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 .
Response to Amendment/Status of Claims
Claims 1,5,36 and 61 were amended. Claims 1,2,4-7,9,11,14,19,20,24,36,40-43,47,58 and 61 are currently pending in the instant application.
Election/Restrictions
Applicant's election with traverse of Group I (claims 1,2,4-7,9,11,14,19,20,24, 36,40-43 and 47 in the reply filed on 05/11/2026 is acknowledged. The traversal is on
the ground(s) that there would be no serious burden on the examiner to search and examine all pending claims. This is not found persuasive because a search/examination burden is not a criterion for restriction/election requirement for this national stage application.
The requirement is still deemed proper and is therefore made FINAL.
Claims 58 and 61 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim.
Applicant's election with traverse of the species of nucleotides 1-450 of SEQ ID NO: 1 (from claim 14) in the reply filed on 05/11/2026 is acknowledged. The traversal is on the ground(s) that there would be no serious burden on the examiner to search and examine all pending claims. This is not found persuasive because a search/examination burden is not a criterion for restriction/election requirement for this national stage application. However, upon further consideration the species in claim 14 have been expanded to include the nucleotide ranges taught by Yao et al.
Claims 1,2,4-7,9,11,14,19,20,24,36,40-43 and 47 are under examination.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 09/30/2024, 11/05/2025 and 05/11/2026 have been considered by the examiner.
Note that all foreign language documents submitted with English language title and abstract are considered only insofar as the English language portion as submitted by applicant.
Note that all NPL documents submitted without English language translation filed on 11/05/2025 are not considered.
Note that the BR foreign patent document filed on 11/05/2025 is in non-English
language in its entirety. Hence. The reference is not considered.
Note that WO 2018/011225 A1 filed on 09/30/2024 pertains to a sensor-based
breastfeeding volume measurement device. The examiner is unable to understand the relevance of this reference to the instant application. Hence, the reference is not considered. If applicant wishes the examiner to consider this particular reference, applicant is required to provide a reason as to how the reference is related to the field of the invention and why the examiner must consider this seemingly unrelated reference.
Priority
This application is a 371 of PCT/US2022/026223, filed 04/25/2022 and claims priority to PCTUS2021028809, filed 04/23/2021 as reflected by the most recent filing receipt.
Claim Objections
Claims 1,2,4-7,9,11,14,19,20,24,36,40-43 and 47 are objected to because of the following informalities: The claim text is not in black font, thereby reading the claims difficult. Applicant is required to use black font in the next reply. Note that application papers including claims must be clearly legible using black colored font text and black lines. See MPEP §608.01.
Claim 43 is objected to because there is a missing space in line 2 between “of and “claim 1”.
Specification
The disclosure is objected to because of the following informalities: Page 110, paragraph 0282 of the instant specification states that the 5’ SARS-CoV-2 sequences in TIP1 are as shown below (SEQ ID NO: 28).
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The sequence above shown on page 110 of the instant specification is not the same sequence that is listed in the Sequence Listing for SEQ ID NO: 28. The sequence listing has SEQ ID NO: 28 as “aaatttcccggg” which is different than the sequence above. Either the specification is incorrect, or the Sequence Listing is incorrect.
Appropriate correction is required.
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.
Written Description Rejection
Claims 1,2,4-7,9,11,14,19,20,24,36,40-43 and 47 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 claim(s) 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The specification discloses recombinant SARS-CoV-2 constructs such as TIP1 and TIP2 which encode varying portions of the 5’ and 3’ UTRs of SARS-CoV-2 and expressing mCherry reporter protein driven from an IRES which meet the written description and enablement provisions of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph. However, claims 1,2,4-7,9,11,14,19,20,24,36,40-43 and 47 are directed to encompass recombinant SARS-CoV-2 constructs which only correspond in some undefined way to specifically instantly disclosed constructs. Other than the recombinant SARS-CoV-2 constructs of TIP1 and TIP2, the recited constructs do not meet the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, due to lacking chemical structural information for what they are and chemical structures are highly variant and encompass a myriad of possibilities. The specification provides insufficient written description to support the genus encompassed by the claim. Note: MPEP 2163.
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, (Fed. Cir. 1991), makes clear 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 [he or she] invented what is claimed." (See Vas-Cath at page 1116.)
Univ. of Rochester v. G.D. Searle, 69 USPQ2d 1886, 1892 (CAFC 2004), further supports this by stating that:
The appearance of mere indistinct words in a specification or a claim, even an original claim, does not necessarily satisfy that requirement. A description of an anti-inflammatory steroid, i.e., a steroid (a generic structural term) described even in terms of its functioning of lessening inflammation of tissues fails to distinguish any steroid from others having the same activity or function. A description of what a material does, rather than of what it is, usually does not suffice…. The disclosure must allow one skilled in the art to visualize or recognize the identity of the subject matter purportedly described. (Emphasis added).
