Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
NEW GROUNDS OF REJECTION NECESSITATED BY THE AMENDMENT
2. 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.
3. 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.
4. Claims 1-8 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Stapert et al. (WO 2009/095840) in view of Salo et al. (US 2011/0275085), and further in view of Fischer et al. (WO 2015/183811), Jackson et al. (US 2019/0144919), and Qian (US 2016/0097049).
Regarding independent claim 1, Stapert discloses a method comprising using primers to perform quantitative PCR detection of a test solution containing host nucleic acid and possibly pathogen nucleic acid, said primers targeting both host and possible pathogen nucleic acids. Host target nucleic acids include immune-system-related genes including TNF, IL6, and IFN. See pages 3-6, 8-9, 17, and 24-31.
While Stapert only discloses targeting host nucleic acid which is DNA rather than mRNA which is required in the claim, Salo discloses that quantitative reverse transcription for measuring mRNA expression of host genes, including immune system-related genes including IFN, was conventional in the prior art, and also that the skilled artisan was aware of the challenges of such mRNA analysis due to the possibility of mRNA instability and degradation, and aware of the proper precautions and procedures to ensure obtaining and maintaining good quality mRNA throughout analysis to optimize results. See paragraphs 0007-0026
While Stapert does not disclose the use of TCEP in extracting nucleic acids as is required in the claim, Fischer discloses a method comprising lysing a sample to be tested for a pathogen to release nucleic acids, extracting the lysed sample, and preparing a test solution for pathogen detection, wherein the lysate comprises TCEP. See abstract and pages 4, 8-9, 16, and 29.
While Stapert does not disclose controlling the environment of a nucleic acid extract such that oxygen content in the extract is less than 1%, Jackson discloses the benefit of adding an oxygen scavenger to a nucleic acid extraction/lysis matrix for the purpose of stabilizing extracted nucleic acids for storage. See paragraphs 0002, 0005, 0028, and 0107-0109.
While Stapert does not disclose using a sealed nucleic acid extraction device as is required in the claim, Qian discloses the use of such a sealed nucleic acid extraction device. See abstract and paragraphs 0008-0016 and 0034-0069.
One of ordinary skill in the art would have been motivated to modify the method of Stapert by targeting host mRNA rather than DNA because Salo disclosed that detection of host mRNA was also conventional in the prior art, and that the skilled artisan was aware of the precautions and procedures for obtaining and maintaining stable, undegraded mRNA, leading to reasonable expectation of success. The skilled artisan would have been further motivated to use TCEP in the extraction process because Fischer disclosed a method comprising lysing a sample to be tested for a pathogen to release nucleic acids, extracting the lysed sample, and preparing a test solution for pathogen detection, wherein the lysate comprises TCEP. The skilled artisan would have been further motivated to include an oxygen scavenger in the nucleic acid extract or lysate because Jackson disclosed that adding an oxygen scavenger when extracting nucleic acids provided the benefit of stabilizing and storing nucleic acids. As far as the limitation of controlling oxygen content to be less than 1%, this would have merely involved routine optimization of known-important reaction parameters, which as well settled in U.S. patent practice does not support unobviousness (M.P.E.P 2144.05). The skilled artisan would have been further motivated to use a sealed nucleic acid extraction device because Qian disclosed the use of such a sealed nucleic acid extraction device to protect, stabilize, and safely store samples. Regarding the limitation of using a sample volume of 1-40 ml, this would have also been determined merely by routine optimization of known-important reaction parameters. Regarding the specific primers of particular SEQ ID Nos required in the claim, in the absence of evidence to the contrary, all possible oligonucleotide probes and primers based on known gene sequences, including those of the well-known recited immune system-related genes, are considered to be equivalent and obvious; the design of such oligonucleotides has long been routine and conventional, and is also merely a matter of routine optimization depending on the desired analysis or detection. Evidence to the contrary may be in the form of unpredictable, surprising, or unexpected results compared to similar primers, or unpredictable discrimination among similar target sequences. It would have been prima facie obvious to one of ordinary skill in the art at the time the application was filed to carry out the claimed methods.
Regarding claim 2, as noted above Fischer discloses adding an oxygen scavenger.
Regarding claims 3 and 5, Fischer discloses the use of a filter in extracting nucleic acids (see last paragraph on page 15).
Regarding claims 4 and 6, Qian discloses the extraction device of claim 4 comprising a receptacle, removable cap, filter column, and shipping container. Qian also discloses the collection device of claim 6 comprising a sample collector and sample storage container detachably interconnected. See abstract and paragraphs 0008-0016 and 0034-0069.
Regarding claim 7, Jackson discloses the use of blood as a sample in paragraph 0003.
Regarding claims 8 and 11, Fischer discloses detecting a virus or bacterium in a human host (see abstract).
5. Claims 15 is rejected under 35 U.S.C. 103 as being unpatentable over Stapert et al. (WO 2009/095840) in view of Salo et al. (US 2011/0275085), and further in view of Fischer et al. (WO 2015/183811), Jackson et al. (US 2019/0144919), Qian (US 2016/0097049), and Zhao et al. (US 2021/0277488; priority to at least 03/16/20).
The teachings of the previously-recited references are discussed above.
These references do not teach detection of COVID-19, nor the use of the COVID-19-specific primers as defined by the recited SEQ ID Nos.
Zhao discloses performing PCR analysis using a clinical sample from a human in which primers and probes target COVID-19 nucleic acid. See abstract and paragraphs 0002, 0004-0007, 0010, and 0019.
One of ordinary skill in the art would have been motivated to modify the method as discussed above by using primers that target a COVID-19 pathogen nucleic acid because Zhao disclosed that COVID-19 was an important pathogen for which detection was desirable, and that the E and N genes can be targeted by primers. Although Zhao does not disclose the exact primers recited in the claim, these are based on known COVID-19 nucleic acid sequences, and as noted above, in the absence of evidence to the contrary said primers are considered to be obvious and equivalent. It would have been prima facie obvious to one of ordinary skill in the art at the time the application was filed to carry out the claimed method.
CONCLUSION
6. No claims are free of the prior art.
7. Aguirre et al. (WO 2019/013613) is now made of record by the Office as a reference of interest, as it discloses simultaneously detecting in a sample an HPV pathogen and a host genetic marker for cancer susceptibility.
8. 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.
9. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENNETH R HORLICK whose telephone number is (571)272-0784. The examiner can normally be reached Mon. - Thurs. 8:30 - 6:30.
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07/14/26
/KENNETH R HORLICK/ Primary Examiner, Art Unit 1681
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