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 .
Claim Status
Applicant’s submission filed 04/10/2026 has been received and entered. Claim 8 has been cancelled. Claims 1-3, 5, 7 and 22 have been amended. Claim 28 has been new added. Accordingly, claims 1-3, 5, 7, 9-11, 13-16, 19 and 22-28 are pending and under current examination.
Status of Prior Rejections/Response to Arguments
The rejection to claims 1-3, 9-11, 13-16, 19 and 23-27 under 35 U.S.C. 102 (a)(1) and (a)(2) by Gao et al. is withdrawn:
Applicant’s amendment to claim 1 limits that “a polymerase protein (L) that comprises at least one heterologous intronic sequence”. Gao et al. do not teach this limitation. Thus Applicant’s amendment is effective to obviate the rejection of record. The rejection is withdrawn.
The rejection to claims 1-3, 5, 7-11, 13-16, 19 and 23-27 under 35 U.S.C. 103 over Gao et al. in view of Ibrahim et al. is maintained:
The rejection to claims 1-3, 9-11, 13-16, 19 and 22-27 are rejected under 35 U.S.C. 103 over Gao et al. in view of Dietzgen et al. is maintained:
The cancellation of claim 8 renders the rejection thereto moot.
Applicant has amended claim 1 and traversed the rejection, asserting that Ibrahim requiring three introns only in the L protein and not in the context of the full viral genome, the minigenome disclosed in Ibrahim does not include the full viral genome (Remarks, p7). In response, the Examiner submits that one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). In instant case, Gao et al. teach an engineered Barley yellow striate mosaic virus (BYSMV) vector with an exogenous RFP gene insertion, the RFP gene was flanked by the N/P gene junction sequences. Gao et al. do not teach the virus core protein polymerase protein (L) of the viral vector comprises at least one heterologous intronic sequence. However, Ibrahim et al. teach cloning the full-length L gene by incorporating three different introns to increase the L gene stability. An artisan would have been taught or motivated by the teachings to modify Gao et al.’s recombinant viral expression vector, and have at least one heterologous intron (i.e., three heterologous introns) inserted into the L protein as taught by Ibrahim et al., with the reasonable expectation that the incorporation of intron(s) can stabilize L gene ORF in the recombinant viral vector.
Applicant has further traversed the rejection, asserting that the results disclosed in Ibrahim for addressing the problem of genome instability are preliminary; Ibrahim provides no data whatsoever to demonstrate successful launch of a viral clone (i.e., a "first step") and also teaches use of a low-copy number strain of E. coli (Remarks, p7). The rejection failed to provide a "detailed enabling methodology for practicing the claimed invention, a suggestion to modify the prior art to practice the claimed invention, and evidence suggesting that it would be successful" (Remarks, p8). In response, the Examiner submits that MPEP2121 states “[W]hen the reference relied on expressly anticipates or makes obvious all of the elements of the claimed invention, the reference is presumed to be operable”. In this case, Ibrahim et al. teach cloning the full-length L gene by incorporating three different introns to increase the L gene stability (p8, parag 3), reads on the limitation that the polymerase protein (L) comprises at least one heterologous intronic sequence. Ibrahim et al.’s teaching of using a low-copy number strain of E. coli does not exclude the enablement of incorporating introns in L gene. Furthermore, Applicant is reminded that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In instant case, given that Gao et al. teach an engineered BYSMV vector for expressing an exogenous polynucleotide sequence (RFP), the vector comprising structural protein viral polymerase L, and Ibrahim et al. teach incorporating introns in L gene helps to increase the L gene stability, an artisan would have been motivated to modify Gao et al.’s recombinant viral expression vector, and incorporate heterologous intron(s) into the L protein as taught by Ibrahim et al., with the reasonable expectation that the incorporation of introns can stabilize L gene ORF. The rejection is maintained in modified form to address amended limitations.
Modified Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-3, 5, 7, 9-11, 13-16, 19 and 23-27 stand rejected and claim 28 is newly rejected under 35 U.S.C. 103 as being unpatentable over Gao et al. (New Phytol. 2019 Sep;223(4):2120-2133, cited in IDS), in view of Ibrahim et al. (PLoS One. 2020 Mar 5;15(3):e0229877), as evidenced by Yang et al. ( Arch Virol. 1998;143(12):2443-51). The rejection is modified as necessitated by Applicant’s amendment.
Gao et al. used Barley yellow striate mosaic Virus (BYSMV) as a model to develop the first recombinant cytorhabdovirus from cloned cDNAs, also engineered BYSMV-based vectors as versatile delivery and expression platforms for genomic studies in planthoppers and cereal plants. In addition, the reverse genetic approach developed in the study provides a template for rescue of other NSR viruses that are transmitted by insect vectors (p2121, left column).