Instant claim 1 recites a recombinant SARS-CoV-2 construct capable of interfering with SARS-CoV-2 replication comprising (a) a 5’ untranslated region (UTR) comprising at least 100 nucleotides of a SARS-CoV-2 5’UTR or a variant thereof, (b) an intervening sequence, and (c) a 3’ UTR region comprising at least 100 nucleotides of a SARS-CoV-2 3’UTR or a variant thereof, wherein the recombinant SARS-CoV-2 construct cannot replicate by itself, wherein the recombinant SARs-CoV-2 construct can replicate in the presence of SARS-CoV-2, and wherein the intervening sequence is about 1 base pair (bp) to about 29000 bp in length, and therefore encompasses a large genus of constructs comprising different parts and lengths and therefore different sequences of the 5’UTR and 3’UTR and variants thereof. Based on the broadest reasonable interpretation of “variants thereof”, this encompasses any variation of the 5’UTR and/or 3’UTR including a shorter length, as a variant does not necessarily require the recited length of 100 nts of the 5’ and 3’ UTRs as it could be any portion thereof. The same interpretation applies to claims 4,6,7 and 14.
In contrast, the specification discloses the 5’ SARS-CoV-2 sequence in TIP1 as SEQ ID NO: 28 and the 3’ SARS-CoV-2 sequence in TIP1 as SEQ ID NO: 29, the 5’ SARS-CoV-2 sequence in TIP2 as SEQ ID NO: 30 and the 3’ SARS-CoV-2 sequences in TIP2 as SEQ ID NO: 31 (Example 2, pages 110-112). Two additional TIP variants are also shown with the 5’ sequence as SEQ ID NO: 32 and SEQ ID NO: 33 (page 112,113). The TIP constructs were tested to see if they can reduce SARS-CoV-2 replication, and results showed that TIP constructs reduced SARS-CoV-2 viral replication but TIP2 construct exhibited the greatest interference with SARS-CoV-2 (paragraph 0288, Fig. 8). Example 5 shows TIP1 and TIP2 can intervene or interfere with different SARS-CoV-2 strains (pages 115-116, FIGS. 13A-13C and that TIP1 and TIP2 significantly reduce the replication of SARS-CoV-2 in a dose-dependent manner. Example 6 shows testing the TIPs on a human lung organoid model (Example 6, pages 116-117, FIG. 14A,C,D) and results were that TIPs reduced SARS-CoV-2 compared to control RNA. Example 9 shows testing in a Hamster model of SARS-CoV-2 infection for in vivo efficacy of SARS-CoV-2 TIPS by intranasal administration and then challenged with SARS-CoV-2, and that control treated hamsters showed weight loss following infection but this was significantly ameliorated by TIP treatment (paragraph 0318, FIG. 17D), significant reduction in SARS-CoV-2 viral load in TIP-treated animals (FIG. 17E).
With the exception of the above specifically disclosed TIP constructs, the skilled artisan cannot envision the detailed chemical structure of the encompassed recombinant SARS-CoV-2 constructs. The specification does not describe a sufficient number of species of the claimed genus which encompasses many different portions and sequences of the 5’UTR and 3’UTR of SARS-CoV-2. Claim 1 only requires a SARS-CoV-2 5’UTR and a SARS-CoV-2 3’UTR and as stated above the “at least 100 nucleotides of a SARS-CoV-2 5’UTR or a variant thereof” and “at least 100 nucleotides of a SARS-CoV-2 3’UTR or a variant thereof” does not necessarily require 100 nucleotides in length based on the broadest reasonable interpretation, and in addition, could be any region of the 5’ UTR and 3’UTR, and the specification does not describe what part of the 5’UTR and 3’UTR or variant thereof is required in order to carry out the recited functions. In addition, claims 4,6,7 and 14 also encompass just a portion or fragment of the recited nucleotide ranges of SEQ ID NO: 1 by reciting “or a variant thereof”. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. The chemical structure itself is required. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Circ. 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016, (Fed. Cir. 1991). In Fiddes v. Baird, 30 USPQ2d 1481, 1483, (Bd. Pat. App. & Int. 1993), claims directed to mammalian FGF's were found unpatentable due to lack of written description for the broad class. The specification provided only the bovine sequence. Finally, University of California v. Eli Lilly and Co., 43 USPQ2d 1398, 1404, 1405 (Fed. Cir. 1997) held that:
...To fulfill the written description requirement, a patent specification must describe an invention and do so in sufficient detail that one skilled in the art can clearly conclude that "the inventor invented the claimed invention." Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997); In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989) (" [T]he description must clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed."). Thus, an applicant complies with the written description requirement "by describing the invention, with all its claimed limitations, not that which makes it obvious," and by using "such descriptive means as words, structures, figures, diagrams, formulas, etc., that set forth the claimed invention." Lockwood, 107 F.3d at 1572, 41 USPQ2d at 1966.
