DETAILED ACTION
Election/Restrictions
Applicant’s election of species in the reply filed on September 16, 2025 is acknowledged. Because Applicant did not distinctly and specifically point out the supposed errors, the election has been treated as an election without traverse.
Drawings
The drawings are objected to for the following reason: Figures 10-13 reference amino acid or nucleic acid sequence positions without a sequence identifier. Figure 17 shows amino acid and nucleotide sequences that are not referenced by a sequence identifier.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
In lieu of filing corrected drawing sheets, the specification can be amended to reference the sequence identifiers in the description of the figures.
Claims Summary
Claim 1 is directed to a method for producing a defective interfering viral genome (DVG) comprising:
Providing a first set of at least three replicate in vitro cell cultures comprising a solid support and cells infected with a reference infectious virus at a high MOI;
Providing a second set of at least three replicate in vitro cell cultures comprising a solid support and cells infected with a reference infectious virus at a low MOI;
Culturing the first and second sets of cultures for at least 5 passages under mutagenic conditions;
Collecting a plurality of DVG candidates from the medium of the first and second sets of cultures;
Deep sequencing the collected DVG candidates; and
Selecting a DVG from the plurality of DVG candidates; the DVG is characterized by an in vitro inhibitory activity of at least 50%, 60%, 70%, 80% or 90% against the reference infectious virus (claim 4); according to claim 3, the method of selecting comprises:
Comparing the sequences of the DVG candidates with the genome sequence of the reference infectious virus;
Identifying at least one DVG candidate having a genome comprising at least one splicing event that is a deletion or a rearrangement;
Determining the relative frequency of at least one DVG candidate having a genome with at least one splicing event among the population of sequenced DVG candidate genomes; and
Selecting at least one DVG for which at least one splicing event is more abundant at high MOI cultures than at low MOI cultures (elected species).
Claim 2 is directed to an embodiment wherein a third set of at least three replicate in vitro cell cultures comprising a solid support and cells infected with a reference infectious virus at a high MOI, and fourth set of at least three replicate in vitro cell cultures comprising a solid support and cells infected with a reference infectious virus at a low MOI, and culturing the third and fourth sets of cultures for at least 5 passages under mutagenic conditions.
The reference infectious virus is ZIKA (elected species). Also claimed is a DVG produced by the method (claim 12), which comprises the nucleotide sequence of ZIKV DVG-K, SEQ ID NO: 32 or at least 90% identical to SEQ ID NO: 32 (claim 13). Also claimed is a defective interfering particle comprising the DVG (claim 14).
Claim 15 is directed to a method of treating a viral infection in a subject by administering an effective therapeutic amount of at least one DVG (claim 15), administered as naked RNA (claim 16). The administered DVG is a defective interfering genome of ZIKV (elected species, claim 17). Also claimed is a pharmaceutical, immunogenic, therapeutic composition or vaccine, comprising at least one DVG (claim 38), or at least one defective interfering particle (claims 39 and 40), respectively, and a pharmaceutically acceptable carrier. Claim 51 is directed to a cell line producing the DVG. Claim 51 is understood to be directed to a cell line comprising the necessary elements to produce DVG. Claim 52 is directed to a method for preparing the drug for the treatment of a patient infected with a target virus comprising a defective interfering particle.
Claim 49 is directed to a polynucleotide comprising SEQ ID NO: 32 or a polynucleotide having at least 90% identity to SEQ ID NO: 32. Also claimed is an expression vector or plasmid comprising the polynucleotide (claim 50).
