The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 8-13-2025 has been entered.
The amendment filed on 8-13-2025 is acknowledged. Claims 1 and 12 have been amended. Claims 15-24 have been added. Claims 1-24 are pending. Claims 9-14 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 1-8 and 15-24 are currently under examination.
Claim Rejections Maintained
35 USC § 112
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.
The rejection of claim 7 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is maintained for reasons of record. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Applicant argues:
1. The polypeptide has been amended to further define that the amino acid provided, i.e. amino acid residues 28-619 of SEQIDNO: 13, can be encoded by a DNA sequence, The claim amendment limits the number of protein variants as the polypeptide, as now defined, is comprised of 22 proteinogenic amino acids.
2. Claim 1 as currently amended provides structural description of the invention via chemical structure in the form of sequence listing of specific amino acid residues and while the claim further provides for variants of the defined sequence, the number of variants is limited.
That is, the number of variants may be large, but that number is finite as each substitution can only be made with the other 21. amino acid residues.
3. Any sequence variant covered by claim 1can be output by a computer algorithm, which for each defined sequence length calculates the maximum number of substitutions and the generates as output an exhaustive list of sequence variants of SEQ ID NO: 13 covered by the claim language.
With regard to Points 1-3, the amendment to claim 1 is insufficient to overcome the rejection of record as the correlation between structure and function is still lacking. As noted by Applicant every residue can be substituted with 21 other proteinogenic amino acids therefore encompass 1.05 x 10156 substitution mutants. Given the instant claims encompass insertional and deletion mutants, as well as fragments thereof, the limited disclosure set forth in the Examples are not representative of the genus of polypeptides capable of inducing a protective adaptive humoral or cellular response against S. aureus. Moreover, while the skilled artisan may be able to envision the variants encompassed by the instant claims, they would not be able to predict which (if any) of said variants would be able to induce a protective adaptive humoral or cellular immune response against S. aureus in a mammal.
As outlined previously, the rejected claim is drawn to compositions that elicit a protective adaptive immune response or protective immune response against Staphylococcus aureus comprising administering to the subject an effective amount of a polypeptide having at least 80% sequence identity to residues 28-619 of SEQ ID NO:13 or at least 80% sequence identity to a fragment of the polypeptide of SEQ ID NO:13 comprising at least 35 contiguous amino acids wherein said polypeptide lacks residues 1-21 of SEQ ID NO:13. Moreover, the genus of proteins at least 80% identical to residues 28-619 of SEQ ID NO: 13 is large and is composed of structurally distinct variants. These includes variants of SEQ ID NO: 13 that are generated by amino acid substitutions, deletions and insertions of one or more amino acids keeping in mind that for insertions and substitutions there are 22 or 21 amino acids (respectively) to choose from.
The specification discloses SEQ ID NO: 13 corresponding to the SAR2723 protein. But is silent with regard to any of its immunological characteristics. Consequently, the specification as filed does not describe the common structure of the genus of fragments and variants of the SAR2723 protein such as the immunoepitope(s) that are critical for eliciting a given immune response. This description of such a common structure is important such that one of skill in the art would appreciate that as of the filing date Applicants have fully described the variants encompassed by the instant claims that are critical for eliciting a given immune response and; thus were in possession of the full scope of the instant invention.
Furthermore, description of the immunoepitope(s) of residues 28-619 of SEQ ID NO: 13 of the time of filing, does not allow one of skill in the art to envision immunoepitopes of a polypeptide with up to 20% of the amino acid sequence variation to residues 28-619 of SEQ ID NO: 13 (sequences which can be mutated via deletion(s), substitution(s), insertions(s) or combinations thereof) or fragments thereof that which are able to raise any of the claimed immune responses.