Furthermore, to the extent that a functional description can meet the requirement for an adequate written description, it can do so only in accordance with PTO guidelines stating that the requirement can be met by disclosing “sufficiently detailed, relevant identifying characteristics,” including “functional characteristics when coupled with a known or disclosed correlation between function and structure.” Univ. of Rochester v. G.D. Searle, 68 USPQ2d 1424, 1432 (DC WNY 2003). In the instant case, there is no core structure or a structure-function correlation for the genus of recombinant SARS-CoV-2 constructs with the recited functions recited in claims 1,2,4-7,9,11,14,19,20,24,36,40-43 and 47 (capable of interfering with SARS-CoV-2 replication; wherein the recombinant SARS-CoV-2 construct cannot replicated by itself, wherein the recombinant SARS-CoV-2 construct can replicate in the presence of SARS-CoV-2 (Claim 1); wherein the recombinant SARS-CoV-2 construct genomic RNA is produced at a higher rate than SARS-CoV-2 genomic RNA when present in a host cell infected with SARS-CoV-2 such that the ratio of the construct SARS-CoV-2 genomic RNA to the SARS-CoV-2 genomic RNA is greater than 1 in the cell (claim 36); wherein the recombinant SARS-CoV-2 construct has a basic reproduction ration (R0)>1 (claim 40); as well as the function of treating or preventing SARS-CoV-2 infection in an individual (claim 47).
Therefore, only the TIP1 and TIP2 constructs described above, but not the full breadth of the claim(s) meet the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph. The species specifically disclosed are not representative of the genus because the genus is highly variant. Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 USC § 112 is severable from its enablement provision. (See page 1115.)
Claim Interpretation
Regarding the wherein clauses and functional limitations recited in instant claims 1,36 and 40, art that teaches the structure recited in the claims would necessarily have the claimed functions and properties of those claims. This applies to claim 1 regarding the functional limitation “capable of interfering with SARS-CoV-2 replication”, the wherein clauses, “wherein the recombinant SARS-CoV-2 construct cannot replicated by itself”, and “wherein the recombinant SARS-CoV-2 construct can replicate in the presence of SARS-CoV-2”; claim 36 regarding “wherein the recombinant SARS-CoV-2 construct genomic RNA is produced at a higher rate than SARS-CoV-2 genomic RNA when present in a host cell infected with SARS-CoV-2, such that the ratio of the construct SAR-CoV-2 genomic RNA to the SARS-CoV-2 genomic RNA is greater than 1 in the cell”, and claim 40 regarding “wherein the recombinant SARS-CoV-2 construct has a basic reproduction ratio (Ro) >1”.
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 1,2,4,6,7,9,11,14,24,36,40 and 42 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yao et al. (bioRxiv, posted on November 23, 2020) as evidenced by GenBank accession number MW250351.
Regarding claims 1,9,24,36 and 40, Yao teaches a "short synthetic" "defective interfering (DI)" construct from parts of the SARS-CoV-2 genome, against SARS-CoV-2, wherein the construct is made from three portions: the 5’ UTR and the adjacent 5' part of nsp1 in ORF1a (which can be considered to be an intervening sequence); a part of nsp15 that includes the putative packaging signal; and the sequence spanning the 3' part of the N sequence, ORF10 (also can be considered an intervening sequence) and the 3’UTR (pages 1 and 3). Yao teaches the DNA sequence of the DI genome as "GenBank accession number; MW250351" having nucleotides "1 to 789", "19674 to 20340", and "28477 to 29903" of "GenBank accession number: NC_045512.2" in the order from the 5' end to the 3' end (page 8). Figure 1a below shows the DNA constructs of the WT and DI which shows the nucleotide lengths as well of each of the parts forming the DI construct, and which meet the structural limitations of claim 1, including for the parts of the construct that read on the intervening sequence (see above) of 1-29000 bp in length as claimed. Yao also teaches the DI genome reduced the amount of SARS-CoV-2 by approximately half within 24 hours of transfection (page 4).
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Regarding claim 2, Yao teaches the length of the synthetic DI is 2882 nt (page 3), and therefore the total length falls within the range recited in instant claim 2.
Regarding claim 4, the instant specification discloses that a DNA sequence for the SARS-CoV-2 genome, with coding regions is available as accession number NC_045512.2 from the NCBI website (Provided as SEQ ID NO: 1 herein) (page 21). Yao teaches the DNA sequence of the DI genome as "GenBank accession number; MW250351" having nucleotides "1 to 789", "19674 to 20340", and "28477 to 29903" of "GenBank accession number: NC_045512.2" in the order from the 5' end to the 3' end (page 8). Instant claim 4 recites wherein the 5’ UTR region comprises nucleotides 1-265 of SEQ ID NO: 1, or a variant thereof. Claim 4 recites “comprises”, which encompasses that additional nucleotides can be included as long as nucleotides 1-265 of SEQ ID NO: 1 are included and Yao teaches nucleotides 1-789 of GenBank accession number: NC_045512.2 that instant SEQ ID NO: 1 corresponds to, and therefore Yao teaches the limitations of claim 4.
Regarding claims 6 and 7, as Yao teaches the DNA sequence of the DI genome as "GenBank accession number; MW250351" having nucleotides "1 to 789", "19674 to 20340", and "28477 to 29903" of "GenBank accession number: NC_045512.2" in the order from the 5' end to the 3' end and as explained above “comprises” encompasses that additional nucleotides are included and that instant SEQ ID NO: 1 corresponds to GenBank accession number: NC_045512.2, Yao teaches the limitations of the ranges of instant claims 6-7.