Please note that claims 12-14 and 38-40 are directed to product-by-process format claims. Claims 15-17 and 52 are directed to methods of using a product, wherein the product is written in a product-by-process format. According to MPEP 2113, the patentability of a product does not depend on its method of production. The structure implied by the process steps should be considered, however, product-by-process claims are not limited to the manipulations of the recited steps, only the structure implied by the steps.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 12, 14 and 38-40 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a law of nature without significantly more. Claim 12 is directed to a defective interfering viral genome made by the method of claim 1. Claim 13 is directed to a defective interfering particle comprising a defective interfering viral genome made by the method of claim 1. Claim 38 is directed to a pharmaceutical, immunogenic or therapeutic composition comprising at least one defective interfering viral genome made by the method of claim 1, and a pharmaceutically acceptable carrier. Claim 39 is directed to a pharmaceutical, immunogenic or therapeutic composition comprising at least one interfering viral genome made by the method of claim 1, and a pharmaceutically acceptable carrier. Claim 40 is directed to a vaccine comprising a pharmaceutical, immunogenic or therapeutic composition comprising at least one interfering viral genome made by the method of claim 1, and a pharmaceutically acceptable carrier.. a product-by-process format. According to MPEP 2113, the patentability of a product does not depend on its method of production. The structure implied by the process steps should be considered, however, product-by-process claims are not limited to the manipulations of the recited steps, only the structure implied by the steps.
The judicial exception in claims 12 and 38 is an interfering viral genome. The method by which it is made does not imply any particular nucleic acid sequence. The interfering viral genome is not markedly different from its naturally occurring counterpart because it has the same structural features (i.e., defective genome) and functional features (i.e., interfering) as that claimed. Pesko et al. (Virology, May 25, 2012, 427(1):10-17) discloses WNV isolates (i.e., particles) comprising nutant genomes with internal deletions, characterized as defective interfering particles that inhibiting full-length virus production when introduced at high MOI in Vero cells (see abstract).
The judicial exception in claims 14, 39 and 40 is also an interfering viral genome. Additionally, the claims recite a pharmaceutically acceptable carrier. This reads on water, which is not markedly different from its naturally occurring counterpart.
This judicial exception is not integrated into a practical application because claims 12 and 14 are directed to the products themselves. Claims 38-40 are directed to pharmaceutical, immunogenic, therapeutic or vaccine compositions, respectively, with pharmaceutically carriers. The labels of “pharmaceutical”, “immunogenic”, “therapeutic” and “vaccine”, do not add any additional elements to the active ingredients. The presence of a pharmaceutically acceptable carrier does not add a meaningful limitation as it is merely a nominal component of the claim.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because a pharmaceutically acceptable carrier is well-understood, routine and convention in the art of compositions (see WO 2018/112225, cited in the IDS filed 9/27/2022, claim 45). Therefore, the claimed embodiments are directed to judicial exceptions without significantly more and are thus patent ineligible.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-4, 6, 14-17, 38, 39, 40, 51 and 52 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 is directed to a method that ends with “selecting a DVG from the plurality of DVG candidates”. There is no method provided for the selection process, in contrast with claim 3 which outlines the steps by which a selection is made. It is not clear how a DVG is selected in claim 1 since no parameters are provided for which a DVG is qualified to be selected. Without further method steps for the selection process, the metes and bounds of claim 1, and dependent claims 2, 4, 6, 14-17, 38, 39, 40, 51 and 52, cannot be determined.
The terms “high multiplicity of infection”, “low multiplicity of infection”, and “more abundant” in claims 1-3 are relative terms which render the claims indefinite. The terms “high”, “low”, “more” and “abundant” are not defined by the claims, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Paragraph [0011] of the published application (US 20230174953) gives examples of high and low MOI, but nothing definitive.
Claim 1 recites, “mutagenic conditions”, and claim 2 recites, “non-mutagenic conditions” however, there are no definitions in the specification for the meaning of these terms. Only examples of mutagenic conditions are given (see paragraph [0048] of the published application, US 20230174953).
Claim 1 recites, “deep sequencing”, however, there is no definition in the specification for the meaning of this term. It is not clear to what degree of sequencing qualifies as deep. The term “RNAseq” is mentioned in the specification, but no particular parameters appear to have been provided.
