DETAILED ACTION
Non-Final Rejection
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
2. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 07/25/2025 has been entered.
Election/Restrictions
3. Applicant’s election without traverse of Group I, claims 1, 2, 5, 7, 10-12, 15, 18, 21-24, 27, 32 and 36 and election of species as applied to claims in elected Group I, mammalian cells (claims 5 and 27), bacteria (claim 22) , viral vaccine vector poxvirus (claim 18) and Ebola virus (claim 36) in the reply filed on 03/12/2024 is applicable in this office action.
In this office action, requirement for election of a viral pathogen species an Ebola virus to identify antigenic pathogen polypeptide capable of inducing broadly neutralizing immune response to a pathogen is withdrawn in view of the available prior art.
Priority
4. Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed in parent Application No. GB1815956.6, filed on 09/28/2018.
Status of Claims
5. Claims 1-2, 5, 7, 10-12, 15, 18, 21-23, 32, 36, 49, and 111 as filed on 07/25/2025 are pending.
6. Applicant cancelled claims 24 and 27. The claim 49 is withdrawn by the applicant.
7. Claims 1-2, 5, 7, 10-12, 15, 18, 21-23, 32, 36 and 111 are under examination in this office action.
Objections to Specification
8. The disclosure is objected to because of the following informalities: The specification on page 49 lines 21-29 has references cited with http://www.” embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Appropriate correction is required.
Claim Interpretation
9. 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 interpreted to be directed to a method for identifying an optimized antigenic pathogen polypeptide capable of inducing a broadly neutralizing immune response to a pathogen and can be used as a lead candidate for vaccine. The method comprises analysis of a pathogen amino acid sequences encoding for immunogenic antigen. The different pathogenic strains and the strains recovered from different years are used for analysis. The immunogenic antigen amino acid sequences of a pathogen are subjected to multiple alignment using a software program and phylogenetic analysis is also performed. Consensus amino acid sequences are identified based on the alignment. The phylogenetic analysis provides multiple phylogenic groups of the amino acid sequences that are grouped based on the sequence identity and ancestral sequence. The consensus amino acid sequence for each phylogenic group is generated and identified. The ancestral amino acid sequence for each phylogenic group is generated and identified. A library of polypeptide library is generated based on conserved sequences. The polypeptide library is screened for binding with one or more broadly neutralizing antibodies that can neutralize the pathogen. A lead candidate is identified based on broad reactivity with broadly neutralizing antibodies and is referred as a lead candidate as optimized immunogenic antigenic polypeptide. A library of polypeptide library comprises plurality of different optimized candidate polypeptides. The polypeptides, inter alia, are modified by incorporating amino acid mutations or modifications to enhance immunogenicity and ability to induce broad neutralizing immune response.
The claim 111 is interpreted to be directed to a method that has scope same as that of the instant claim 1.
Claim Rejections - 35 USC § 112, Written description
10. 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 claims 1-2, 5, 7, 10-12, 15, 18, 21-23, 32, 36 and 111 are rejected 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. The claims1-2, 5, 7, 10-12, 15, 18, 21-23, 32, 36 and 111 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.
The claims 1 and 111 are drawn to a method for identifying a lead candidate optimized antigenic pathogen polypeptide capable of inducing a broadly neutralizing immune response to a pathogen.
The breadth of the claims: The claims 1 and 111 are very broad due to the claim limitations reciting a genus “a pathogen” and a genus “an antigenic polypeptide” without specifying a structure”, however, defines the function “binding to a broadly neutralizing antibody” or “inducing a broadly neutralizing immune response to a pathogen” One of the ordinary skills in the art cannot envision “a species” or the structure of broad genus “a pathogen” and a genus “an antigenic polypeptide”. A pathogen can encompass any viral pathogen from any known family of a virus. The specification does not provide specific examples for the range of species and the structure of species that would encompass the genera “a pathogen” and “an antigenic polypeptide”. It is unpredictable in the art and not possible to envision by one of the ordinary skills in the art as to which species of “a pathogen” and what amino acid sequence of a claimed genus “an antigenic polypeptide” the applicant has claimed.
Guidance in the specification: As indicated in the written description rejection above, the specification does not describe a specific structure of all species of a genus “a pathogen” and all species of a genus “an antigenic polypeptide”.
The applicable standard for the written description requirement can be found in MPEP 2163; University of California v. Eli Lilly, 43 USPQ2d 1398 at 1407; PTO Written Description Guidelines; Enzo Biochem Inc. v. Gen-Probe Inc., 63 USPQ2d 1609; Vas- Cath Inc. v. Mahurkar, 19 USPQ2d 1111; and University of Rochester v. G.D. Searle & Co., 69 USPQ2d 1886 (CAFC 2004).
