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 .
Election/Restrictions
Applicant’s election without traverse of a variant of SARS-CoV-2 in the reply filed on July 25, 2026 is acknowledged.
Status of Claims
Claims 1-20 are currently pending and under examination on the merits in the instant application.
Specification
The abstract of the disclosure is objected to because the word “novel” is not descriptive of an invention. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Drawings
The petition to accept color drawings filed on December 21, 2023 has been dismissed. See the decision mailed on February 14, 2024. Accordingly, the drawings filed on December 21, 2023 are not accepted.
Information Disclosure Statement
The listing of references in the specification, see pages 58-62, is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-3, 5, 7-9, and 11-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Xie et al. (Cell Host & Microbe, 2020,27:841-848, applicant’s citation).
Xie teaches an in vitro assembly of the molecular clone of the wild-type SARS-CoV-2 gene comprising dividing the full-length cDNA genome into seven partially overlapping fragments as templates, each of which is flanked by a type IIS restriction endonuclease site (e.g., BsaI) in opposite orientation; digesting the fragments with the enzyme, thereby generating sticky ends; purifying and in vitro ligating the fragments; and generating the full-length cDNA of the wild-type SARS-CoV-2 by cloning all fragments into a single vector, wherein the first fragment is operably linked to a promoter. See page 842; Figure 1.
Xie teaches the in vitro assembly methodology can be applied to assemble a mutant SARS-CoV-2 cDNA having the ORF7 sequence replaced with an exogenous gene. See pages 843-844; Figure 3.
Accordingly, claims 1-3, 5, 7-9, and 11-20 are described by Xie et al.
Claims 1-3, 5, 7-9, 11-14, and 16-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ju et al. (PLOS Pathogens, 2021, 17(3):e1009439, applicant’s citation).
Ju teaches a ligation-based assembly of the molecular clone of SARS-CoV-2 lacking N gene comprising dividing the full-length cDNA genome into five partially overlapping fragments as templates, each of which is flanked by a type IIS restriction endonuclease site, which is BsaI or BsmBI; amplifying the five fragments by PCR; digesting the fragments with BsaI or BsmBI, thereby generating sticky ends; purifying and ligating the fragments that are operably linked to a T7 promoter; and generating the full-length cDNA of SARS-CoV-2 lacking N gene. See pages 2-3; Figure 1A.
Accordingly, claims 1-3, 5, 7-9, 11-14, and 16-20 are described by Ju et al.
Claims 1-3, 5, 7, 11-14, and 16-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Baric et al. (US 2002/0177230 A1).
Baric discloses a “method of directionally assembling a recombinant viral genome” that “comprises a mutation”, wherein the viral genome is “a coronavirus genome”, wherein coronaviruses “cause about 30% of the common colds in humans”, wherein the method comprises dividing the viral genome into “at least five subclones”, “wherein each termini of each subclone is a restriction enzyme recognition site” including “Bbs1”, which overlap with the adjacent subclone, wherein the subclones are ligated and assembled, wherein the assembled recombinant viral genome is infected into a host cell. See claims 1-24; Figures 1-2; paragraphs 0010-0013 and 0068-0071.
Accordingly, claims 1-3, 5, 7, 11-14, and 16-20 are described by Baric et al.
Claims 1-3, 5-7, and 13-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lohman et al. (US 2022/0098577 A1).
Lohman discloses an “efficient assembly of the viral genome from many parts”, wherein the viral genome includes SARS-CoV-2 (“Genbank ID: NC_045512”) and the many parts include 12 fragments, wherein such assembly is useful for research and vaccine development, wherein the assembly utilizes the methodologies illustrated in Figures 1A-2C, which comprise using multiple fragments/inserts each comprising overlapping sequences with the adjacent fragment/insert each flanked by BsaI cut sites in opposite orientations, wherein the fragments/inserts are . See paragraph 0393. See also Figures 1A-2C reproduced below.
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Lohman teaches that the assembly methods can be used to assemble “different genomes” including different “virus genomes”. See paragraph 0013.
Accordingly, claims 1-3, 5-7, and 13-20 are described by Lohman et al.
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.
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 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Lohman et al. (US 2022/0098577 A1) in view of Pastorio et al. (Cell Host & Microbe, 2022, 30:1255-1268).
Lohman discloses an “efficient assembly of the viral genome from many parts”, wherein the viral genome includes SARS-CoV-2 (“Genbank ID: NC_045512”) and the many parts include 12 fragments, wherein such assembly is useful for research and vaccine development, wherein the assembly utilizes the methodologies illustrated in Figures 1A-2C, which comprise using multiple fragments/inserts each comprising overlapping sequences with the adjacent fragment/insert each flanked by BsaI cut sites in opposite orientations, wherein the fragments/inserts are . See paragraph 0393. See also Figures 1A-2C.
Lohman teaches that the assembly methods can be used to assemble “different genomes” including different “virus genomes”. See paragraph 0013.
Lohman does not teach that the assembly comprises the Omicron variant, nor does Lohman teach that the assembly comprises a deletion of the ORF encoding the S protein.
Pastorio teaches that the SARS-CoV-2 Omicron variant “currently dominates the COVD-19 pandemic” due to its “enhanced transmission and immune evasion”, which are “driven by numerous mutations in the Omicron Spike protein.” See abstract.
Pastorio teaches that “further studies are required to fully understand the full consequences of all the complex changes in the Omicron Spike on viral infectivity, tropism, transmission, and pathogenesis”. See page 1265.
It would have been obvious to one of ordinary skill in the art before the effective filing date to utilize Lohman’s viral genome assembly method comprising using the prevalent Omicron variant of the SARS-CoV-2. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success in order to study the mutation-containing Omicron variant because it was an art-recognized to study the Omicron variant as it was deemed the most prevalent variant of SARS-CoV-2 with the “enhanced transmission and immune evasion” as reported by Pastorio. It would also have been obvious to utilize Lohman’s viral genome assembly method using an artificially designed SARS-CoV-2 mutant having a deletion of the Spike protein-encoding ORF in order to investigate the impact of the Spike protein in SARS-CoV-2 infectivity and transmission because mutations in the Spike protein, in particular in the Omicron variant, were suggested to contribute to the “enhanced transmission and immune evasion” thus “further studies” pertaining to the Spike protein’s role in particular in the Omicron variant were suggested to be necessary “to fully understand” the nexus between the Spike protein’s mutations and viral infectivity, tropism, transmission, and pathogenesis” of SARS-CoV-2 as evidenced by Pastorio.
In view of the foregoing, claims 1-20 taken as a whole would have been prima facie obvious before the effective filing date.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DANA H SHIN whose telephone number is (571)272-8008. The examiner can normally be reached Monday-Thursday: 8am - 6:30pm.
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/DANA H SHIN/Primary Examiner, Art Unit 1635