The art recognizes that defining epitopes is not easy and there is a confusing divergence between the textbook definition of epitope and the definition that is in use in published descriptions of experimental investigations and that epitopes must be empirically determined (Greenspan et al, Nature Biotechnology 17:936-937, 1999). Antibody epitopes are characterized by the art as either continuous or discontinuous (see pages 23-25, 27-33, Harlow et al., Antibodies A Laboratory Manual, Cold Spring Harbor Laboratory Press Inc., 1988). T cell epitopes are continuous peptide fragments of a polypeptide or antigen that have been processed by an accessory cell. Colman et al. (Research in Immunology 145: 33-36, 1994, p.33 column 2, p. 35 column 1) disclose that a single amino acid change in an antigen can effectively abolish the interaction with an antibody entirely and that a very conservative amino acid substitution may abolish antibody binding and a non-conservative amino substitution may have little effect in antibody binding. This underlies the importance of the description of the immunoepitopes that are protective and which and where and how many changes can the immunoepitopes tolerate and still retain the ability to raise an immune response against any Staphylococcus bacterium. Houghten et al. (New Approaches to Immunization, Vaccines 86, Cold Spring Harbor Laboratory, p. 21-25, 1986) taught the criticality of individual amino acid residues and their positions in peptide antigen-antibody interactions. Houghten et al state (see page 24): "One could expect point mutations in the protein antigen to cause varying degrees of loss of protection, depending on the relative importance of the binding interaction of the altered residue. A protein having multiple antigenic sites, multiple point mutations, or accumulated point mutations at key residues could create a new antigen that is precipitously or progressively unrecognizable by any of the antibodies in the polyclonal pool.
Even though one could screen for said variants of SEQ ID NO:13 that elicit a given immune response, the courts have held that possession of a genus may not be shown by merely describing how to obtain members of the claimed genus or how to identify their common structural features. The written description requirement is separate and distinct from the enablement requirement (See also Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 920-23, 69 USPQ2d 1886, 1890-93 (Fed. Cir. 2004) and adequate written description requires more than a mere reference to a potential method for identifying candidate polypeptides. The purpose of the written description requirement is broader than to merely explain how to ‘make and use’ [the invention] Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1560, 19 USPQ2d 1111, 1114 (Fed. Cir. 1991). The disclosure of only one member of the genus to which the claims are drawn is insufficient to describe the large and variant genus of proteins the scope of which is set forth above. In such an unpredictable art, as set forth supra, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See Noelle v Lederman. 355 F. 3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) and In re Alonso (Fed. Cir. 2008-1079).
Moreover, the instant claim is drawn to compositions that elicit a protective immune response against Staphylococcus aureus (i.e. vaccines). To adequately describe the genus of vaccines, Applicant must adequately describe the immunoepitopes within the SAR2723 polypeptide that induce a protective immune response against Staphylococcus aureus. The specification, however, does not disclose distinguishing and identifying features of a representative number of members of the genus of vaccines to which the claims are drawn, such as a correlation between the structure of the variant SAR2723 polypeptide (or fragments thereof) and its recited function (inducing a protective immune response), so that the skilled artisan could immediately envision, or recognize at least a substantial number of members of the claimed genus of antibodies. Moreover, the specification fails to disclose which amino acid residues in said domain are essential for antibody binding, or which amino acids might be added, replaced or deleted so that the resultant domain peptide retains the binding specificity of its parent, or by which other amino acids the essential amino acids might be replaced so that the resultant peptide retains the binding specificity of its parent. Therefore, the specification fails to adequately describe at least a substantial number of members of the genus of antibodies to which the claims refer; and accordingly the specification fails to adequately describe at least a substantial number of members of the claimed genus of vaccines. The term “vaccinate” is defined as the use of a specific antigen to induce protective immunity to infection or disease induction. The specification does not provide substantive evidence that the claimed vaccines are capable of inducing protective immunity. This demonstration is required for the skilled artisan to be able to use the claimed vaccines for their intended purpose of preventing infections. Without this demonstration, the skilled artisan would not be able to reasonably predict the outcome of the administration of the claimed vaccines, i.e. would not be able to accurately predict if protective immunity has been induced. The ability to reasonably predict the capacity of a single bacterial immunogen to induce protective immunity from in vitro antibody reactivity studies is problematic. Ellis (Vaccines, W.B. Saunders Company, Chapter 29, 1988, pages 568-574) exemplifies this problem in the recitation that "the key to the problem (of vaccine development) is the identification of the protein component of a virus or microbial pathogen that itself can elicit the production of protective antibodies"(page 572, second full paragraph). Unfortunately, the art is replete with instances where even well characterized antigens that induce an in vitro neutralizing antibody response fail to elicit in vivo protective immunity. See Boslego et al (Vaccines and Immunotherapy, 1991, Chapter 17), wherein a single gonococcal pillin protein fails to elicit protective immunity even though a high level of serum antibody response is induced (page 212, bottom of column 2). Accordingly, the art indicates that it would require empirical testing to formulate and use a successful vaccine without the prior demonstration of vaccine efficacy.