To provide adequate written description and evidence of possession of a claimed genus, especially where the genus, especially where the genus requires a difficult to achieve and thus unpredictable function (e.g. function of binding of a “binding moiety” to a “generic or specific “biological target”) the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of using the claimed product, or any combination thereof. In this case, the only factor present in the claims is a genus “a pathogen” to a “generic “an antigenic polypeptide”. Accordingly, in the absence of sufficient recitation of distinguishing identifying characteristics for the claimed genera the specification does not provide adequate written description.
A definition by function alone does not suffice to sufficiently describe a coding sequence because it is only an indication of what the gene does, rather than what it is. EliLily, 119 F.3 at 1568, 43 USPQ2d at 1406. The court clearly states in Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, that "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 page 1117.) The specification does not clearly allow persons of ordinary skill in the art to recognize that the inventors invented what is claimed. As discussed above, the skilled artisan cannot envision the detailed chemical structure encompassed by all species of a genus “a pathogen” and all species of a genus “an antigenic polypeptide” capable of carrying out the claimed function of broad neutralization or binding to a pathogen or a virus”. Given that the specification has only described the function of a component, the full breadth of the claims does not meet the written description provision of 35 U.S.C. 112, first paragraph.
The applicant/inventor needs to show that they have truly invented the claimed genus “a pathogen” and “ an antigenic polypeptide”, i.e., that one has conceived and described sufficient representative species encompassing the breadth of the genus. Otherwise, the applicant/inventor has only a research plan, leaving it to others to explore and figure out the unknown contours of the claimed genus." AbbVie Deutsch/and GmbH & Co. v. Janssen Biotech, 759 F.3d 1285, 1300 (Fed. Cir. 2014). "In other words, the test for sufficiency is whether the disclosure of the application relied upon reasonably conveys to those skilled in the art that the inventor had possession of the claimed subject matter as of the filing date." Ariad, 598 F.3d at 1351.
Further, for a broad generic claim, the specification must provide adequate written description to identify the genus of the claim. In Regents of the University of California v. Eli Lilly & Co., the court stated: “A written description of an invention involving a chemical genus, like a description of a chemical species requires a precise definition, such as by structure, formula, [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials. Fiers, 984 F.2d at 1171, 25 USPQ2d at 1606; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284-85 (CCPA 1973) ("In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or sub-combinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus. . . ."). Regents of the University of California v. Eli Lilly & Co., 43 USPQ2d 1398.
The MPEP further states that if a biomolecule is described only by a functional characteristic, without any disclosed correlation between function and structure of the sequence, it is “not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed sequence.” MPEP 2163. The MPEP does state that for generic claim the genus can be adequately described if the disclosure presents a sufficient number of representative species that encompass the genus. MPEP 2163. If the genus has a substantial variance, the disclosure must describe a sufficient variety of species to reflect the variation within that genus. See MPEP 2163. Although the MPEP does not define what constitute a sufficient number of representatives, the Courts have indicated what do not constitute a representative number of species to adequately describe a broad generic. In Gosteli, the Court determined that the disclosure of two chemical compounds within a subgenus did not describe that subgenus. In re Gosteli, 872 F.2d at 1012, 10 USPQ2d at 1618.
Claim Rejections - 35 USC § 112
11. 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.
Claim 18 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.
Regarding claim 18, the phrase "such as" in line 5 renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim Rejections - 35 USC § 103
12. 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.
13. Claims 1-2, 5, 7, 10-12, 15, 21, 23, 32, and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Flyak et al 2018 (published in Nature Microbiology, June 2018 June; 3(6): 670–677), and further in view of Gaschen et al 2002 (Science, 2002, 28;296(5577):2354-60), Nickle et al 2003 (Science, 2003, vol 299 (5612), p. 1515-1518), Kothe et al 2006 (Virology 352 (2006) 438 – 449), Kesturu et al 2006 (Virology 348 (2006) 437–448), Sun et al 2011 (Virol J, 2011 Mar 6:8:100), Charles-Nino et al 2011 (Vaccine 29 (2011) 5313–5321), Giles et al 2011 (published in Vaccine 29, pages 3043–3054), Giles et al 2012 (published in Journal of Infectious Diseases, 205, pages 1562-1570), Khan et al 2017 (published in BMC Medical Genomics, 2017, 10 (4):78), Ripolli et al 2017 (published in Human Vaccines and Immunotherapeutics, 2017, Vol 13 (12), 2953-2966), Grant-Klein et al 2015 (published in Human Vaccines & Immunotherapeutics,2015, 11:8, 1991-2004), Dowling et al 2007 ( published in Journal of Virology, Vol 81 (4), p. 1821–1837) and Orozco et al 2005 (published in J Virology, vol 79 (15), p 9503-9514).