Regarding claim 1, Gao et al. teach a recombinant plant cytorhabdovirus, Barley yellow striate mosaic virus (BYSMV) (Abstract). Gao et al. teach classical plant rhabdoviruses are negative strand RNA viruses (NSR) and comprise the Cytorhabdovirus and Nucleorhabdovirus genera based on cytoplasmic or nuclear replication and morphogenesis sites. All rhabdovirus genomes encode five conserved structural proteins, including the nucleoprotein(N), the phosphoprotein (P), the matrix protein (M), the glycoprotein (G) and the viral polymerase (L) in a conserved order 3’-N-P-M-G-L-5’ (p2120, right column- p2121, left column). Gao et al. teach an engineered BYSMV vector with an RFP gene insertion (p2122, right column, and figure 1a). This teaching reads on a recombinant viral expression vector (herein BYSMV vector with an RFP gene insertion) comprising: a negative strand RNA virus (NSV) backbone (BYSMV) comprising polynucleotide sequences encoding core proteins, wherein the core proteins comprise a polymerase protein L; and at least one expression cassette comprising an exogenous polynucleotide sequence (RFP)” in instant claim. Gao et al. teach in the engineered BYSMV vector with an RFP gene insertion, the RFP gene was flanked by the N/P gene junction sequences and this derivative was inserted between the BYSMV N and P genes (p2122, right column- p2123, left column, and Figure 1a). This teaching reads on “at least one expression cassette (RFP) comprising an exogenous polynucleotide sequence flanked by viral gene junctions from the NSV backbone”. Gao et al. also teach the BYSMV-based vectors (see figure 2a), the exogenous GFP and RFP gene were inserted between the N/P gene junctions and the derivative was cloned between the BYSMV N and P genes to produce pBY-GFP and pBY-GR (figure 2a), the GFP and RFP signal were expressed from BY-GFP and BY-GR infections in the small brown planthoppers (SBPHs). This teaching reads on the NSV backbone vector pBY-RFP and pBY-GR are capable of infecting a target organism (herein SBPHs) and expressing the exogenous polynucleotide sequence (GFP and RFP). Moreover, the limitation “wherein the NSV backbone encodes a virus capable of infecting a target organism and expressing the exogenous polynucleotide sequence” is also considered as an inherent property of the claimed recombinant viral expression vector. “[W]here the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977)”. See MPEP 2112.01.
Gao et al. do not teach the polymerase protein (L) comprises at least one heterologous intronic sequence. However, this was disclosed by Ibrahim et al. at the time of the instant invention.
Ibrahim et al. developed a negative sense minigenome cassette for Lettuce necrotic yellows virus (LNYV), introduced introns into the unstable viral ORF and employed Agrobacterium tumefaciens to co-infiltrate Nicotiana with the genes for the N, P, and L proteins together with the minigenome cassette. The minigenome cassette included the Discosoma sp. red fluorescent protein gene (DsRed) cloned in the negative-sense between the viral trailer and leader sequences which were placed between hammerhead and hepatitis delta ribozymes (Abstract).
Regarding claim 1, Ibrahim et al. teach cloning the full-length L gene by incorporating three different introns into the 5’ half of the E. coli pcnB gene and using a strain with modified gene for reduction of plasmid copy number (p8, parag 3). Ibrahim et al. teach the origin of the three introns: the third intron of the Phaseolus vulgari nitrite reductase (NIR) gene, the second intron of the Solanum tuberosum light-inducible tissue-specific ST-LS1 gene, and the first intron of Nicotiana tabacum ribulose 1, 5-bisphosphate carboxylase small subunit (NtRbcS) gene respectively (see the legend of figure 1). This teaching reads on the polymerase protein (L) comprises at least one heterologous intronic sequence.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Gao et al.’s recombinant viral expression vector, and have at least one heterologous intron (i.e., three heterologous introns) inserted into the L protein as taught by Ibrahim et al.. The skilled artisan would have been motivated to have at least one heterologous intron (i.e., three heterologous introns) inserted into the L protein since Ibrahim et al. teach introns can stabilize L gene ORF (see p4, parag 3). There would be a reasonable expectation of success of have at least one heterologous intron (i.e., three heterologous introns) inserted into the L protein since Ibrahim et al. teach the method to introduce introns to L protein (see p3, Gene constructs).
Regarding claim 2, following the discussion above, Gao et al. teach classical plant rhabdoviruses are negative strand RNA virus (NSR) viruses. All rhabdovirus genomes encode five conserved structural proteins, including the nucleoprotein(N), the phosphoprotein (P), the matrix protein (M), the glycoprotein (G) and the viral polymerase (L) in a conserved order 3’-N-P-M-G-L-5’ (p2121, left column).