MPEP § 2163.02 states, “[a]n objective standard for determining compliance with the written description requirement is, 'does the description clearly allow persons of ordinary skill in the art to recognize that he or she invented what is claimed' ”. The courts have decided:
The purpose of the “written description” requirement is broader than to merely explain how to “make and use”; the applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the “written description” inquiry, whatever is now claimed.
See Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Federal Circuit, 1991). Furthermore, the written description provision of 35 USC § 112 is severable from its enablement provision; and adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
MPEP 2163.02 further states, “[p]ossession may be shown in a variety of ways including description of an actual reduction to practice, or by showing the invention was 'ready for patenting' such as by disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention” See, e.g., Pfaff v. Wells Elecs., Inc., 525 U.S. 55, 68, 119 S.Ct. 304, 312, 48 USPQ2d 1641, 1647 (1998); Regents of the Univ. of Cal. v. Eli Lilly, 119 F.3d 1559, 1568, 43 USPQ2d 1398, 1406 (Fed. Cir. 1997); Amgen, Inc. v. Chugai Pharm., 927 F.2d 1200, 1206, 18 USPQ2d 1016, 1021 (Fed. Cir. 1991) (one must define a compound by "whatever characteristics sufficiently distinguish it"). Moreover, because the claims encompass a genus of variant species, an adequate written description of the claimed invention must include sufficient description of at least a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics sufficient to show that Applicant was in possession of the claimed genus. However, factual evidence of an actual reduction to practice has not been disclosed by Applicant in the specification; nor has Applicant shown the invention was “ready for patenting” by disclosure of drawings or structural chemical formulas that show that the invention was complete; nor has Applicant described distinguishing identifying characteristics sufficient to show that Applicant were in possession of the claimed invention at the time the application was filed.
Additionally, MPEP 2163 states:
"A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed." In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004)”
And:
For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See, e.g., Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are "representative of the full variety or scope of the genus," or by the establishment of "a reasonable structure-function correlation." Such correlations may be established "by the inventor as described in the specification," or they may be "known in the art at the time of the filing date." See AbbVie, 759 F.3d at 1300-01, 111 USPQ2d 1780, 1790-91 (Fed. Cir. 2014) (Holding that claims to all human antibodies that bind IL-12 with a particular binding affinity rate constant (i.e., koff) were not adequately supported by a specification describing only a single type of human antibody having the claimed features because the disclosed antibody was not representative of other types of antibodies in the claimed genus, as demonstrated by the fact that other disclosed antibodies had different types of heavy and light chains, and shared only a 50% sequence similarity in their variable regions with the disclosed antibodies.).
As evidenced by the teachings of Skolnick et al., the art is unpredictable. Skolnick et al. (Trends in Biotechnology 18: 34-39, 2000) discloses the skilled artisan is well aware that assigning functional activities for any particular protein or protein family based upon sequence homology is inaccurate, in part because of the multifunctional nature of proteins (see, e.g., the abstract; and page 34, Sequence-based approaches to function prediction). Even in situations where there is some confidence of a similar overall structure between two proteins, only experimental research can confirm the artisan's best guess as to the function of the structurally related protein (see, in particular, the abstract and Box 2). Thus, one skilled in the art would not accept the assertion, which is based only upon an observed similarity in amino acid sequence that a variant of a given polypeptide would necessarily have a given immunological property. The instant specification has failed to teach or disclose vaccine compositions comprising the SAR2723 protein (or variants and fragments thereof) that are protective against infections caused by Staphylococcus aureus. The specification fails to teach or disclose data that demonstrates that the claimed vaccines can provide protection against infections caused by Staphylococcus aureus. There is no disclosure of subjects that have been immunized with the claimed vaccines nor is there a disclosure of challenge studies that have been conducted to establish the claimed vaccines’ ability to provide protection against S. aureus infections. The specification is limited to the ability of a fragment of SAR2723 (residues 28-619 of SEQ ID NO:13) which merely increases the survival if vaccinated mice. Consequently, there is no correlation between structure and function as required by the Written Description requirement.