14. Claim 1 is directed to a method for identifying a lead candidate optimized antigenic pathogen polypeptide capable of inducing a broadly neutralizing immune response to a pathogen, inter alia, comprising providing a polypeptide library, an optimized pathogen polypeptide library, screening of the polypeptide library, identifying candidate antigenic pathogen polypeptide library bound by antigen binding molecules, plurality of different candidate optimized antigenic pathogen polypeptide library, and codon optimization, gene optimization of different generated nucleotide sequences, modification of nucleic acid sequences encoding polypeptide library.
Flyak et al 2018 teaches instant claim 1 limitation step (i) providing a polypeptide library with different amino acid sequences from different pathogen isolates of the same family to which it is desired to induce broadly neutralizing immune response. Flyak et al 2018 teaches, Ebola virus (EBOV) glycoprotein (GP) amino acid residues 33-676 based library (See, page 8, last paragraph, Epitope mapping ….. library, lines 1-4), different Ebola viruses (BDBV, EBOV, RESTV, SUDV) belonging to same family Filoviridae and Genus Ebolavirus with different amino acid sequences for GP based on multiple sequence alignment (page 16, figure 3-a) and peptides from these virus strains /isolates with different amino acid sequences (page 16, figure 3-d, table with column 1 and 2, peptide sequence entries).
Flyak et al 2018 teaches instant claim 1 limitation step (ii) screening the candidate optimized antigenic pathogen polypeptides library for binding by one or more broadly neutralizing antigen-binding molecules, each of which is able to bind and/or neutralize a pathogen of the same family as the pathogen to which it is desired to induce a broadly neutralizing immune response. Flyak et al 2018 teaches screening of the Ebola virus GP HR2/MPER antigenic pathogen polypeptides from different Ebola viruses (BDBV, EBOV, SUDV) for binding with three anti-Ebola viruses neutralizing monoclonal antibodies (NmAbs) and demonstrate cross-reactive binding (page 16, figure 3, c: Charts, d: table). These three monoclonal antibodies also show broad neutralizing property (page 16, figure 3, b: Charts); and further the different Ebola virus GP HR2/MPER peptide specific mAbs BDBV223, BDBV317 or BDBV340 broadly neutralize Ebolavirus strains/isolates BDBV, EBOV, RESTV or SUDV (see page 15, figure 2-a) and these NmAbs also afford protection from mortality after post-exposure with the Ebola viruses (passive immunization or treatment with the NmAbs) in mice (see page 15, figure 2-b, c) or ferrets (see page 15, figure 2-d).
Flyak et al 2018 teaches instant claim 1 limitation step (iii) identifying a candidate optimized antigenic pathogen polypeptide that is bound by one or more of the antigen-binding molecules in step (ii) as being a lead candidate optimized antigenic pathogen polypeptide capable of inducing a broadly neutralizing immune response to the pathogen. Flyak et al 2018 teaches that immunization with an Ebola virus glycoprotein peptide comprising the HR2/MPER antigenic site elicits neutralizing antibodies in rabbits (page 2, summary paragraph, lines 10-13; page 10, see paragraph on Polyclonal Ab generation). Flyak teaches use of Ebola virus HR2/MPER BDBV2p peptides (TDKIDQIIHDFIDKPL) or SUDV2 peptide (TDKINQIIHDFIDNPL) (also see page 16, figure 3-d for a table with column 1-2 showing peptide sequences from different viruses BDBV, EBOV, SUDV, from Ebola virus genus with varying antigenic peptide sequences for top 3 Ebola virus strain sequences in the table) to immunize rabbits for generation of neutralizing polyclonal antibodies and demonstrates neutralization of recombinant Ebola virus (EBOV) expressing green fluorescent protein was assessed in a neutralization assay (see page 11, lines 1-12; page 17 figure 4-d).
Flyak et al teaches multiple sequence alignment of GP2 from 4 different viruses BDBV, EBOV, RESTV and SUDV belonging to Genus Orthoebolaviruses and identification of antigenic peptides that bind to NmAb and induce broadly neutralizing antibody response against viruses belonging to belonging to Genus Orthoebolaviruses (See, page 16, figure 3 a-b, d; and page 17, figure 4, d).
Flyak et al 2018 teaches expression of Ebola virus GP polypeptides in mammalian cells HEK-293 (See, page 8, paragraph on Epitope mapping lines 5 and 7-9).
Flyak et al does not teach bioinformatics tools and methodology pipeline for sequence diversity analysis, phylogenetic analysis to derive consensus sequence from ancestor sequences, deriving consensus optimized pathogen polypeptides from ancestral pathogen nucleotide sequences, multiple sequence alignment from pathogens of the family or genus, identification of peptides or epitopes that bind to neutralizing mAbs and polyclonal sera, and codon optimization of nucleic acid sequence to express in mammalian cells.