Regarding claim 11, the sequences taught by Yao in the DI construct that read on the intervening sequence (the adjacent 5' part of nsp1 in ORF1a, or the sequence spanning the 3' part of the N sequence, ORF10) are SARS-CoV-2 sequences (See Fig 1a and page 8, first paragraph).
Regarding claim 14, “comprises” encompasses that additional nucleotides can be included as long as nucleotides 1-450 of SEQ ID NO: 1, or nucleotides 29543-29903 of SEQ ID NO: 1 or nucleotides 29191-29903 of SEQ ID NO: 1 are included. As stated above, the DI construct of Yao of GenBank accession number MW250351 has nucleotides "1 to 789", "19674 to 20340", and "28477 to 29903" of "GenBank accession number: NC_045512.2 which instant SEQ ID NO: 1 corresponds to, and therefore meets the limitations of (i), (iii) and (iv) of claim 14 as the DI construct comprises nucleotides 1-450 of SEQ ID NO: 1, nucleotides 29543-29903 of SEQ ID NO: 1 and nucleotides 29191-29903 of SEQ ID NO: 1.
Regarding claim 43, Yao teaches Vero-E6 cells in culture, electroporated with the RNA produced by in vitro transcription of the DI and that the efficiency of transcription was 90% (page 8), and therefore teaches an isolated cell comprising the recombinant construct.
Since Yao's construct comprising GenBank accession number MW250351 fully satisfies all structural limitations set forth in the rejected claims, it necessarily follows that Yao's construct inherently possesses the functions and properties recited in the rejected claims, absent objective evidence to the contrary. See claim interpretation above regarding the wherein clauses and functions recited in claims 1, 36 and 40.
"[T]he patentability of apparatus or composition claims depends on the claimed structure, not on the use or purpose of that structure." Catalina Mkt. Int 'l, Inc. v. Coolsavings.com, Inc., 289 F.3d 801, 809 (Fed. Cir. 2002). That is, "[f]rom the standpoint of patent law, a compound and all of its properties are inseparable; they are one and the same thing." In re Papesch, 315 F.2d 381, 391 (CCPA 1963).
Accordingly, claims 1,2,4,6,7,9,11,14,24,36,40 and 42 are anticipated by Yao et al.
Claims 1,2,4,11,14,19,20,24,36,40 and 42 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Zhang et al. (US 2024/0192196 A1, Filed 30 Sep 2020).
Regarding claims 1,2,11,19,20,36 and 40, Zhang discloses a "SARS-COV-2 replicon construct" of SEQ ID NO:30 comprising a " 5′-UTR at the 5′ end of SARS-COV-2; downstream was a ribosome entry site (IRES); further downstream was GFP reporter gene, wherein four translation stop codons were inserted at an end of the GFP reporter gene; further downstream was firefly luciferase gene connected to the transcription regulatory region (TRS) for M protein of SARS-COV-2; and the 3′ end was the non-coding region 3′-UTR at the 3′ end of SARS-COV-2". The GFP reporter gene and firefly luciferase gene is being considered to be the intervening sequence and which is a heterologous sequence encoding one or more functional proteins (instant claims 11 and 20). The construct of SEQ ID NO: 30 is 4364 nucleotides in length (paragraphs 0026, 0038, 0117; claim 1). The nucleotide sequence of the 5’UTR of novel coronavirus SARS-CoV-2 is SEQ ID NO: 26 (265 nt long) and the nucleotide sequence of the 3’UTR of novel coronavirus SARS-CoV-2 was shown in SEQ ID NO: 27 (294 nt long) (paragraphs 0038-0039,0117-0118) and therefore teaches the length requirements of claims 1 and 2.
Regarding claim 4, Zhang et al. teach the SARS-COV-2 replicon construct has the 5’UTR of SEQ ID NO: 26 which is 265 nucleotides long. SEQ ID NO: 26 of Zhang et al. (Db) which is the 5’-UTR sequence is 100% identical to nucleotides 1-265 of instant SEQ ID NO: 1 (Qy):
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Regarding claim 14, Zhang's construct of SEQ ID NO:30 (Db) comprises 450-nt of instant SEQ ID NO: 1 (Qy) at positions 7-456:
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Regarding the limitations of claim 19, in which the intervening sequence comprises a heterologous sequence which does not encode a functional protein, the above construct is taught as containing an IRES, in which the nucleic acid sequence of a ribosomal entry site was further connected between the 5’UTR of novel coronavirus SARS-CoV-2 and re porter gene A, the sequence of which is SEQ ID NO: 28 (paragraphs 0115, 0117).
Regarding claim 24, Zhang et al. teach the construct of SEQ ID NO: 30 is a DNA sequence (paragraph 0118).
Regarding claim 42, Zhang et al. teach an HEK293T cell line used as a packaging cell for verification of the replication system of Example 1 (Example 2, paragraph 0123) and therefore teach an isolated cell comprising the recombinant SARS-CoV-2 construct of claim 1.