Therefore, because the art is unpredictable, in accordance with the MPEP and current case law, the description of claimed vaccines is not deemed representative of the genus of variants and fragments of the polypeptide of residues 28-619 of SEQ ID NO:13 to which the claims refer.
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.
The rejection of claims 1-8 and 15-24 under 35 U.S.C. 102(a)(1) as being anticipated by Meinke et al. (WO 02/059148 – IDS filed on 10-26-2023) is maintained for reasons of record.
Applicant argues:
1. As currently amended, claim 1 is directed towards a polypeptide derived from SEQ ID NO. 13, specifically residues 28-619 or an amino acid sequence having a sequence identity of at least 80%. Claim 1 also requires that residues 1-27 in SEQ ID NO: 13 are not present. Meinke fails to provide such teaching and therefore fails to anticipate all the limitations of claim.
2. Nothing in Meinke directly teaches or implies that the signal peptide can be removed from the polypeptide of SEQ ID NO:13.
3. Disclosing a signal protein can be removed does not mean that this version of the protein is used in vaccine compositions.
Applicant’s argument has been fully considered and deemed non-persuasive.
With regard to Point 1, Meinke et al. disclose that variants of their polypeptides that lack their N-terminal signal sequence (see page 46 for example) thereby meeting the limitation of the protein not containing amino acids 1-27 of SEQ ID NO:13.
With regard to Point 2, the removal of the signal peptides as set forth on page 46 applies to all of the disclosed proteins including those disclosed in Table 2 (of which SEQ ID NO:61 is one). The generalized disclosure is applied to all proteins that are recombinantly expressed and therefor encompasses the claimed polypeptides.
With regard to Point 3, the instant claims are drawn to immunogenic compositions not vaccines. Given that all proteins are immunogenic to one degree or another, Meinke et al. anticipates all the limitations of the rejected claims. Moreover, in response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., the claimed compositions are vaccine compositions) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
As outlined previously, Meinke et al. disclose Staphylococcus aureus antigens with 99.2% sequence identity to SEQ ID NO:13 (see SEQ ID NO:61 and the alignment below). Meinke et al. further disclose that the N-terminal amino acids that comprise a signal peptide can be removed (see page 46); the use of their antigens (and fragments thereof) in vaccine preparations (see page 22); and that said preparations can comprise carriers and/or an adjuvant such as alum (see page 28). With respect to the specific immune responses set forth in claim 7, given the high degree of homology between the disclosed polypeptide and the claimed polypeptide it is deemed, in absence of evidence to the contrary, that they would necessarily possess the same immunological characteristics. Consequently, Meinke et al. anticipates all the limitations of the rejected claims.
ABJ18915
XX
OS Staphylococcus sp.
XX
CC PN WO200259148-A2.
XX
CC PD 01-AUG-2002.