Gaschen et al 2002 is in the art and teaches that globally, human immunodeficiency virus-type 1 (HIV-1) is extraordinarily variable, and this diversity poses a major obstacle to AIDS vaccine development. HIV-1 envelope proteins can differ in more than 30% of their amino acids. To contend with the diversity, country-specific vaccines are being considered, but evolutionary relationships may be more useful than regional considerations. Consensus and ancestor aminoa acid sequences could be used in vaccine design to minimize the genetic differences between vaccine strains and contemporary isolates, effectively reducing the extent of diversity by half. Gaschen et al 2002 teaches maximum likelihood phylogenetic analysis of the sequences and generation of consensus and ancestral amino acid sequences or polypeptides (See, abstract, entire article and supporting online materials and figures for the article).
Nickle et al 2003 is in the art and teaches and teaches consensus and ancestral State HIV vaccines and emphasize that ancestral state method has an advantage over a consensus vaccine because the ancestral state is an estimate of an actual sequence that existed in the past. It is likely that the protein generated from an ancestral sequence will have native folding and function, and the ancestral sequence is unlikely to change and also proposed a new approach COT Center of the Tree (COT), on the unrooted phylogeny (See, entire article and Fig 1).
Kothe et al 2006 is in the art and teaches ancestral and consensus envelope immunogens for HIV-1 subtype C. Kothe et al 2006 teaches the construction and characterization of the first full-length ancestral (AncC) and consensus (ConC) env genes of HIV-1 (group M) subtype C. The codon-usage-optimized genes expressed high levels of envelope glycoproteins that were incorporated into HIV-1 virions, mediated infection via the CCR5 co-receptor and retained neutralizing epitopes as recognized by plasma from patients with chronic HIV-1 subtype C infection. When tested by immunoblot analysis, sera from AncC and ConC env immunized guinea pigs recognized a greater number of primary subtype C envelope glycoproteins than sera from guinea pigs immunized with a contemporary subtype C env control. Mice immunized with AncC and ConC env DNA developed gamma interferon T cell responses that recognized overlapping peptides from the cognate ConC and a heterologous subtype C Env control (See, abstract and entire article).
Kesturu et al 2006 is in the art and teaches minimization of genetic distances by the consensus, ancestral, and center-of-tree (COT) sequences for HIV-1 variants within an infected individual and the design of reagents to test immune reactivity. Kesturu et al 2006 derived and analyzed consensus (CON), ancestral (ANC), and center-of-tree (COT) sequences to represent intra-individual HIV-1 env variants encoding a range of diversities and phylogenetic structures. Each reconstructed sequence significantly minimized genetic distances to extant sequences throughout the first 5 years of infection of an individual. COT or CON sequences derived from autologous virus samplings may be useful for increasing the sensitivity of assessments of immune reactivity against HIV (See, abstract, entire article).
Sun et al 2011 is in the art and teaches identification of a conserved JEV serocomplex B-cell epitope by screening a phage-display peptide library with a mAb generated against West Nile virus capsid protein (See, abstract, Fig 3-4, 7, entire article).
Charles-Nino et al 2011 is in the art and teaches variable epitope libraries, a new vaccine immunogen capable of inducing broad human immunodeficiency virus type 1-neutralizing antibody response. Charles-Nino et al 2011 teaches phage display combinatorial libraries demonstrated that sera from mice immunized with these VELs are capable of neutralizing 5 out of 10 viral isolates from Tier 2 reference panel of subtype B envelope clones, including HIV-1 isolates which are known to be resistant to neutralization by several potent monoclonal antibodies, described previously. These data indicate the feasibility of the application of immunogens based on VEL concept as an alternative approach for the development of molecular vaccines against antigenically variable pathogens. One of the ordinary skills can apply a similar approach can be used for developing polypeptide library and screening that is derived from a pathogen consensus and ancestral immunogenic polypeptide sequences (See, abstract, entire article).