Regarding claims 3 and 5, Gao et al. teach schematic diagrams of the pBY-RFP (p2124, figure 1a), for the core proteins including N, P, M, G and L, the polynucleotide sequence encoding the N protein is upstream of the polynucleotide sequences encoding the other core proteins, and the polynucleotide sequence encoding the L protein is downstream of the polynucleotide sequences encoding the other core proteins.
Regarding claim 7, Ibrahim et al. teach introns stabilize L gene ORF in E. coli and are correctly spliced in planta. The expected cDNA size of each segment with introduced introns was 500 bp, while 279, 312, and 407 bp respectively if introns were spliced out (see Fig 1A). All three introns were removed giving bands of the expected size (p4, parag 4), this teaching indicates that the at least one intronic sequence is inserted into the L protein at a splice site or a predicted splice site, as recited in instant claim.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Gao et al.’s recombinant viral expression vector, and have at least one heterologous intron (i.e., three heterologous introns) inserted into the L protein at a splice site as taught by Ibrahim et al.. The skilled artisan would have been motivated to have at least one heterologous intron (i.e., three heterologous introns) inserted into the L protein at a splice site since Ibrahim et al. teach introns can stabilize L gene ORF (see p4, parag 3). There would be a reasonable expectation of success of have at least one heterologous intron (i.e., three heterologous introns) inserted into the L protein at a splice site since Ibrahim et al. teach the method to introduce introns to L protein (see p3, Gene constructs).
Regarding claim 9, following the discussion above, Gao et al. teach the RFP gene is positioned between the N protein and the P protein (see figure 1a), reads on the at least one expression cassette is positioned between the N protein and the P protein, as recited in instant claim.
Regarding claim 10, Gao et al. teach in the pBY-RFP plasmid (figure 1a), the full-length BY-RFP cDNA contains duplicate N/P gene junctions flanking the red fluorescent protein (RFP) gene between the N and P genes of Barley yellow striate mosaic virus (BYSMV) antigenome cDNA (p2125, legend of figure 1).
Regarding claim 11, Gao et al. teach pBY-GR plasmid (see p2126, figure 2), which comprises a first expression cassette comprising a first exogenous polynucleotide sequence GFP, and a second expression cassette comprising a second exogenous polynucleotide sequence RFP, there are triple N/P gene junctions in the vector so that the second expression cassette RFP is also flanked by N/P junctions, as recited in instant claim.
Regarding claim 13, following the discussion above, Gao et al. teach the pBY-RFP plasmid comprising RFP, which is a gene-of interest (figure. 1a).
Regarding claim 14, following the discussion of claim 11, Gao et al. teach pBY-GR plasmid (see p2126, figure 2), which comprises a first expression cassette comprising a first exogenous polynucleotide sequence GFP, and a second expression cassette comprising a second exogenous polynucleotide sequence RFP, reads on the second exogenous polynucleotide sequence encodes a second gene-of-interest.
Regarding claims 15 and 19, Gao et al. teach BYSMV derivatives expressing CRISPR-Cas9 nucleases and guide RNAs (gRNAs) can mediate genome editing in plants (p2126, left column). Gao et al. generated the pBY-Cas9-RFP vector, in which the Cas9 nuclease and a single guide RNA (sgRNA) were substituted, respectively, for the GFP and CFP genes of pBY-GRC (see p2128, figure 4a). This teaching reads on the exogenous polynucleotide encodes Cas9 nuclease and a sgRNA, the two components of a CRISPR-Cas system, as recited in instant claim.
Regarding claims 16, following the discussion above, Gao et al. generated the pBY-Cas9-RFP vector comprising Cas9 nuclease and a sgRNA (see p2128, figure 4a). Gao et al. also teach the gRNA contains a guide sequence matching a 20 bp region within the GFP gene in N. benthamiana 16c plants. In addition, the sgRNA targeting sequence contains an NdeI restriction site that will be abolished by successful genome editing (p2126, right column -2128, left column, and figure 4b). This teaching reads on the CRISPR-Cas system is a genome engineering system, as recited in instant claim.
Regarding claims 23 and 25, Gao et al. teach the engineered BYSMV vectors could express the c. 600-amino-acid b-glucuronidase (GUS) protein and a red fluorescent protein stably in systemically infected leaves and roots of cereals, including wheat, barley, foxtail millet, and maize plants (Abstract), reads on the target organism of the recombinant viral expression vector can be a plant as recited in instant claim 23, such as maize as recited in instant claim 25.
Regarding claims 24 and 26, Gao et al. teach BY-GFP, BY-GR and BY-GRC infections in the small brown planthoppers (SBPHs), and the expression of GFP, RFP and CFP in SBPHs (see p2126, figure 2b). This teaching indicates the target organism is an insect (planthoppers), and the expression of GFP and RFP indicates the vector is transmissible to insects, as recited in instant claims.