Claim 2 is directed to further method steps of claim 1, wherein a third set of at least three replicate in vitro cell cultures comprising a solid support and cells infected with a reference infectious virus at a high MOI, and fourth set of at least three replicate in vitro cell cultures comprising a solid support and cells infected with a reference infectious virus at a low MOI, and culturing the third and fourth sets of cultures for at least 5 passages under mutagenic conditions. It is not clear where the methods steps from claim 2 fit in with claim 1. Without further guidance, the metes and bounds of claim 2 cannot be determined.
Claim Rejections - 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.
Claims 1-4, 6, 12, 14-17, 38-40, 51 and 52 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method of producing and selecting a defective interfering viral genome wherein a method step of testing inhibition of a parental virus is performed, does not reasonably provide enablement for a method wherein no selection criteria are required, or wherein only a splicing event observed to be more abundant in high MOI cultures than a low MOI cultures is used as the selection criteria. Please note that the examiner is not suggesting the use of the language “testing inhibition of parental virus”, rather, that further testing is needed to confirm that the candidate DVG has the interfering function. Further, even if DVGs were obtained by the method, the claims are enabling for a pharmaceutical composition and an immunogenic composition comprising a DVG, but not a vaccine. Further, even if DVGs were obtained by the method, the claims are enabling for a method of inducing an immune response in a subject against ZIKV, but not for treating a viral infection, such as ZIKV. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
The breadth of the claims encompasses the production of defective interfering viral genomes (DVGs) by producing DVG candidates in various cell cultures at a high or low MOI under mutagenic conditions, deep sequencing the candidates and selecting a DVG without any criteria for the selection (claim 1, for example). In one embodiment, the selection is based on splicing events being more abundant at high MOI cultures than low MOI cultures (claim 3). The breadth of the claims encompasses DVGs produced by the methods, methods of treating a viral infection, such as a ZIKV infection in a human, therapeutic compositions, as well as a vaccine comprising the DVG for humans.
The nature of the invention is the production of DVGs that are interfering. The nature of the invention is the use of the interfering DVGs such that they treat existing infections in humans, against viral infections, or such that they induce an immune response that serves to prevent disease caused by a subsequent infection.
The specification, at paragraphs [0002]-[0005] of the published application (US 20230174953) indicate that defective interfering viral genomes (DVG) (as in claim 1) and particles comprising DVGs (as in claim 14) interfere with the generation of infectious progeny virus particles, as stated in paragraph [0003]:
Because they lack part of their genome or its encoded functions, DVGs must co-infect cells with their parental virus, in order to take advantage of the proteins encoded by the full-length virus. Hence, DVGs that hijack the replication machinery or use proteins encoded by the parental virus, may compete with wild type virus for resources, which can result in inhibition of the parental virus.
Thus, the claimed methods produce DVGs that not only have defective genomes, but have the function of interfering with the generation of infectious progeny virus particles or inhibit parental virus. In that case, the claimed methods do not appear to recite method steps that show that the selected DVGs actually interfere with the generation of infectious progeny virus particles. The claimed methods produce candidate DVGs and select a DVG, or in the case of claim 3, look for splicing events at various MOIs, but there are no steps indicating how the DVGs are determined to be interfering. Paragraph [0005] of the published application states the following:
Our combined experimental evolution and computational approach identifies thousands of different DVGs for any virus. First, our experimental approach generates all possible DVGs in a virus population. Expectedly, our list includes DVGs that resemble those identified by more classic methods. Second, our computational analysis allows us to predict which DVGs would work best as defective interfering particles, using temporal frequencies estimated from the sequence data. Using this combined approach, we have generated a list of top candidates for a wide range of viruses belonging to different virus families, of which up to 90% have confirmed capacity to interfere with wild type virus replication.