Giles et al 2011 is in the virology and vaccine art. Giles teaches the steps for generating optimized pathogen antigen polypeptide library. Giles discloses computationally optimized broadly reactive antigen (COBRA) based H5N1 VLP vaccine that elicits broadly reactive antibodies in mice and ferrets (mammals). Giles teaches obtaining influenza A H5 HA nucleotide sequences (H5N1 human isolates) from the NCBI Influenza Virus Resource database. Nucleotide sequences were translated into protein sequences using the standard genetic code. Full length sequences from H5N1 clade 2 human infections from 2004 to 2006 were acquired and used for subsequent consensus generations. Giles further teaches the sequences analysis and grouping into the phylogenetic clades. HA amino acid sequences alignment for each individual outbreak group and determining the most common
amino acid at each position and thus generating primary consensus sequences that represented each outbreak group within each subclade (See, fig. 1A, phylogenetic analysis using ancestral sequences to generate consensus/conserved H5 HA sequences). Primary consensus sequences within each
subclade was then aligned, and the most common amino acid was chosen resulting in secondary consensus sequences representing each subclade (See, Fig. 1A). The secondary consensus sequences were aligned and the most common amino acid at each position was selected resulting in the final consensus sequence referred to as clade 2 COBRA HA (See, Fig. 1A). Phylogenetic analysis of the COBRA HA with all human isolates of H5N1 HA proteins indicated that COBRA retained a clade 2-like sequence without being grouped specifically within any clade 2 subclade cluster (Fig. 1B), (See, page 3046 results; page 3047 fig 1, results). Thus, Giles obtained polypeptide library comprising a plurality of different candidate optimized influenza A H5 HA polypeptides/protein, in the form of primary consensus sequences, secondary consensus sequences, and final consensus sequences. The final amino acid sequence, termed computationally optimized broadly reactive antigen (COBRA), was reverse translated and codon optimized for expression in mammalian cells, including codon usage for mammalian cells and RNA optimization. This construct was then synthesized and inserted into the pTR600 expression vector and expressed in human embryonic kidney (HEK) 293T cells (See, Giles et al 2011, page 3044 methods). Giles further teaches comparison of immunogenicity and improved performance of the optimized candidate influenza A H5 HA polypeptides/protein (polypeptide library, COBRA VLPs) for plurality (different) H5 HA clades 1, 2.2, 2.2 and 2.3 specific IgG antibodies (end point titers) and virus receptor blocking specificity (See, page 3049, Fig 5, table 1, page 3050, fig 6-7, table 2; fig 8).
Giles et al 2012 similarly teaches influenza A H5 HA COBRA VLP vaccine elicits broadly reactive antibodies that protect nonhuman primates from H5N1 infection (See, Giles et al 2012, entire research paper, specifically, abstract, methods, fig 1, fig 5, page 1566 fig 3).
Although the teachings of Giles et al 2011 and Giles et al 2012 are directed to influenza A virus one of the ordinary skills in the art would apply the teachings to Ebola virus to develop broadly reactive vaccines using the multiple sequences from different genetic and antigenic clades by performing ancestorial sequence analysis and design and evaluate the computationally optimized broad reactive immunogenic Ebola virus GP polypeptides.
Khan et al 2017 teaches a generic methodology outline and pipeline for analysis of viral sequence diversity for vaccine target discovery. Khan et al 2017 teaches bioinformatics tools and sequence data collection from NCBI and sequence data processing to remove redundant sequences, and perform multiple sequence alignment on curated sequences, variant sequence analysis, identification of species specific and highly conserved sequences, relevance to circulating strain analysis and finally immune-relevance analysis of pathogen specific, highly conserved sequences (See page 3, figure 1, a and b; page 4, table 1). Khan et al 2017 teaches approach for multiple alignment and analysis of HIV-1, Dengue or influenza HA glycoprotein sequences (page 6, column 1, lines 5-40) and immune relevance analysis for HLA-class I T cell epitopes (page 12, See section on Immune relevance analysis).
Ripolli et al 2017 teaches obtaining 1189 full-length sequences from the National Center for Biotechnology Information (NCBI) corresponding to the Ebolavirus genus GP from BDBV, Sudan, Reston, and Tai Forest virus, elimination of identical sequences using program MUSCLE31 to carry out multiple sequence alignments and deriving information on amino acid residue conservation (See page 2964, column 1, section on sequence analysis; page 2962, figure 7, summary of multiple sequence analysis) and identification of epitopes that bind to neutralizing mAbs and polyclonal sera (See page 2958, table 3 and table 4).
Grant-Klein et al 2015 teaches codon optimization of Ebola virus glycoprotein GP for expression in mammalian cells, Cynomolgus macaques. Further, Grant-Klein teaches deletion of mucin-like domain from GP and evaluation of the codon optimized nucleic acid sequences encoding the EBOV GP and EBOV GPᐃMucin as a DNA vaccine to induce neutralizing antibodies and to protect Cynomolgus macaques, a mammal, against virulent challenge with Ebola virus (see, page 1991, research paper title and abstract lines 1-2). Thus, Grant-Klein et al 2015 teaches codon optimization of the viral nucleotide sequences encoding antigenic polypeptide for expression in mammal and deletion of nucleic acid sequence encoding amino acid sequence that inhibits production and/or function of anti-pathogen polypeptide antibody deletion of a mucin-like domain.
Dowling et al 2007 teaches influences of glycosylation on antigenicity, immunogenicity,
and protective efficacy of ebola virus glycoprotein (GP) DNA vaccines. Dowling et al 2007 teaches that mutation of two N-linked sites on GP1, which flank previously defined protective antibody epitopes on GP, may enhance immunogenicity, possibly by unmasking epitopes (See, Dowling et al 2007, abstract, and figures, entire research paper).
