DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status and Election
Claims 1, 16, 24, 32-34, 41-42, 62, 64, 66 and 72-92 are pending.
Applicant’s election of group 1, encompassing claims 1, 16, 24, 32-34, 41-42, 62, 64 and 66 directed to SARS-CoV-2 replicons is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). Claims 72-92 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected groups, there being no allowable generic or linking claim.
Claims 1, 16, 24, 32-34, 41-42, 62, 64 and 66 are under examination.
Specification
The disclosure is objected to because of the following informalities:
First, the nucleic acid sequence of T7 on page 23 needs to be identified with a SEQ ID NO from the sequence listing.
Second, the use of the terms pSMART-BAC®, Gibson Assembly®, mMessage mMachine®, Monarch®, MaxCyte®, and Nucleobond®, which are trade names or marks used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Appropriate correction is required.
Claim Interpretation
Claim 1 recites “A coronavirus reporter replicon comprising: (a) one or more SARS-CoV-2 genes… wherein the one or more SARS-CoV-2 genes comprise ORF1ab…, ORF3a…, ORF7a/b…, ORF8…, and ORF 10… wherein one or more of a spike ORF, an envelope ORF, and a membrane ORF is replaced with the reporter gene.” The Specification does not specifically define “and” and “or” as being equivalent. The broadest reasonable interpretation of “one or more SARS-CoV-2 genes…, wherein the one or more SARS-CoV-2 genes comprises…” is at minimum one of the genes from the list. Thus, claim 1 is interpreted as a coronavirus reporter replicon that is replication competent comprising at minimum one of ORF1ab, ORF3a, ORF7a/b, ORF8, and ORF 10 and replacement of at minimum one of spike ORF, an envelope ORF, and a membrane ORF with the reporter protein.
If Applicant intends for all the ORFs listed in claim 1 to be included in the replicon, the following claim language is suggested: “A coronavirus reporter replicon comprising: (a) SARS-CoV-2 genes for coronavirus viral RNA replication including ORF1ab…, ORF3a…, ORF7a/b…, ORF8…, and ORF 10…, or sequence that are at least 90% homologous to each of those genes; and (b) at least one reporter gene; and wherein one or more of a spike ORF, an envelope ORF, and a membrane ORF is replaced with the reporter gene.”
Finally, the Specification does not define spike ORF, envelope ORF or membrane ORF as specific ORFs, genes or sequences of the SARS-CoV-2 genome. Thus, an ORF that encodes a spike protein or a protein involved in the production of, or is located in, the envelope or membrane is broadly, but reasonably, encompassed by “a spike ORF, an envelope ORF and a membrane ORF”. If Applicant intends for the spike ORF, an envelope ORF and a membrane ORF to refer to specific ORFs like S, M and E, it is suggested to use recite positions relative to SEQ ID NO 1, like the claim recites for the possible included ORFs.
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.
(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.
Claims 1, 16, 24, 41, 42, 62, 64 and 66 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Shi (US 20230416692 A1, priority to US provisional applications 63/000713 filed March 27, 2020 and 63/041667 filed June 19, 2020) and evidenced by Redondo (Redondo et al., Frontiers in Immunology (2021), 12:708624, pages 1-8). Claim 16 is evidenced by Genbank (NC_045512.2, severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome, https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2, [retrieved January 8, 2026]).
Shi claims priority to the two US provisional applications recited above. Each of the point citations in the rejection below are fully supported in one or both of the US provisional applications.
Regarding claim 1, Shi teaches a SARS-CoV-2 replicon comprising ORF 1a, 1b, S, 3, E, M, 6, 8a/b, N, 9b and 10 (i.e., at least one of ORF1ab, ORF3b, ORF8 and ORF10) (FIG. 5A). Shi teaches the SARS-CoV-2 replicon also comprises a gene encoding NanoLuc (i.e., a reporter gene) in place of ORF7a/b (FIG. 5A). Shi teaches the nucleic acid sequence of the SARS-CoV-2 replicon from which the reporter replicon was derived is SEQ ID NO 1 ([0051]), which is 100% identical to SEQ ID NO 1 of the instant application. Therefore, Shi teaches the replicon having each of the genes that are 100% identical with the recited positions from SEQ ID NO 1 of the examined application. Shi teaches the NanoLuc SARS-CoV-2 replicon can form plaques similar to wild type and is therefore replication competent (FIG. 5B-E). Shi is silent regarding the function of the missing ORF7a/b.