According to paragraph [0005], candidates are generated but need to be confirmed as to their interfering capability (see paragraph [0011]). Example 3 is directed to ZIKV, where DVGs were produced, tested for being non-replicating, tested for dependency on a wild-type for replication, and tested for inhibitory activity of wild-type virus in a mouse model of infection, and in mosquitos, including the elected species of SEQ ID NO: 32 (ZIKV DVG-K).
Applicant’s own work, Rezelj et al. (Nature Communications, 2021, 12:2290, 14 pages) describes the process that Applicant used to identify DVGs against flavivirus infection in mammalian and mosquito hosts (see abstract). The process includes a final step of demonstrating that the candidate DVG is antiviral in vivo (abstract). While there are many computations that go into generating likely candidates, the confirmation of their activity requires experimental evidence in vivo.
Even if DVGs were obtained using the claimed methods, they are not enabled for ZIKV therapeutic or vaccine purposes, nor for treating a ZIKV infection. (While the therapeutic and vaccine compositions are not directed to ZIKV in particular, the examiner is addressing it because it is encompassed. Further, ZIVV is an elected species, thus it is addressed in this context for purposes of compact prosecution.) Particular challenges to ZIKV prevention include lack correlates of protection in humans, minimal opportunities for efficacy testing due to reduced prevalence of ZIKV infection in humans (waning epidemic), complications with ADE, and the varying manifestations of ZIKV infection, including congenital diseases and GBS (see Pattnaik et al., Vaccines, 2020, 8, 266; 10 pages, see pages 3, third full paragraph, and pages 10-11). The specification does not provide any working examples that would correlate to protection against ZIKV in humans, nor treatment of existing infections/disease.
In view of the breadth of the claims, the nature of the invention, the teachings of the specification, the working examples, and the low level of predictability, it would require undue experimentation to practice the invention as claimed.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 12, 14, 15, 17, 38, 39, 51 and 52 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Weinberger et al. (WO 2018/112225, cited in the IDS filed 9/27/2022, “Weinberger”). The claims are summarized above and correlated with the teachings of the prior art in bold font below. Please note that claims 12, 14, 15, 17, 38, 39, 51 and 52 are directed to products or methods that use products that are written in a product-by-process format. According to MPEP 2113, the patentability of a product does not depend on its method of production. The structure implied by the process steps should be considered, however, product-by-process claims are not limited to the manipulations of the recited steps, only the structure implied by the steps. Please also note that the claims are rejected on the basis of their recited components and steps, not any functional language that is addressed in the scope of enablement rejection above.
Weinberger discloses methods and compositions for generating defective interfering particles and identifying defective interfering particles, including genomes of viruses, such as ZIKV (see abstract, page 19, lines 9-15, and page 29, line 24) (claims 12, 14 and 52). Although the method by which the defective interfering particles and genomes are produced differ from the method by which Applicant produces them, there are no particular structural features recited in the claims that would distinguish Weinberger’s products from Applicant’s products, since both are defective viral genomes/particles that interfere.
Weinberger discloses pharmaceutical formulations with pharmaceutically acceptable excipients, as well as a cell line to generate viral stocks (see page 29, lines 18-27, and page 35, item 45) (claims 38, 39 and 51). Also disclosed is a method of reducing viral load in a subject by administering the defective interfering particle (see Weinberger claim 48) (claims 15 and 17). Therefore, the claims are anticipated by the prior art.
Claims 12, 14-16, 51 and 52 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tangy et al. (WO 2017/221076, “Tangy”). The claims are summarized above and correlated with the teachings of the prior art in bold font below. Please note that claims 12, 14-16, 51 and 52 are directed to products or methods that use products that are written in a product-by-process format. According to MPEP 2113, the patentability of a product does not depend on its method of production. The structure implied by the process steps should be considered, however, product-by-process claims are not limited to the manipulations of the recited steps, only the structure implied by the steps. Please also note that the claims are rejected on the basis of their recited components and steps, not any functional language that is addressed in the scope of enablement rejection above.
