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 Inventive Group 1 in the reply filed on 10/01/2025 is acknowledged.
Claim Interpretation
Claim 7 states that the composition comprising an isolated Anellovirus ORF1 molecule does not substantially comprise a genetic element. Per the specification, a “genetic element” refers to a “difference or modification relative to a wild-type viral genome” (pg. 33) and “a nucleic acid molecule that is or can be enclosed with… a proteinaceous exterior to form an anellovector” (pg 34) and lastly, “a nucleic acid construct…comprising a genetic element sequence or fragment thereof”. (Pg 34) Therefore, any prior art reading solely on an Anellovirus ORF arginine-rich region OR an isolated Anellovirus ORF1 molecule comprising a molecular weight of at least 101kDa will satisfy the requirements of claim 7.
Specification
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 7 and 37 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. Claims 7 and 37 are directed to an arginine-rich Anellovirus ORF1 molecule with a molecular weight of at least 101 kDa. While the specification does state in the Enumerated Embodiments on page 15 that the composition must have a molecular weight of at least 101 kDa, examples of the invention given in the specification are directed to a peptide aptamer having a weight of 12-14 kDa (pg 179) and the location of the anellovirus promoter 9 at 20 kDa (pg 194). Furthermore, the prior art does not provide examples of Anellovirus ORF1 proteins measuring at least 101 kDa. The closest prior art, Mushahwar et al., discloses TTV particles isolated from human serum measuring between 30-50 nM. (Pg 3179, Results) In addition to this, Kahvejian et al. discloses an embodiment of the invention with a molecular weight of less than 2000 Daltons, which would be less than 2 kDa. (Pg 297, ln 25-30) Therefore, there are no examples disclosed in either the specification, claims, or prior art that demonstrate possession of the claimed invention.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 7, 17, 23-26, 36, and 37 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claim(s) recite(s) an isolated Anellovirus ORF1 molecule comprising a jelly-roll fold. This judicial exception is not integrated into a practical application because as evidenced by Butkovic et al., comprising a jelly-roll fold is an inherent feature of all Anelloviridae. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because all Anelloviridae naturally comprise a jelly-roll fold as a feature of their structure.
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.
Claims 7, 17, 23, and 36 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Mushahwar et al., (Molecular and biophysical characterization of TT virus: Evidence for a new virus family infecting humans, 1999) as evidenced by Butkovic et al. (Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein, 2023)
Regarding claim 7: Mushahwar discloses a method of isolation of a novel DNA virus from the serum of a patient and that the novel virus is a TTV virus, which is in the Anellovirus family. (Pg 3177, Abstract) As Mushahwar simply isolated the virus, no genetic manipulation was done to alter the virus from its natural state, reading on the requirement of claim 7 of the anelloviral composition not substantially comprising a genetic element. In addition to this, Mushahwar discloses that, during the isolation of the TTV virus, the ORF1 protein of the isolates comprises an arginine-rich region. (Pg 3180, Results) This further reads on the teachings of claim 7 of an isolated Anellovirus ORF1 molecule comprising an ORF1 arginine rich region.
Regarding claim 17: Claim 17 is directed towards an Anellovirus ORF1 molecule comprising a jelly-roll domain. Per the discussion above, Mushahwar discloses an isolated Anellovirus ORF1 molecule that was derived from the serum of a patient and isolated. (Pg 3177, Abstract) As evidenced by Butkovic, Anelloviruses inherently comprise a jelly-roll domain as part of the structure of the ORF1 region of the plasmid, therefore making it inherent that the isolated Anellovirus ORF1 molecule as taught by Mushahwar also comprises a jelly-roll domain in the ORF1 region.
Regarding claim 23: Mushahwar discloses the generation of the full genomic sequence of the TTV virus by means of genomic extension, which was carried out via TTV-specific primers, isolated nucleic acids, and anchored primers for both upstream and downstream of the sample sequences. (Pg 2, Genomic Extension) As completion of the full genomic sequence includes the ORF1 region, this reads on claim 23 of the anellovirus ORF1 molecule being full-length.
