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 .
DETAILED ACTION
Acknowledgement is hereby made of receipt and entry of the communication filed on Jul. 16, 2026. Claims 1, 3, 5-7 and 9-20 are pending. Claims 19-20 are withdrawn. Claims 1, 3, 5-7 and 9-18 are currently examined.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
(Previous Rejection – Withdrawn) Claims 1, 3, 5-7 and 9-18 were rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
This rejection is withdrawn in view of the amendments filed on Feb. 23, 2026.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102 of this title, 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.
(Previous Rejection – Maintained) Claims 1, 3, 5-7 and 9-18 are rejected under 35 U.S.C. 103 as being unpatentable over Gohl et al. (BMC Genomics (2020) 21:863; submitted in IDS filed on Mar. 10, 2023), Itokawa et al. (PLoS ONE, 2020, 15(9): e0239403), and/or Freed et al. (Biol Methods Protoc. 2020 Jul 18; 5(1): bpaa014), in view of Akhras et al. (PLoS ONE, 2007, 2(2): e223).
Applicant argues that Claim 1 has been amended to recite in part that "molecular inversion probes (MIPs) [are bound] at spaced intervals along the viral genome, wherein at least 1000 MIPs are used to cover at least 99% of the viral genome," and that, upon sequencing, each nucleotide is sequenced at a depth of at least 22x." Applicant argues that Applicant submits that Akhras does not teach or disclose a tiled MIP assay capable of near-complete genome reconstruction with deep, multiple overlapping MIPs to allow for a 22x or greater sequencing depth as claimed herein, that one of skill in the art would not have been motivated to modify the teachings of Akhras to arrive at the near-complete, deep genome sequencing method of amended claim 1. Applicant argues that Gohl, Itokawa and Freed fail to cure these deficiencies of Akhras.
Applicant’s arguments are not persuasive. Teachings of Akhras indicate that an MIP technique, the PathogenMip assay, existed at the time of instant invention, which can be used in the detection and/or characterization of virus nucleic acid together with nucleic acid sequencing.
As to the argument that Akhras fails to teach the claimed number of MIPs that cover at least 99% of the genome of SARS-CoV-2 virus and that each nucleotide is sequenced at a depth of at least 22x, Gohl teaches that amplicon approaches in which cDNA is made from SARS-CoV-2 positive samples and amplified using primers that generate tiled PCR products are being used to sequence SARS-CoV-2 to obtain sequence of the SARS-CoV-2 genome (see page 2, left column, para 1), that the 4-pool amplification scheme (tailed amplicon v2) achieved coverage metrics close to the untailed ARTIC v3 approach at comparable read depths with 99.60% coverage at a minimum of 10x and 95.64% coverage at a minimum of 100x (Fig. 2a-b, Supplemental Table 1, Supplemental Table 2) (see page 3, left column, para 2), and that the average coverage at a subsampled read depth of 100,000 raw reads was 99.89% (10x) and 75.90% (100x) for all six test samples (see page 4, right column). One of skill in the art after reading Gohl would have have expected that the number of primers/probes used to generate PCR amplicons as well as depths of sequence read can be varied depending on goals of the study and within the purview of a skilled artisan who performs the study. In other words, one of skill in the art would have found it obvious to change the number of MIPs and depths of sequence read when applying the MIP technique taught in Akhras to sequencing assays for SARS-CoV-2 taught in Gohl, Itokawa and Freed, and the values as claimed can be arrived based on study needs (e.g., to cover as much of the genome sequence and obtain as many reads as possible for a complete sequencing study).
Conclusion
No claims are allowed.
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 extension fee 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIANXIANG (NICK) ZOU whose telephone number is (571)272-2850. The examiner can normally be reached on Monday - Friday, 8:30 am - 5:00 pm, EST. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MICHAEL ALLEN, on (571) 270-3497, can be reached. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/NIANXIANG ZOU/
Primary Examiner, Art Unit 1671
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