Redondo teaches that ORF7a encodes an N-terminal signal peptide, an ectodomain, a type-I transmembrane protein region and an ER-localization signal (page 4, ¶4). Therefore, ORF7a is a membrane ORF, and Xie’s NanoLuc SARS-CoV-2 replicon inherently had a membrane ORF replaced by the NanoLuc reporter.
Regarding claim 16, Shi teaches the ORF nearest the 5’ terminus of the coronavirus (i.e., ORF1a) is translated into a large polyprotein that is cleaved into multiple proteins, and together functions as an RNA-dependent RNA polymerase ([0050]). Shi is silent as to what ORF1a encodes. Genbank teaches the genome sequence of the SARS-CoV-2 isolate Wuhan-Hu-1 (title), which is 100% identical to Shi’s SEQ ID NO 1 and to SEQ ID NO 1 of the present application.
Genbank teaches that ORF1a encodes an ORF1ab polyprotein (page 2), that comprises a sequence that is 100% identical to SEQ ID NO 9 (i.e., an RNA-dependent RNA polymerase) (page 3, highlighted in attached Genbank reference). Therefore, Shi’s coronavirus replicon inherently comprises a gene that encodes an RNA-dependent RNA polymerase that is at least 90% identical to SEQ ID NO 9.
Regarding claim 24, Shi teaches that NanoLuc is a short for nanoluciferase ([0007]).
Regarding claim 41, Shi teaches the NanoLuc SARS-CoV-2 replicon encoded as cDNA (i.e., a vector) ([0095]).
Regarding claim 42, Shi teaches the NanoLuc SARS-CoV-2 replicon cDNA included a T7 promoter and a poly(A) terminator ([0056])
Regarding claims 62 and 64, the Specification does not provide a limiting definition of “vector”, which is interpreted broadly as any means to provide the sequence to a cell. Shi teaches in vitro transcription of the viral RNA (i.e., a vector) was introduced (i.e., transfected) into a Vero cell ([0095]).
Regarding claim 66, Shi teaches the NanoLuc SARS-CoV-2 replicon can be used to screen therapies ([0067]). Shi teaches combining the Vero cells comprising the NanoLuc SARS-CoV-2 replicon with remdesivir or chlorophane (i.e., a candidate agent for inhibiting SARS-CoV-2) and determining ability of the replicon to replicate based on luciferase activity levels ([0077]; Fig 8C and 8D).
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 32 and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Shi (US 20230416692 A1, priority to US provisional applications 63/000713 filed March 27, 2020 and 63/041667 filed June 19, 2020), as applied to claims 1, 16, 24, 41, 42, 62, 64 and 66 above, and further in view of Fernandes (Fernandes et al., Viruses (2020), 12:598, pages 1-22, published May 30, 2020) and Genbank2 (AY909580.1, Synthetic construct neomycin-kanamycin phosphotransferase type II mRNA, complete cds, https://www.ncbi.nlm.nih.gov/nuccore/AY909580.1, available July 5, 2005, [retrieved February 12, 2026]).
Claims 32 and 34 recite a SARS-CoV-2 replicon comprising a sequence that is at least 90% identical to nucleotides 284-26118 of SEQ ID NO 5. According to the Specification, nucleotides 284-26118 of SEQ ID NO 5 comprise the coding sequences for, starting from the 5’ end: ORF1a/b (including all the nsps), nanoLuciferase, ORF3a, Neomycin, ORF6, ORF7a, ORF7b, ORF8, N gene and ends just before ORF10 (Table 5, pages 116-117).
The teachings of Shi are recited above as for claims 1, 16, 24, 41, 42, 62, 64 and 66 and are incorporated here. Briefly, Shi teaches a SARS-CoV-2 replicon comprising all of the SARS-CoV-2 genes except for ORF7, which is replaced with the coding sequence for the reporter protein NanoLuc. Shi also teaches the sequence of the NanoLuc reporter coding sequence is SEQ ID NO 6, which has 100% identity to nucleotide positions 21581-22093 of SEQ ID NO 5 of the examined application (See OA Appendix, page 1).