Orozco et al 2005 is in the virology and vaccine art. Orozco et al teaches epitope swapping to develop HPV vaccine (See, abstract and methods and figures). Although, the teachings of Orozco et al are directed to HPV virus one of the ordinary skills in the art would apply the teachings are applicable to Ebola virus to develop broadly reactive vaccines using the epitopes from different genetic and antigenic clades by performing ancestorial sequence analysis and design and evaluate the computationally optimized broad reactive immunogenic Ebola virus GP polypeptide.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the prior art teachings of Flyak et al by incorporating the teachings of Giles et al, Khan et al, Ripolli et al, Grant-Klein et al, Dowling et al 2007, Orozco et al 2005, Gaschen et al 2002, Nickle et al 2003, Kothe et al 2006, Kesturu et al 2006, Sun et al 2011, and Charles-Nino˜ et al 2011 as recited supra to arrive at the invention of instant claim 1. The motivation would be to develop optimized pathogen polypeptides to develop a vaccine that elicits broadly reactive antibody response against a pathogen (e.g. Ebola virus) as disclosed by Glies for influenza A H5N1 virus (See, Glies et al 2011, abstract). The motivation to incorporate teachings of Khan et al would be to analyze large and variant viral polypeptide and nucleotide sequence data sets including available in the public domains by using a computational and systematic bioinformatics pipeline of methods steps approach for better selection of candidate vaccine targets (See, Khan et al, abstract). The motivation for codon optimization for increased expression and stability of the foreign genes such as encoding for Ebola virus glycoprotein (See, Grant-Klein et al 2015, page 1997, col 2, last para, To enhance the immunogenicity …..) and enhance protective immune response by unmasking epitopes by deletion of ebola virus GP glycans (See, Dowling et al 2007, abstract, entire research paper). There would have been a reasonable expectation of success given the disclosures of the applied prior art teachings as recited supra. Thus, the invention of claim 1 as a whole was clearly prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention. This is analogous to some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the invention as claimed in claims 1. See KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007) (see MPEP § 2143, example of rationales, A, C-G).
15. Claim 2: The instant claim 2 (dependent on claim 1) recites an added limitation, wherein: the one or more broadly neutralizing antigen-binding molecules include an antibody that has been obtained, or derived from an antibody that has been obtained, from a subject that has been exposed to a pathogen of the same family as the pathogen to which it is desired to induce a broadly neutralizing immune response; and/or the one or more broadly neutralizing antigen-binding molecules include non-antibody antigen-binding proteins.
The combined teachings of Flyak et al 2018, Gaschen et al 2002, Nickle et al 2003, Kothe et al 2006, Kesturu et al 2006, Sun et al 2011, Charles-Nino et al 2011, Giles et al 2011, Giles et al 2012, Khan et al 2017, Ripolli et al 2017, Grant-Klein et al 2015, Dowling et al 2007 and Orozco et al 2005 teaches instant claim 1 as recited supra.
The prior art teachings as applied to render obvious claim 1 (recited above) are incorporated here in entirety as applicable to instant claim 2.
Flyak et al 2018 further teaches obtaining three broadly cross reactive and broadly neutralizing antibodies from human survivors of Ebola virus infection and disease. These three human monoclonal antibodies are non-clonally related cross-reactive mAbs designated BDBV223, BDBV317 and BDBV340 were isolated from two donors who survived BDBV Ebola infection. These human derived mAbs are identified to target an antigenic site in the canonical heptad repeat 2 (HR2) regions near the membrane proximal external region (MPER) of GP. The mAb binding is mapped to peptide sequences from different viruses BDBV, EBOV, SUDV, from Ebola virus genus with varying antigenic peptide sequences (See page 16, figure 3-d for the table) and broad neutralizing activity of the mAbs against Ebola virus strains/isolates BDBV, EBOV, RESTV or SUDV (see page 15, figure 2-a). In addition, these mAbs also afforded protection from mortality after post-exposure with the Ebola viruses (passive immunization or treatment with the NmAbs) in mice (see page 15, figure 2-b, c) or ferrets (see page 15, figure 2-d). region (MPER) of GP (See page 2, summary paragraph, lines 8-10 and Main text lines 2-6).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further modify the combined teachings prior arts as applied to claim 1 above to incorporate additional teachings of Flyak et al 2018 to obtain the neutralizing antibodies from human survivors of Ebola virus infection and evaluate the broad neutralizing activity of the mAbs against Ebola virus strains/isolates BDBV, EBOV, RESTV or SUDV (See, Flyak et al 2018, page 15, figure 2-a, entire paper). The motivation would be to ensure broad reactivity and neutralization of the viruses to afford protection to the virus infection. There would have been a reasonable expectation of success given the disclosures of the applied combined prior art teachings as recited supra. This is analogous to some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the invention as claimed in claim 2. See KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007) (see MPEP § 2143, example of rationales, A, C-G).