Since Zhang's construct comprising SEQ ID NO:30 fully satisfies all structural
limitations set forth in the rejected claims, it necessarily follows that Zhang's construct
inherently possesses the functions and properties recited in the rejected claims, absent objective evidence to the contrary. See claim interpretation above regarding the wherein clauses and functions recited in claims 1, 36 and 40.
Accordingly, claims 1,2,4,11,14,19,20,24,36,40 and 42 are anticipated by Zhang et al.
Claims 1,2,4,6,7,9,11,14,24,36,40-43 and 47 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Jordan et al. (WO 2021/259883 A1, EFD 23 June 2020) as evidenced by GenBank accession number NC_045512.2 (cited on an IDS).
Regarding claims 1,2,4,11,14,24,36 and 40, Jordan teaches the basis for design of the synthetic nucleic acid molecule of the present invention is the SARS-CoV-2 isolated Wuhan-Hu-1 (Genbank NC_045512.2) (Example 1, page 40) which is the same accession number disclosed in the instant specification and provided as instant SEQ ID NO: 1 (See page 21 of instant specification). Jordan teaches the artificial sequence was constructed stepwise into a mosaic of 4 sequences, Mosaic-1 (SEQ ID NO: 1), Mosaic-2 (SEQ ID NO: 2), Mosaic-3 (SEQ ID NO: 3) and Mosaic-4 (SEQ ID NO: 4) each of which is described on page 40. Regarding the recited intervening sequence, Jordan teaches the Mosaic-1 (SEQ ID NO: 1) includes the 5’ UTR with proposed promoter sequences for replication and the TRS-L element and extends into ORF1a to also include a promoter element; Mosaic-2 (SEQ ID NO: 2 includes the ribosomal slippage site at the junction of ORF1a and 1b; Mosaic-4 (SEQ ID NO:4) also contains other components other than the 3’UTR including the stop codon of ORF8 and intergenic region upstream of the N gene, in addition to the 3’UTR (page 40). Any of these components that are not the 5’ UTR and 3’UTR sequence reads on the intervening sequence. Jordan also recites a synthetic nucleic acid molecule comprising a polynucleotide (i) containing a nucleotide sequence of the 5’ untranslated region (UTR) of a nidovirus, a nucleotide sequence of the 3’ untranslated region (UTR) of a nidovirus, and a nucleotide sequence of a packaging signal localized in ORFlb of a nidovirus (claim 1), wherein the nidovirus is a virus of the family of Coronaviridae (claim 17), wherein the virus of the family Coronaviridae is selected from the group consisting of MERS-CoV….SARS-CoV-2…(Claim 18).
SEQ ID NO: 1 of Jordan (Db) is taught as including the 5’-UTR of the SARS-CoV-2 construct (pages 39-40), and is 100% identical to nucleotides 1-450 of instant SEQ ID NO: 1 (Qy). See alignment below.
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Regarding the 3’UTR of instant claims 1,6 and 7, SEQ ID NO: 4 of Jordan (Db) is taught as the 3’ terminal region starting with the stop codon of ORF8 and including the intergenic region upstream of the N gene, and the 3’UTR of SARS-CoV-2 construct (pages 39-40). Nucleotides 1419-1647 of SEQ ID NO: 4 of Jordan are 100% identical to nucleotides 29675-29903 of instant SEQ ID NO: 1 (Qy). See alignment below.
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Jordan teaches the synthetic nucleic acid molecule of the invention is incapable of autonomous replication (page 14).
Regarding claim 9, SEQ ID NO: 3 of Jordan is taught as Mosaic-3 and containing the packaging signal of SARS-CoV-2 (pages 39-40).
Regarding claim 41, Jordan teaches the virus-like particle of the present invention comprises the nucleic acid molecule of the present invention which is incapable of autonomous replication. It further comprises an envelope of a nidovirus (page 17).
Regarding claim 42, Jordan recites a cell comprising a synthetic nucleic acid molecule of any one of claims 1-19 (claims 22-24).
Regarding claim 43, Jordan recites a pharmaceutical composition comprising a synthetic nucleic acid molecule of any of claims 1-19 and one or more pharmaceutical acceptable excipient(s), diluent(s), and/or carrier(s) (claim 25).
Regarding claim 47, Jordan recites a combination comprising (i) a synthetic nucleic acid molecule of any one of claims 1 to 19, particles of claims 20 or 21, or a pharmaceutical composition of claim 25, and (ii) a nidovirus or a combination of claim 35 for use in the treatment, prophylaxis, and/or prevention of an infection or disease caused by a nidovirus and for vaccination against nidovirus infection (claim 36) and teaches a method for the treatment, prophylaxis, and/or prevention of an infection or a disease caused by a nidovirus comprising the steps of: (i) providing a synthetic nucleic acid molecule according to the first aspect, particles according to the second aspect, or a pharmaceutical composition according to the fourth aspect and (ii) administering the synthetic nucleic acid molecule according to the first aspect, the particles according to the second aspect, or the pharmaceutical composition according to the fourth aspect (in a therapeutically effective amount) to a subject in need thereof (page 31). The term “therapeutically effective amount”, as used herein, means that the amount of the nucleic acid molecule or particle of the present invention contained in the pharmaceutical composition administered is of sufficient quantity to achieve the intended purpose, such as, in this case, to cause treatment, prophylaxis, and/or prevention of an infection or a disease caused by a nidovirus (page 20).