XX
CC PI Meinke A, Nagy E, Von Ahsen U, Klade C, Henics T, Zauner W;
CC PI Minh DB, Vytvytska O, Etz H, Dryla A, Weichhart T, Hafner M;
CC PI Tempelmaier B;
XX
SQ Sequence 619 AA;
Query Match 99.2%; Score 3075; Length 619;
Best Local Similarity 99.2%;
Matches 587; Conservative 1; Mismatches 4; Indels 0; Gaps 0;
Qy 1 DTPQKDTTAKTTSHDSKKSTDDETSKDTTSKDIDKADNNNTSNQDNNDKKVKTIDDSTSD 60
||||||||||||||||||| ||||||||||||||||| |||||||||||| |||||||||
Db 28 DTPQKDTTAKTTSHDSKKSNDDETSKDTTSKDIDKADKNNTSNQDNNDKKFKTIDDSTSD 87
Qy 61 SNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRNGEKSTN 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 88 SNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRNGEKSTN 147
Qy 121 DSNKNSDNSIKNDTDTQSSKQDKADNQKAPKSNNTKPSTSNKQPNSPKPTQPNQSNSQPA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 148 DSNKNSDNSIKNDTDTQSSKQDKADNQKAPKSNNTKPSTSNKQPNSPKPTQPNQSNSQPA 207
Qy 181 SDDKVNQKSSSKDNQSMSDSALDSILDQYSEDAKKTQKDYASQSKKDKNEKSNTKNPQLP 240
|||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 208 SDDKANQKSSSKDNQSMSDSALDSILDQYSEDAKKTQKDYASQSKKDKNEKSNTKNPQLP 267
Qy 241 TQDELKHKSKPAQSFNNDVNQKDTRATSLFETDPSISNNDDSGQFNVVDSKDTRQFVKSI 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 268 TQDELKHKSKPAQSFNNDVNQKDTRATSLFETDPSISNNDDSGQFNVVDSKDTRQFVKSI 327
Qy 301 AKDAHRIGQDNDIYASVMIAQAILESDSGRSALAKSPNHNLFGIKGAFEGNSVPFNTLEA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 328 AKDAHRIGQDNDIYASVMIAQAILESDSGRSALAKSPNHNLFGIKGAFEGNSVPFNTLEA 387
Qy 361 DGNQLYSINAGFRKYPSTKESLKDYSDLIKNGIDGNRTIYKPTWKSEADSYKDATSHLSK 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 388 DGNQLYSINAGFRKYPSTKESLKDYSDLIKNGIDGNRTIYKPTWKSEADSYKDATSHLSK 447
Qy 421 TYATDPNYAKKLNSIIKHYQLTQFDDERMPDLDKYERSIKDYDDSSDEFKPFREVSDNMP 480
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||:||
Db 448 TYATDPNYAKKLNSIIKHYQLTQFDDERMPDLDKYERSIKDYDDSSDEFKPFREVSDSMP 507
Qy 481 YPHGQCTWYVYNRMKQFGTSISGDLGDAHNWNNRAQYRDYQVSHTPKRHAAVVFEAGQFG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 508 YPHGQCTWYVYNRMKQFGTSISGDLGDAHNWNNRAQYRDYQVSHTPKRHAAVVFEAGQFG 567
Qy 541 ADQHYGHVAFVEKVNSDGSIVISESNVKGLGIISHRTINAAAAEELSYITGK 592
||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 568 ADQHYGHVAFVEKVNSDGSIVISESNVKGLGIISHRTINAAAAEELSYITGK 619
Claims 1-8 and 15-24 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Masignani et al. (WO 02/094868 – IDS filed on 10-26-2023) for the reasons set forth in the previous Office action in the rejection of claims 1-8.
Applicant argues:
1. Claim 1 is directed towards a polypeptide derived from residues 28-619 of SEQ ID NO:13 or an amino acid sequence having a sequence identity of at least 80% that is at least 35 amino acids in length. Claim 1 also requires that residues 1-27 in SEQ ID NO: 13 are not present and Masignani fails to provide such a teaching and therefore fails to anticipate all the limitations of claim.
Applicant’s argument has been fully considered and deemed non-persuasive.
With regard to Point 1, Masignani et al. disclose a polypeptide with 99.2% sequence identity to residues 28-619 of SEQ ID NO:13 and that said polypeptide that lack their N-terminal signal sequence (see page 1 for example) (thereby meeting the limitation of the protein not containing amino acids 1-27 of SEQ ID NO:13). Consequently, Masignani et al. anticipates all the limitations of the rejected claims.
As outlined previously, Masignani et al. disclose Staphylococcus aureus antigens with 99.2% sequence identity to residues 28-619 of SEQ ID NO:13 (see SEQ ID NO:3914 and the alignment below). Masignani et al. further disclose that the N-terminal amino acids that comprise a signal peptide can be removed (see page 1); the use of their antigens (and fragments thereof) in vaccine preparations (see abstract and page 3 for example); and that said preparations can comprise carriers (such as tetanus toxin) and/or an adjuvant such as alum (see page 23 for example).