Tangy discloses an immunogenic composition and vaccine comprising, among other components, defective interfering measles virus particles, and defective interfering naked RNA from measles virus (see Tangy abstract, claim 29, and paragraphs [9] and [66]) (claims 12 and 14). The composition is administered to a human patient for inducing an immune response, treating a viral infection, etc. (see paragraph [50]) (claims 15 and 16). Methods of producing the defective interfering particles/genomes and a cell line producing them is disclosed (see Tangy claim 26, for example) (claims 51 and 52). Therefore, the claims are anticipated by the prior art.
Claim 49 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ladner et al. (Genome Announcements, 4(3):e00377-16, 2 pages), evidenced by GenBank KU955594.1 (Zika virus isolate Zika virus/M.mulatta-tc/UGA/1947/MR-766, 2016).
Claim 49 is directed to a polynucleotide comprising SEQ ID NO: 32 or a polynucleotide having at least 90% identity to SEQ ID NO: 32. Ladner discloses a complete genome sequence of ZIKV isolate MR-766, which is 92.9% identical to SEQ ID NO: 32. An alignment is provided at the end of this Office Action.
Claim Rejections - 35 USC § 103
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.
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 38-40 are rejected under 35 U.S.C. 103 as being unpatentable over
Tangy et al. (WO 2017/221076, “Tangy”) in view of Weinberger et al. (WO 2018/112225, cited in the IDS filed 9/27/2022, “Weinberger”). Please note that claims 38-40 are directed to products written in a product-by-process format. According to MPEP 2113, the patentability of a product does not depend on its method of production. The structure implied by the process steps should be considered, however, product-by-process claims are not limited to the manipulations of the recited steps, only the structure implied by the steps. Please also note that the claims are rejected on the basis of their recited components and steps, not any functional language that is addressed in the scope of enablement rejection above.
Tangy discloses an immunogenic composition and vaccine comprising, among other components, defective interfering measles virus particles, and defective interfering naked RNA from measles virus (see Tangy abstract, claim 29, and paragraphs [9] and [66]). Tangy mentions solutions but not explicitly a pharmaceutically acceptable carrier. However, it would have been obvious to have used a pharmaceutically acceptable excipient, which is reasonably a pharmaceutically acceptable carrier, as in Weinberger et al. (page 35, item 45), since the composition is intended for administration to human subject (see Tangy, paragraph [50]), with a reasonable expectation of success. Therefore, the claimed embodiment would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claim 50 is rejected under 35 U.S.C. 103 as being unpatentable over Ladner et al. (Genome Announcements, 4(3):e00377-16, 2 pages), evidenced by GenBank KU955594.1 (Zika virus isolate Zika virus/M.mulatta-tc/UGA/1947/MR-766, 2016) as applied to claim 49 above, in view of Weinberger et al. (WO 2018/112225, cited in the IDS filed 9/27/2022, “Weinberger”).
Claim 50 is directed to an embodiment wherein the polynucleotide is in an expression vector or plasmid. Ladner’s teachings are outlined above but Ladner does not suggest an expression vector or plasmid comprising Ladner’s sequence of ZIKV isolate MR-766. It would have been obvious to have put the sequence into a plasmid or expression vector so that it could be used to generate and identify DIP sequences, as in Weinberger, with a reasonable expectation of success (see abstract and pages 1-2). One would have been motivated to generate DIP sequences using Ladner’s sequence because ZIKV is a human pathogen of interest (see Ladner’s abstract), and Weinberger suggests ZIKV (see page 29, line 24).
Therefore, the claimed embodiment would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Alignment of GenBank KU955594.1
“Qy” is Applicant’s SEQ ID NO: 32. “Db” is Ladner’s sequence.
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Conclusion
No claim is allowed.
SEQ ID NO: 32 is free of the prior art of record.
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/STACY B CHEN/Primary Examiner, Art Unit 1672