Since Jordan's molecule fully satisfies all structural limitations set forth in the rejected claims, it necessarily follows that Jordan's molecule inherently possesses the functions and properties recited in the rejected claims, absent objective evidence to the contrary. See claim interpretation above regarding the wherein clauses and functions recited in claims 1, 36 and 40.
Accordingly, claims 1,2,4,6,7,9,11,14,24,36,40-43 and 47 are anticipated by Jordan et al.
Claims 1,2,4,6,9,11,14,24,36,40,42,43 and 47 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Giat et al. (WO2021209984, EFD 12 April 2020) as evidenced by NCBI NC_045512.2), cited on an IDS.
Regarding claims 1,2,4,11,14,24,36 and 40, Giat et al. teach parasitic pseudo-viral transcript (PSCT, also referred to as a “decoy transcript”) that is harmless and unable to replicate in the absence of the wild type virus from which it is a decoy of and includes all necessary sequences for efficient replication and packaging (page 2). Giat et al. teach the PSCT acts as a parasite that competes with wild-type virus for its replication and as a result within a few virus replication cycles, the majority of virions will encapsulated mostly the decoy transcript, thus slowing down the spread of the WV potentially even to the point of its eradication by the host immune system (page 2). Giat et al. teach CoV-SARS-2 having NCBI Reference Sequence NC_045512.2, GenBank MN908947.3 (page 12). Giat et al. recites a viral decoy transcript derived from a ssRNA virus (WV), the transcript comprising a 5’ end comprising a 5’UTR of the WV, a genomic packaging signal (GPS) of the WV, a 3’UTR of the WV, an extrinsic stop codon and a poly-A tail, and comprising a nucleotide sequence having at least 80% sequence similarity to the nucleotide sequence set forth in SEQ ID NO: 2 or 6 (claim 5), or comprising a nucleotide having at least 80% sequence similarity to any one or more of the nucleotide sequences set forth in SEQ ID NOs: 3-5 and 7 (claim 6). Table 1 on pages 26-29 shows the description and sequences for the recited sequences, with SEQ ID NO: 2 being the full length decoy transcript; SEQ ID NO: 3 being the 5’UTR of the decoy transcript and SEQ ID NO: 5 being the 3’UTR of the decoy transcript and SEQ ID NO: 4 being the GPS of the decoy transcript, and therefore shows and meets the length requirements of the regions recited in claims 1 and 2.
Regarding the 5’UTR region of claims 4 and 14, SEQ ID NO: 3 of Giat et al. (Db) which is identified as the 5’UTR of the decoy transcript has 100% identity with nucleotides 1-450 nucleotide of instant SEQ ID NO: 1 (Qy), see below:
PNG
media_image8.png
612
743
media_image8.png
Greyscale
Regarding the 3’UTR region of claim 6, SEQ ID NO: 5 of Giat et al. (Db) which is identified as the 3’UTR of the decoy transcript has 100% identity with all 196 nucleotides at positions 29675-29870 of instant SEQ ID NO: 1 (Qy):
PNG
media_image9.png
386
732
media_image9.png
Greyscale
Regarding claim 9, the decoy of Giat et al. comprises a packaging signal (GPS) for SARS-CoV-2 as SEQ ID NO: 4 is the GPS of the decoy transcript (claim 6 and Table 1, page 28).
Regarding claim 42, Giat et al. recite a cell or cell population comprising the decoy transcript of any one of claims 1-21 (claims 25-27).
Regarding claim 43, Giat et al. recite a composition comprising the decoy transcript of any one of claims 1-21 and a suitable transport vehicle and/or carrier, wherein the carrier is water (claims 28-29). As there is no definition in the instant specification for “excipient”, based on the broadest reasonable interpretation, water reads on excipient in claim 43.
Regarding claim 47, Giat et al. recite a method for treating, attenuating and/or inhibiting spread of a ssRNA viral infection in a subject, the method comprising providing to the subject the decoy transcript of any one of claims 1-21 or the composition of any one of claims 28-36, wherein the treated subject is a subject infected with the WV (claim 38).
Since Giat’s molecule fully satisfies all structural limitations set forth in the rejected claims, it necessarily follows that Giat’s molecule inherently possesses the functions and properties recited in the rejected claims, absent objective evidence to the contrary. See claim interpretation above regarding the wherein clauses and functions recited in claims 1, 36 and 40.
Accordingly, claims 1,2,4,6,9,11,14,24,36,40,42,43 and 47 are anticipated by Giat 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.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Yao et al. as applied to claims 1,2,4,6,7,9,11,14,24,36,40 and 42 above, and further in view of Liu et al. (Molecular Biology of the SARS-Coronavirus 2009 July 22: 47-61).
The teachings of Yao et al. as applicable to claims 1,2,4,6,7,9,11,14,24,36,40 and 42 have been described above.