With respect to the specific immune responses set forth in claim 7, given the high degree of homology between the disclosed polypeptide and the claimed polypeptide it is deemed, in absence of evidence to the contrary, that they would necessarily possess the same immunological characteristics. Consequently, Masignani et al. anticipates all the limitations of the rejected claims.
ABM72717
ID ABM72717 standard; protein; 619 AA.
XX
DE Staphylococcus aureus protein #1957.
XX
OS Staphylococcus aureus.
XX
CC PN WO200294868-A2.
XX
CC PD 28-NOV-2002.
XX
CC PI Masignani V, Mora M, Scarselli M;
XX
SQ Sequence 619 AA;
Query Match 99.2%; Score 3075; Length 619;
Best Local Similarity 99.2%;
Matches 587; Conservative 1; Mismatches 4; Indels 0; Gaps 0;
Qy 1 DTPQKDTTAKTTSHDSKKSTDDETSKDTTSKDIDKADNNNTSNQDNNDKKVKTIDDSTSD 60
||||||||||||||||||| ||||||||||||||||| |||||||||||| |||||||||
Db 28 DTPQKDTTAKTTSHDSKKSNDDETSKDTTSKDIDKADKNNTSNQDNNDKKFKTIDDSTSD 87
Qy 61 SNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRNGEKSTN 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 88 SNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRNGEKSTN 147
Qy 121 DSNKNSDNSIKNDTDTQSSKQDKADNQKAPKSNNTKPSTSNKQPNSPKPTQPNQSNSQPA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 148 DSNKNSDNSIKNDTDTQSSKQDKADNQKAPKSNNTKPSTSNKQPNSPKPTQPNQSNSQPA 207
Qy 181 SDDKVNQKSSSKDNQSMSDSALDSILDQYSEDAKKTQKDYASQSKKDKNEKSNTKNPQLP 240
|||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 208 SDDKANQKSSSKDNQSMSDSALDSILDQYSEDAKKTQKDYASQSKKDKNEKSNTKNPQLP 267
Qy 241 TQDELKHKSKPAQSFNNDVNQKDTRATSLFETDPSISNNDDSGQFNVVDSKDTRQFVKSI 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 268 TQDELKHKSKPAQSFNNDVNQKDTRATSLFETDPSISNNDDSGQFNVVDSKDTRQFVKSI 327
Qy 301 AKDAHRIGQDNDIYASVMIAQAILESDSGRSALAKSPNHNLFGIKGAFEGNSVPFNTLEA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 328 AKDAHRIGQDNDIYASVMIAQAILESDSGRSALAKSPNHNLFGIKGAFEGNSVPFNTLEA 387
Qy 361 DGNQLYSINAGFRKYPSTKESLKDYSDLIKNGIDGNRTIYKPTWKSEADSYKDATSHLSK 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 388 DGNQLYSINAGFRKYPSTKESLKDYSDLIKNGIDGNRTIYKPTWKSEADSYKDATSHLSK 447
Qy 421 TYATDPNYAKKLNSIIKHYQLTQFDDERMPDLDKYERSIKDYDDSSDEFKPFREVSDNMP 480
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||:||
Db 448 TYATDPNYAKKLNSIIKHYQLTQFDDERMPDLDKYERSIKDYDDSSDEFKPFREVSDSMP 507
Qy 481 YPHGQCTWYVYNRMKQFGTSISGDLGDAHNWNNRAQYRDYQVSHTPKRHAAVVFEAGQFG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 508 YPHGQCTWYVYNRMKQFGTSISGDLGDAHNWNNRAQYRDYQVSHTPKRHAAVVFEAGQFG 567
Qy 541 ADQHYGHVAFVEKVNSDGSIVISESNVKGLGIISHRTINAAAAEELSYITGK 592
||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 568 ADQHYGHVAFVEKVNSDGSIVISESNVKGLGIISHRTINAAAAEELSYITGK 619
Conclusion
No claim is allowed.
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/ROBERT A ZEMAN/Primary Examiner, Art Unit 1645 March 5, 2026