Shi does not teach 1) including a neomycin resistance gene in the replicon along with the NanoLuc reporter, or 2) replacement of the spike (S), membrane (M) and envelope (E) ORFs of the SARS-CoV-2 genome.
Fernandes teaches the start of the art of developing single-stranded replicon reporters for positive RNA virus, including SARS-CoV-2 (Abstract). Fernandes teaches that replicons are self-replicative subgenomic systems in which the genes encoding viral structural proteins are replaced by a reporter gene (page 2, ¶2). Fernandes teaches the correct 5’ and 3’ ends of the viral genome are crucial to the success of replicon constructs since many viruses have specific structures at their terminals for replication and/or translation (page 2, ¶2). Fernandes teaches a reporter gene is introduced in place of the deleted structural genes to allow luminometric (luciferases) or fluorescent (fluorescent proteins) detection of RNA replication (page 2, ¶3). Fernandes also teaches that replicons can be stably maintained in cells by introducing a drug resistance gene into the system, such as neomycin phosphotransferase (Neo), thereby simplifying high-throughput antiviral screenings (page 2, ¶4). Fernandes teaches that Coronavirdiae replicons have been developed in which a GFP reporter and a resistance gene replaced the genomic region from the Spike (S) gene through ORF8, including the Envelop (E), and Membrane (M) ORFs (Figure 2c; page 9 ¶4). Fernandes teaches another SARS-CoV replicon system was developed in which other the S gene was replaced by a GFP reporter. Fernandes teaches other viral replicon reporters that included both a luciferase reporter and a neomycin gene had the transgenes arranged such that they were not adjacent or co-translational with each other (Figure 2a).
Genbank2 teaches the neomycin-kanamycin phosphotransferase, type II coding sequence for gene targeting in mammalian cells (i.e., a neomycin resistance gene), which is 83% identical (662/796 nucleotides) to positions 22957 - 23751 of SEQ ID NO 5 (See OA appendix, page 2).
Regarding claims 32 and 34, it would have been obvious to one skilled before the effective filing date of the claimed invention to have modified the SARS-CoV-2 reporter of Shi by 1) replacing the Spike ORF with the NanoLuc coding sequence instead of ORF7a/b and 2) included the neomycin resistance coding sequence as taught in Genbank in place of the Envelope (E) and Membrane (M) ORFs. Such an arrangement using the sequences of the SARS-CoV-2 genome and NanoLuc disclosed in Shi, and the sequence of the neomycin resistance gene, disclosed in Genbank2 would result in a SARS-CoV-2 reporter replicon having 25701 out of 25835, or 99.5%, identical nucleotides as SEQ ID NO 5. It would have amounted to the simple combination of known elements by known means to yield predictable results. The skilled artisan would have predicted that a SARS-CoV-2 reporter replicon missing the spike, envelope and membrane ORFs would be replication competent because Fernandes teaches that the S, E and M genes encoding the structural proteins of coronaviruses can be removed from replicons and be used to assay viral replication. The skilled artisan would have been motivated to include a neomycin resistance gene so that stable cell lines comprising the SARS-CoV-2 replicon reporter could be generated, as taught in Fernandes. It also would have been entirely predictable that separate NanoLuc and Neomycin cassettes could be separated from each other in the viral genome because Fernandes teaches that is a functional arrangement in replicon reporters of other enveloped viruses. Finally, the skilled artisan would have been motivated to retain the remaining non-structural ORFS, such as ORF3a, ORF7a/b, ORF8 and ORF10 of SARS-CoV-2 so their function in viral replication could be assayed using the reporter replicon.
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Shi (US 20230416692 A1, priority to US provisional applications 63/000713 filed March 27, 2020 and 63/041667 filed June 19, 2020), Fernandes (Fernandes et al., Viruses (2020), 12:598, pages 1-22) and Genbank2 (AY909580.1, Synthetic construct neomycin-kanamycin phosphotransferase type II mRNA, complete cds, https://www.ncbi.nlm.nih.gov/nuccore/AY909580.1, [retrieved February 12, 2026]), as applied to claims 1, 16, 24, 32, 34, 41, 42, 62, 64 and 66 above, and further in view of Nakamura (US 20160281066 A1, published September 29, 2016) and Nakao (US 20170340687 A1, published November 30, 2017).