Yao et al. do not teach wherein the 5’UTR region comprises two or more copies of 5’UTR sequences, each comprising at least 100 nucleotides of a SARS-CoV-2 5’UTR or a variant thereof, and/or the 3’UTR region comprises two or more copies of 3’UTR sequences, each comprising at least 100 nucleotides of a SARS-CoV-2 3’UTR or a variant thereof.
Before the effective filing date, Liu et al. taught that the 5’ and 3’ untranslated regions (UTRs) of all coronavirus genomes contain cis-acting sequences required for viral transcription and replication (page 48, Section 4.2). Liu et al. taught additional cis-acting sequences such as packaging signals needed for assembly have been identified, and many of these cis-acting sequence have been defined by studying defective interfering (DI) RNAs, which are extensively deleted, retain the 5’ and 3’ UTRs plus some additional genomic RNA and are replication competent in the presence of a helper virus to provide replicase components in trans, and thus they retain cis-acting sequences needed for genome replication (page 48, Section 4.2).
It would have been obvious to one of ordinary skill in the art before the effective filing date, to have modified the 5’ and/or 3’ region of the SARS-CoV-2 short synthetic defective interfering (DI) construct of Yao et al. to include two or more copies of the 5’ UTR and/or 3’UTR sequence taught by Yao et al. based on the teachings of Liu et al. with a reasonable expectation of success. There would be a reasonable expectation of success because both Yao et al. and Liu et al. pertain to SARS-CoV and both discuss defective interfering RNA. One of ordinary skill in the art would have been motivated to do so because Liu et al. taught that 5’ and 3’ UTRs of all coronavirus genomes contain cis-acting sequences required for viral transcription and replication, and therefore one of ordinary skill in the art would expect that providing two or more copies thereof would result in increased viral transcription and replication of the SARS-CoV construct.
Accordingly, the limitations of claim 5 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. as applied to claims 1,2,4,11,14,19,20,24,36,40 and 42 above, and further in view of Liu et al. (Molecular Biology of the SARS-Coronavirus 2009 July 22: 47-61).
The teachings of Zhang et al. as applicable to claims 1,2,4,11,14,19,20,24,36,40 and 42 have been described above.
Zhang et al. do not teach wherein the 5’UTR region comprises two or more copies of 5’UTR sequences, each comprising at least 100 nucleotides of a SARS-CoV-2 5’UTR or a variant thereof, and/or the 3’UTR region comprises two or more copies of 3’UTR sequences, each comprising at least 100 nucleotides of a SARS-CoV-2 3’UTR or a variant thereof.
Before the effective filing date, Liu et al. taught that the 5’ and 3’ untranslated regions (UTRs) of all coronavirus genomes contain cis-acting sequences required for viral transcription and replication (page 48, Section 4.2). Liu et al. taught additional cis-acting sequences such as packaging signals needed for assembly have been identified, and many of these cis-acting sequence have been defined by studying defective interfering (DI) RNAs, which are extensively deleted, retain the 5’ and 3’ UTRs plus some additional genomic RNA and are replication competent in the presence of a helper virus to provide replicase components in trans, and thus they retain cis-acting sequences needed for genome replication (page 48, Section 4.2).
It would have been obvious to one of ordinary skill in the art before the effective filing date, to have modified the 5’ and/or 3’ region of the SARS-COV-2 replicon construct of Zhang et al. to include two or more copies of the 5’ UTR and/or 3’UTR sequence taught by Yao et al. based on the teachings of Liu et al. with a reasonable expectation of success. There would be a reasonable expectation of success because both Zhang et al. and Liu et al. pertain to SARS-CoV. One of ordinary skill in the art would have been motivated to do so because Liu et al. taught that 5’ and 3’ UTRs of all coronavirus genomes contain cis-acting sequences required for viral transcription and replication, and therefore one of ordinary skill in the art would expect that providing two or more copies thereof would result in increased viral transcription and replication of the SARS-CoV construct.
Accordingly, the limitations of claim 5 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Jordan et al. as evidenced by GenBank accession number NC_045512.2 as applied to claims 1,2,4,6,7,9,11,14,24,36,40-43 and 47 above, and further in view of Liu et al. (Molecular Biology of the SARS-Coronavirus 2009 July 22: 47-61).
The teachings of Jordan et al. as evidenced by GenBank accession number NC_045512.2 as applicable to claims 1,2,4,6,7,9,11,14,24,36,40-43 and 47 have been described above.
Jordan et al. as evidenced by GenBank accession number NC_045512.2 do not teach wherein the 5’UTR region comprises two or more copies of 5’UTR sequences, each comprising at least 100 nucleotides of a SARS-CoV-2 5’UTR or a variant thereof, and/or the 3’UTR region comprises two or more copies of 3’UTR sequences, each comprising at least 100 nucleotides of a SARS-CoV-2 3’UTR or a variant thereof.