16. Claim 5: The instant claim 5 (dependent on claim 1) recites an added limitation, wherein the candidate optimized antigenic pathogen polypeptides of the polypeptide library have been expressed in, or on the surface of, mammalian cells, or bacterial, yeast, or insect cells.
The combined teachings of Flyak et al 2018, Gaschen et al 2002, Nickle et al 2003, Kothe et al 2006, Kesturu et al 2006, Sun et al 2011, Charles-Nino et al 2011, Giles et al 2011, Giles et al 2012, Khan et al 2017, Ripolli et al 2017, Grant-Klein et al 2015, Dowling et al 2007 and Orozco et al 2005 teaches instant claim 1 as recited supra.
The prior art teachings as applied to render obvious claim 1 (recited above) are incorporated here in entirety as applicable to instant claim 5.
Flyak et al 2018, Giles et al 2011, Sun et al 2011 and Charles-Nino et al 2011 teaches the claim 5 added limitation.
Flyak et al 2018 further discloses expression of Ebola virus GP polypeptide library, covering 641 amino acid residues, in mammalian cells HEK-293 using 384-well cell culture plate (See, page 8, paragraph on Epitope mapping lines 5 and 7-9). Giles et al 2011 teaches the H5 HA final amino acid sequence, termed computationally optimized broadly reactive antigen (COBRA) optimized for expression in mammalian cells, including codon usage and RNA optimization, the construct was then synthesized and inserted into the pTR600 expression vector, the construct was transfected in human HEK 293T cells and optimized antigens (COBRA antigens) were expressed. The functional characterization of the expressed H 5HA VLPs or protein was characterized for immunogenicity and reactivity (See, Giles et al 2011, page 3044, methods and results).
Sun et al 2011 teaches identification of a conserved JEV serocomplex B-cell epitope by screening a phage-display peptide library with a mAb generated against West Nile virus capsid protein (See, abstract, Fig 3-4, 7, entire article).
Charles-Nino et al 2011 teaches HIV-1 variable epitope libraries a new vaccine immunogen capable of inducing broad human immunodeficiency virus type 1-neutralizing antibody response that can be used to teach the instant claim limitation on consensus or ancestral immunogenic pathogen polypeptide libraries (See, abstract, entire article).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further modify the combined teachings prior arts as applied to claim 1 above to incorporate additional teachings of Flyak et al 2018, Giles et al 2011 Sun et al 2011 and Charles-Nino et al 2011 as recited supra to arrive at the invention of claim 5. The motivation would be to ensure broad immune reactivity to afford broad protection to the virus infection (See, Giles et al 2011, abstract and discussion). There would have been a reasonable expectation of success given the disclosures of applied prior art teachings as recited supra. This is analogous to some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the invention as claimed in claim 5. See KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007) (see MPEP § 2143, example of rationales, A, C-G).
17. Claim 7: The instant claim 7 (dependent on claim 1) recites an added limitation, wherein the pathogen is a virus, the candidate optimized antigenic pathogen polypeptides are candidate optimized antigenic virus polypeptides, and the pathogen peptides are virus polypeptides.
The combined teachings of Flyak et al 2018, Gaschen et al 2002, Nickle et al 2003, Kothe et al 2006, Kesturu et al 2006, Sun et al 2011, Charles-Nino et al 2011, Giles et al 2011, Giles et al 2012, Khan et al 2017, Ripolli et al 2017, Grant-Klein et al 2015, Dowling et al 2007 and Orozco et al 2005 teaches instant claim 1 as recited supra.
The prior art teachings as applied to render obvious claim 1 (recited above) are incorporated here in entirety as applicable to instant claim 7.
Flyak et al 2018 and Giles et al 2011 Gaschen et al 2002, Nickle et al 2003, Kothe et al 2006, Kesturu et al 2006, Sun et al 2011, and Charles-Nino et al 2011 teaches the claim 7 added limitation.
Flyak et al 2018 further teaches candidate antigenic pathogen polypeptides are derived from a virus, an Ebola virus HR2/MPER BDBV2p peptides (TDKIDQIIHDFIDKPL) or SUDV2 peptide (TDKINQIIHDFIDNPL) (also see page 16, figure 3-d for a table with column 1-2 showing peptide sequences from different viruses BDBV, EBOV, SUDV, from Ebola virus genus with varying antigenic peptide sequences for top 3 Ebola virus strain sequences in the table).
