in lower doses, and it mimics the natural infection in triggering more than only B-cell immunity (col. 2 ln. 57 to col. 3 ln. 55). To achieve this goal, Segers teaches using bacteria that produce the RTX-A toxin in a non-activated form, and reduces this to practice in A. pleuropneumoniae by deleting the ApxIC gene (Example 2) or both the ApxIC and ApxIIC genes (Example 3) (i.e. an additional gene is modified, see claim 10). In the double deletion, the strain still produced ApxIA and ApxIIA (col. 12 ln. 39-44), but the deletions led to strong or complete losses of hemolytic activity (col. 12 ln. 1-7). Segers teaches that the double deletion mutant “MBHPP147” (defined in the title of Table 2) “can be used as a live vaccine which confers significant homologous and heterologous protection.” (col. 14 ln. 6-8). Segers also teaches: “Alternatively, it is possible to modify the target-site of the RTX Activator protein, i.e. the acylation-site at the RTX-toxin. If this site is modified to the extent that acylation is decreased or absent, this also results in the production of an RTX-toxin in a non-activated form. The acylation site can easily be mutated using recombinant DNA techniques. Mutation can e.g. be obtained by deletion of a restriction fragment that comprises the acylation site, or by site-directed mutagenesis of the acylation site.” (col. 5 ln. 7-14). Regarding claim 2, the ApxIA and ApxIIA are located at the normal chromosomal locus. Regarding claims 3 and 7, Segers teaches that the bacteria produce ApxIA and ApxIIA that is inactive (because the proteins are not activated). There is no evidence of record that the inactive ApxIA and ApxIIA taught by Segers is not capable of cross-reacting with the wild-type proteins having SEQ ID NOs: 1-3 as in claim 7. Regarding claim 8-9, the microorganism is the Actinobacillus strain A. pleuropnuemoniae that express endogenous ApxIA and ApxIIA and is derived by modifying a serotype 1 strain (Example 3). Regarding claims 12-13, the bacteria can be used in a live attenuated vaccine (col. 6 ln. 44-46, Example 3). Segers teaches that the vaccine also comprises a pharmaceutically acceptable carrier or diluent such as water, culture fluid, or physiological salt (col. 6 ln. 58-65) and optionally an adjuvant may be added to the vaccine (col. 7 ln. 5-6). Regarding claim 19, the A. pleuropneumoniae attenuated strain further comprises the rest of the genome which encodes additional A. pleuropneumoniae antigens (col. 4 ln. 28-30). For example, Segers teaches that hemolysins, cytotoxins, and outer membrane proteins could be used as antigens in a vaccine (col. 2 ln. 61-63). Segers also teaches that the vaccine may be modified to additionally carry genetic information encoding one or more additional antigens from other bacteria (col. 7 ln. 36-43).
Regarding claims 4-6, Oh teaches that the acylation modification sites for ApxIA are at K560 and K686, the acylation modification sites for ApxIIA are at K557 and N687, and the acylation modification sites for ApxIIIA are at K571 and K702 (Figure 2B).
One of ordinary skill in the art at the time of filing would consider it prima facie obvious to improve the MacInnes A. pleuropneumoniae bacteria comprising cell-wall associated ApxIA and ApxIIA by expressing recombinant ApxIIIA as taught in Hur as the specific example of the other toxin that MacInnes teaches can be expressed, thereby arriving at the invention for claims 1-2, 7-10, 12-14, and 19, because both MacInnes and Hur teach a vaccine comprising all three Apx toxins, and because MacInnes teaches that additional antigens can be expressed in general while Hur provides the specific methodological details to recombinantly express ApxIIIA. Therefore, combining the three Apx toxins in a single strain would be desirable to improve the immune response relative to a two-toxin vaccine and to result in a single-strain vaccine that is easier to prepare and administer by removing the step of separately growing and mixing multiple different strains. See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.”
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that applying a known technique to a known device, method or product ready for improvement is obvious because a particular known technique is recognized as part of the ordinary capabilities of one skilled in the art. In the instant case, MacInnes contains a “base” product of a live attenuated vaccine strain comprising ApxIA and ApxIIA; and Hu contains a similar product wherein the technique of recombinantly expressing ApxIIIA is taught as advantageous in order to produce a vaccine strain that can raise an immune response against ApxIIIA. Thus, one of ordinary skill in the art would have recognized that applying the known technique taught by Hu would have yielded predictable results (i.e. the same advantages) and an improved system.
As on optional additional modification, one of ordinary skill in the art at the time of filing would consider it prima facie obvious to improve the Apx toxins being expressed in the MacInnes strain(s) by inactivating the toxins by deleting or substituting the acylation sites as taught by Segers and using the specific acylation site amino acids taught by Oh, thereby further arriving at the invention for claims 3-7, because a live attenuated vaccine strain producing an inactive toxin would still be effective, as shown by Segers, while being safer because the toxins cannot perform their toxic activities. Therefore, following the strategy of Segers to delete or substitute the acylated amino acids disclosed in Oh would be desirable to make a safer live attenuated strain with inactive Apx toxin proteins. See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.” The resulting proteins would be inactive proteins which have common antigenic cross-reactivity with SEQ ID NOs: 1-3 or at least the variant wild-type sequences taught in MacInnes in the absence of any evidence to the contrary and in view of the minor modification being made (substitution or deletion of a single amino acid).
The modifications to express ApxIIIA in the live attenuated strain of MacInnes and to delete or substitute the amino acids could be performed with a reasonable expectation of success because the required genetic modification techniques were well known at the time of filing. Note that MacInnes and Segers both explicitly teach that the bacteria can be modified to express new genes, even though they were both filed more than 20 years before the effective filing date, and that MacInnes specifically teaches the wild-type sequences of the Apx toxins, and that Oh specifically teaches the locations for modification.
Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
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Alignment 1: Alignment of instant SEQ ID NO: 1 and SEQ ID NO: 2 of MacInnes. The sequences have 97.9% identity.
Alignment 2: Alignment of instant SEQ ID NO: 2 and SEQ ID NO: 8 of MacInnes
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. The sequences have 100% identity.
Alignment 3: Alignment of instant SEQ ID NO: 3 and SEQ ID NO: 11 of MacInnes
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. The sequences
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMELIA NICOLE DICKENS whose telephone number is (571)272-0381. The examiner can normally be reached M-R 8:30-4:30, and every other F 8:30-4:30 (EDT/EST).
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/AMELIA NICOLE DICKENS/Examiner, Art Unit 1645
/VANESSA L. FORD/Supervisory Patent Examiner, Art Unit 1674