Before the effective filing date, Liu et al. taught that the 5’ and 3’ untranslated regions (UTRs) of all coronavirus genomes contain cis-acting sequences required for viral transcription and replication (page 48, Section 4.2). Liu et al. taught additional cis-acting sequences such as packaging signals needed for assembly have been identified, and many of these cis-acting sequence have been defined by studying defective interfering (DI) RNAs, which are extensively deleted, retain the 5’ and 3’ UTRs plus some additional genomic RNA and are replication competent in the presence of a helper virus to provide replicase components in trans, and thus they retain cis-acting sequences needed for genome replication (page 48, Section 4.2).
It would have been obvious to one of ordinary skill in the art before the effective filing date, to have modified the 5’ and/or 3’ region of the SARS-COV-2 replicon construct to include two or more copies of the 5’ UTR and/or 3’UTR sequence taught by Jordan et al. as evidenced by GenBank accession number NC_045512.2 based on the teachings of Liu et al. with a reasonable expectation of success. There would be a reasonable expectation of success because Jordan et al. and Liu et al. pertain to SARS-CoV. One of ordinary skill in the art would have been motivated to do so because Liu et al. taught that 5’ and 3’ UTRs of all coronavirus genomes contain cis-acting sequences required for viral transcription and replication, and therefore one of ordinary skill in the art would expect that providing two or more copies thereof would result in increased viral transcription and replication of the SARS-CoV construct.
Accordingly, the limitations of claim 5 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Giat et al. as evidenced by NCBI NC_045512.2 as applied to claims 1,2,4,6,9,11,14, 24,36,40,42,43 and 47 above, and further in view of Liu et al. (Molecular Biology of the SARS-Coronavirus 2009 July 22: 47-61).
The teachings of Giat et al. as evidenced by NCBI NC_045512.2 as applicable to claims 1,2,4,6,9,11,14,24,36,40,42,43 and 47 have been described above.
Giat et al. as evidenced by NCBI NC_045512.2 do not teach wherein the 5’UTR region comprises two or more copies of 5’UTR sequences, each comprising at least 100 nucleotides of a SARS-CoV-2 5’UTR or a variant thereof, and/or the 3’UTR region comprises two or more copies of 3’UTR sequences, each comprising at least 100 nucleotides of a SARS-CoV-2 3’UTR or a variant thereof.
Before the effective filing date, Liu et al. taught that the 5’ and 3’ untranslated regions (UTRs) of all coronavirus genomes contain cis-acting sequences required for viral transcription and replication (page 48, Section 4.2). Liu et al. taught additional cis-acting sequences such as packaging signals needed for assembly have been identified, and many of these cis-acting sequence have been defined by studying defective interfering (DI) RNAs, which are extensively deleted, retain the 5’ and 3’ UTRs plus some additional genomic RNA and are replication competent in the presence of a helper virus to provide replicase components in trans, and thus they retain cis-acting sequences needed for genome replication (page 48, Section 4.2).
It would have been obvious to one of ordinary skill in the art before the effective filing date, to have modified the 5’ and/or 3’ region of the CoV-SARS-2 decoy construct of Giat et al. as evidenced by NCBI NC_045512.2 to include two or more copies of the 5’ UTR and/or 3’UTR sequence based on the teachings of Liu et al. with a reasonable expectation of success. There would be a reasonable expectation of success because Giat et al. and Liu et al. pertain to SARS-CoV. One of ordinary skill in the art would have been motivated to do so because Liu et al. taught that 5’ and 3’ UTRs of all coronavirus genomes contain cis-acting sequences required for viral transcription and replication, and therefore one of ordinary skill in the art would expect that providing two or more copies thereof would result in increased viral transcription and replication of the SARS-CoV construct.
Accordingly, the limitations of claim 5 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1,2,4-7,9,11,14,19,20,24,36,40-43 and 47 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16,19 and 32 of copending Application No. 17/920,682.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims overlap in scope with the '682 claims. The instant claims are drawn to a recombinant SARS-CoV-2 construct comprising a 5' UTR region (e.g., "nucleotides 1-450 of SEQ ID NO: 1", which appears to correspond to SEQ ID NO:28 claimed in claim 14 of ‘682) and a 3' UTR region (also disclosed as SEQ ID NO: 31 on page 112 of instant specification) which appears to correspond to SEQ ID NO:31 claimed in claim 15 of ‘682), wherein the construct is capable of interfering with SARS-CoV-2 replication and replicates in the presence of SARS-CoV-2. Instant claim 9 also recites a packaging signal for SARS-CoV-2 as does claim 6 of ‘682. Instant claim 47 recites a method of treating or preventing SARS-CoV-2 infection in an individual comprising administering to the individual an effective amount of the pharmaceutical composition of claim 43 and claim 32 of ‘682 recites a method comprising administering to a subject a pharmaceutical composition comprising a pharmaceutically acceptable excipient and a therapeutically effective amount of at least one interfering, recombinant SARS-CoV-2 construct comprising cis-acting elements comprising a 5’UTR, a 3’UTR or a combination thereof.
Conclusion
Claims 1,2,4-7,9,11,14,19,20,24,36,40-43 and 47 are rejected.
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/STEPHANIE L SULLIVAN/Examiner, Art Unit 1635
/ABIGAIL VANHORN/Primary Examiner, Art Unit 1636
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