Giles et al 2011 teaches the pathogen is a H5N1 influenza A virus and candidate antigenic pathogen polypeptides are derived from a virus or VLPs derived from H5 HA optimized polypeptides, protein (See, abstract, fig 1, methods, figure 5-showing COBRA H5 HA VLPs obtained from clades 1, 2.1, 2.2, 2.3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further modify the combined teachings prior arts as applied to claim 1 above to incorporate additional teachings of Flyak et al 2018 or Giles et al 2011 as recited supra to arrive at the invention of claim 7. The motivation would be to ensure broad immune reactivity to afford broad protection to the viral infection that cause global public health threat (See, Giles et al 2011, abstract and discussion). There would have been a reasonable expectation of success given the disclosures of applied prior art teachings as recited supra. This is analogous to some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the invention as claimed in claim 7. See KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007) (see MPEP § 2143, example of rationales, A, C-G).
18. Claim 10: The instant claim 10 (dependent on claim 1) recites an added limitation, wherein the candidate optimized antigenic pathogen polypeptides are screened for binding by the one or more antigen-binding molecules by a flow cytometric assay.
The combined teachings of Flyak et al 2018, Gaschen et al 2002, Nickle et al 2003, Kothe et al 2006, Kesturu et al 2006, Sun et al 2011, Charles-Nino et al 2011, Giles et al 2011, Giles et al 2012, Khan et al 2017, Ripolli et al 2017, Grant-Klein et al 2015, Dowling et al 2007 and Orozco et al 2005 teaches instant claim 1 as recited supra.
The prior art teachings as applied to render obvious claim 1 (recited above) are incorporated here in entirety as applicable to instant claim 10.
Flyak et al 2018 further teaches the claim 10 added limitation by disclosing expression Ebola virus GP antigenic polypeptide library and screening using mAb as primary antibody directed against GP and Alexa Fluor 488-conjugated secondary antibody using flow cytometry (See, page 8, paragraph on Epitope mapping lines 8-9; page 9, lines 1-6).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further modify the combined teachings prior arts as applied to claim 1 above to incorporate additional teachings of Flyak et al 2018 on flow cytometry screening of the optimized pathogen polypeptide as recited supra to arrive at the invention of claim 10. The motivation would be to ensure confirmation of the epitope on the optimized pathogen polypeptide for binding with the specific antibodies from recovered survivor subjects (See, abstract) or mAbs (see, page 8-9, epitope mapping) and additionally for assessing utility of the expressed optimized polypeptides in a cell-based assay for antibody, ADCC and cellular immune response studies. There would have been a reasonable expectation of success given the disclosures of applied prior arts as recited supra. This is analogous to some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the invention as claimed in claim 10. See KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007) (see MPEP § 2143, example of rationales, A, C-G).
19. Claims 11: The instant claim 11 (dependent on claim 1) recites an added limitation, which further comprises generating the polypeptide library.
The combined teachings of Flyak et al 2018, Gaschen et al 2002, Nickle et al 2003, Kothe et al 2006, Kesturu et al 2006, Sun et al 2011, Charles-Nino et al 2011, Giles et al 2011, Giles et al 2012, Khan et al 2017, Ripolli et al 2017, Grant-Klein et al 2015, Dowling et al 2007 and Orozco et al 2005 teaches instant claim 1 as recited supra.
The prior art teachings as applied to render obvious claim 1 (recited above) are incorporated here in entirety as applicable to instant claim 11.
The claim 11 added limitation on generating a polypeptide library is taught by prior arts applied to claim 1 and the teachings are incorporated here in entirety by reference.
Flyak et al 2018 further teaches generating Ebola virus GP peptide library using amino acid residues 33-676 to create a library of clones (See page 8, paragraph on Epitope mapping, line 4-6).
Giles et al 2011 teaches generating the H5 HA influenza A virus generation of candidate optimized pathogen polypeptides (See, fig 1, page 3044 methods, col 2, antigen constructs and synthesis) are derived from a virus or VLPs derived from H5 HA optimized polypeptides protein expressing nucleic acid constructs in plasmid pTR600 mammalian expression vector and expresses in mammalian cells, and can be considered as teaching the generating polypeptide library of the instant claim 11 (See, abstract, fig 1, methods, figure 5-showing COBRA H5 HA VLPs/ the polypeptide library obtained from clades 1, 2.1, 2.2, 2.3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further modify the combined teachings prior arts as applied to claim 1 above to incorporate additional teachings of Flyak et al 2018 or Giles et al 2011 as recited supra to arrive at the invention of claim 11. The motivation would be to obtain a repository of the optimized pathogen polypeptide library to identify the candidate polypeptide showing broad cross reactivity with available antiserum against the pathogen and to have access to the library for future use in viral disease epidemic caused by virus mutation (See, Giles et al 2011, Flyak et al 2018). There would have been a reasonable expectation of success given the disclosures of the applied prior arts. This is analogous to some te