Regarding claim 27, Gao et al. teach the pBY-RFP plasmid was transformed into A. tumefaciens and co-infiltrated into N. benthamiana leaves (Fig. 1b). By 14 dpi, high-intensity RFP fluorescence was observed in the cells agroinfiltrated with pBY-RFP. This teaching reads on a cell of the N. benthamiana leaves comprising the pBY-RFP plasmid, wherein the cell is a plant cell.
Regarding claim 28, Gao et al. do not teach the polymerase protein (L) comprises at least one heterologous intronic sequence. However, Ibrahim et al. teach overcoming L gene instability by introducing three introns and using an E. coli strain that enabled downregulation of plasmid copy-number (p2, parag 3). Ibrahim et al. use three introns in their experiments, but the principle they based on is that strategies (of cloning whole L gene) including the use of single point mutations, insertion of introns, and use of low-copy plasmid have been used to overcome these problems (see p8, parag 3). Gao et al. cite the reference of Yang et al. (reference 26). Yang et al. teach construction of a full length cDNA copy of the genomic RNA of lettuce mosaic virus (LMV), the intron II of the bean nitrite reductase gene was engineered into the LMV FL cDNA (summary). Yang et al. teach the method of the construction of the intron-containing FL cDNA, the 221 bp intron II of bean nitrite reductase gene, engineered to have PstI and NsiI sites in its splicing borders (p2446, parag 3). Therefore it is also appliable that a single heterologous intronic sequence can be used in the polymerase protein (L).
Claims 1-3, 5, 7, 9-11, 13-16, 19 and 22-27 stand rejected and claim 28 is newly rejected under 35 U.S.C. 103 as being unpatentable over Gao et al. (New Phytol. 2019 Sep;223(4):2120-2133, as cited in IDS), in view of Ibrahim et al. (PLoS One. 2020 Mar 5;15(3):e0229877), as evidenced by Yang et al. ( Arch Virol. 1998;143(12):2443-51), as applied to 1-3, 5, 7, 9-11, 13-16, 19 and 23-28 above, further in view of Dietzgen et al. (Virus Res. 2020 May;281:197942, as cited in IDS). The rejection is modified as necessitated by Applicant’s amendment.
The teaching of Gao et al. and Ibrahim et al. is set forth above.
Regarding claim 22, Gao et al. teach engineered BYSMV vectors, wherein the BYSMV is plant cytorhabdovirus (see Abstract), which belongs to plant rhabdoviruses (p2120, right column). Gao et al. and Ibrahim et al. do not teach the NSV backbone is derived from a virus from the genus Alphanucleorhabdovirus. However, this was disclosed by Dietzgen et al. at the time of instant invention.
Dietzgen et al. review selected, better studied examples of plant rhabdoviruses, their genetic diversity, epidemiology and interactions with plant hosts and arthropod vectors (Abstract).
Regarding claim 22, Dietzgen et al. teach alphanucleorhabdovirus belongs to rhabdoviruses: two unique rhabdoviruses are known to infect rice and cause yield losses, the cytorhabdovirus rice stripe mosaic virus (RSMV) and the alphanucleorhabdovirus rice yellow stunt virus (RYSV) (p5, left column). Dietzgen et al. also teach RYSV is an alphanucleorhabdovirus that encodes 7 ORFs in the antigenome in the same order as the cytorhabdovirus RSMV (p5, left column).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Gao et al.’s recombinant viral expression vector, and use alphanucleorhabdovirus as the NSV backbone as taught by Dietzgen et al.. The only difference between instant claim and Gao et al.’s recombinant viral expression vector having cytorhabdovirus BYSMV backbone is instant claim uses alphanucleorhabdovirus as the NSV backbone. Given that Gao et al. teach all rhabdovirus genomes encode five conserved structural proteins, including the nucleoprotein(N), the phosphoprotein (P), the matrix protein (M), the glycoprotein (G) and the viral polymerase (L) in a conserved order 3’-N-P-M-G-L-5’ (p2121, left column), and Dietzgen et al. teach alphanucleorhabdovirus is similar to cytorhabdovirus, which also belongs to rhabdovirus, has similar function of infecting rice and causing yield losses, and also encodes 7 ORFs in the antigenome in the same order as the cytorhabdovirus RSMV (p5, left column), one of ordinary skill in the art would have substituted cytorhabdovirus BYSMV backbone, and use alphanucleorhabdovirus as the NSV backbone depends on their research interest. This simple substitution of one known element (use alphanucleorhabdovirus as the NSV backbone) for another known element (use cytorhabdovirus BYSMV as the NSV backbone) is likely to be obvious when predictable results are achieved. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 — 97 (2007) (see MPEP § 2143, B.).
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/Q.G./Examiner, Art Unit 1633
/FEREYDOUN G SAJJADI/Supervisory Patent Examiner, Art Unit 1699
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