Claim 33 recites a SARS-CoV-2 replicon comprising a sequence that is at least 90% identical to nucleotides 284-28130 of SEQ ID NO 2. According to the Specification, nucleotides 284-28130 of SEQ ID NO 2 comprise the coding sequences for, starting from the 5’ end: ORF1a/b (including all the nsps), Luciferase-GFP fusion protein, ORF3a, Neomycin, ORF6, ORF7a, ORF7b, ORF8, N gene and ends just before ORF10 (Table 5, pages 116-117).
The teachings of Shi, Fernandes and Genbank2 are recited above as for claims 1, 16, 24, 32, 34, 41, 42, 62, 64 and 66 and are incorporated here. Shi also teaches SARS-CoV-2 replicons having the fluorescent reporter mNeonGreen instead of the NanoLuc reporter ([0008], FIG 3). Fernandes also teaches viral reporters have used the fluorescent proteins GFP and EGFP or the Renilla luciferase and firefly luciferase reporters (Figures 2 and 3; page 5, ¶2). The obviousness of replacing the Spike ORF with NanoLuc coding sequence and the Envelope and Membrane ORFs with the Neomycin resistance gene is recited above as for claims 32 and 34 and incorporated here.
Shi, Fernandes and Genbank2 do not teach using, or the the coding sequence for, a Luciferase-GFP fusion gene in a viral replicon reporter.
Nakamura teaches developing vaccinia viral vectors to carry transgenes for the treatment of cancer (Abstract). Nakamura teaches incorporating the coding sequence for a Luciferase-EGFP (Luc-GFP) fusion protein into a vaccinia viral replicon such that the coding sequence for Luc-GFP disrupts the coding sequence for the viral protein VGF (FIG 2B and D). Nakamura teaches the recombinant viral genomes comprising the Luc-GFP cassette were collected from cells infected with the Luc-GFP viral replicons ([0070]), indicating that the viral replicon is replication competent. Nakamura teaches measuring GFP levels in fibroblast cell lines infected with the Luc-GFP viral replicon ([0071]) and measuring luciferase expression levels in mice infected with the Luc-GFP viral replicon ([0074]).
Nakao also teaches the vaccina viral replicon having Luc-GFP fusion protein integrated at and disrupting the VGF gene (FIG 2). Nakamura teaches the sequence of the viral genome having the Luc-GFP coding sequence integrated at the VGF gene is set forth in SEQ ID NO 21 ([0166]). Nakamura teaches the sequence of SEQ ID NO 21 (pages 22-111). SEQ ID NO 21 comprises a sequence that is 97% (2379/2412) identical to positions 21581 – 23992 (i.e., the Luciferase-GFP coding sequence) (See OA Appendix, pages 3-8).
It would have been obvious to one skilled before the effective filing date of the claimed invention to have further modified the SARS-CoV-2 reporter of Shi by substituting the NanoLuc reporter sequence for the Luc-GFP coding sequence taught in Nakamura and Nakao. Such an arrangement using the known sequences of the SARS-CoV-2 genome taught in Shi, the Luc-GFP sequence taught in Nakao, and the sequence of the neomycin resistance gene, as taught in Genbank2 would result in a SARS-CoV-2 reporter replicon having 27680 out of 27847, or 99.4%, identical nucleotides as SEQ ID NO 2. It would have amounted to the simple combination of known elements and the substitution of one reporter for another by known means to yield predictable results. It would have been entirely predictable that a Luc-GFP dual fusion reporter could be used in place of the NanoLuc reporter in the obvious variant of Shi’s coronavirus reporter because 1) Nakamura and Nakao use the Luc-GFP reporter in a different viral replicon reporter, and 2) Shi demonstrates both fluorescent and luminescent reporters in a SARS-CoV-2 reporter. The skilled artisan would have been motivated to use Nakamura and Nakao’s Luc-GFP reporter in order to use both fluorescent and luminometric assays to assess viral replication.
Conclusion
No claims are allowable.
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/CATHERINE KONOPKA/Primary Examiner, Art Unit 1635