Regarding claim 36: Following the discussion of claim 7 above, the teachings of Mushahwar further read on claim 36 of the Anellovirus ORF1 comprising an arginine-rich region, as shown in the Results section on page 3180 stating “the ORF1 protein of both isolates possess an arginine-rich region”.
Claims 7 and 18-25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kahvejian et al. (WO 2018/232017)
Regarding claim 7: Kahvejian discloses an embodiment of the invention in which the synthetic curon binds to an arginine-rich region of the proteinaceous exterior. (Pg 14, claim 45) In addition to this, Kahvejian discloses that the curon may match 100% to an Anellovirus ORF1 protein. (Pg 46, ln 17-19) Taken together, this reads on claim 7 of a composition comprising an isolated Anellovirus ORF1 molecule comprising an arginine-rich region that does not substantially comprise a genetic element.
Regarding claim 18: Kahvejian discloses synthetic curons which can be used as delivery vehicles for delivering a therapeutic agent to a cell which may comprise a payload such as a nucleic acid effector. (Pg 1, ln 19-24) Kahvejian further discloses an embodiment in which the nucleic acid molecule may share between 70-100% sequence to an Anellovirus ORF1 protein. (Pg 46, ln 17-19) In addition to this, Kahvejian discloses that the synthetic curon is defined as having at least one structural difference when compared to a wild-type virus. (Pg 1, ln 32-33) Therefore, Kahvejian reads on synthetic Anellovirus ORF1 protein comprising at least one difference relative to a wild-type Anellovirus ORF1 protein, as taught by claim 18.
Regarding claim 19: Kahvejian discloses that the synthetic curon of the invention must have at least one structural difference when compared to a wild-type virus such as a deletion, insertion, or substitution (Pg 1, ln 32-33) and that the synthetic curon may share 70-100% sequence to an Anellovirus ORF1 protein. (Pg 46, ln 17-19) Taken together, this reads on the limitations of claim 19 of the composition comprising a mutation or chemical modification relative to a wild-type Anellovirus ORF1 protein.
Regarding claims 20 and 21: Kahvejian discloses that the curon of the claimed invention may comprise a deletion. (Pg 1, ln 32-33)
Regarding claim 22: Kahvejian discloses an embodiment of the invention which comprises a wild-type Anellovirus sequence which may be optionally less than the full length of the genome. (Pg 17, claim 66) As the requirement is optional and not required for the invention, this reads on the claimed method of use of a full-length Anellovirus ORF1 protein.
Regarding claim 24: Kahvejian discloses Anellovirus amino acid sequences sourced from the Anellovirus Alphatorquevirus in Table 6 and further specifies that the disclosed sequences are exemplary embodiments of the invention (pg 71, Table 6), and SEQ ID NO. 22 fully reads on the claimed SEQ ID NO. 185 as shown in the alignment chart below:
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836
596
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Regarding claim 25: Kahvejian discloses exemplary Anellovirus amino acid sequences sourced from the Anellovirus Betatorquevirus in Table 12 (pg 81) and SEQ ID NO. 45 fully matches the claimed SEQ ID NO. 215 as shown in the alignment chart below:
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778
584
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Greyscale
Allowable Subject Matter
Claim 12 is allowed. There is no existing prior art which links, in order, a first transposase recognition sequence, an Anellovirus genetic element region comprising a promoter operable linked to a sequence encoding an exogenous effector, and a second transposase recognition sequence.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to HANNA M THUESON whose telephone number is (571) 272-3680. The examiner can normally be reached M-F 7:30-5 EST. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Tracy Vivlemore, can be reached on (571) 272-2914. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/HANNA MARIE THUESON/ Examiner, Art Unit 1638
/Tracy Vivlemore/ Supervisory Primary Examiner, Art Unit 1638