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
Priority
This Application is a national phase application filed under 35 U.S.C. § 371 claiming priority to International Application No. PCT/EP2021/087880, filed on December 30, 2021, which claims priority to European Application No. EP20306715.2, filed on December 31, 2020 that is hereby acknowledged by the Examiner.
Status of the Claims
The amendment dated 06/30/2023 is acknowledged. Claims 18-34 are pending and under examination.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 06/30/2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement(s) is/are being considered by the Examiner.
Specification
The disclosure is objected to because of the following informalities: The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see page 2). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Appropriate correction is required.
Claim Objections
Claims 25 and 34 are objected to for the following informalities:
Claim 25 recites “SARS-CoV1”. To be consistent in notation, the term should recite “SARS-CoV-1”.
Claim 34 recites “SARS-Co-2”. The term should be written as “SARS-CoV-2”.
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.
Claims 21, 22, 25 are rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Regarding claims 21-22 and 25, the term "preferably" is a relative term which renders the claim indefinite. The term "preferably" is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Thus, the claim is rendered indefinite.
Regarding claim 25, the phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Regarding claim 25, the phrase “e.g.” renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
Claims 18-26 and 34 are rejected under 35 U.S.C. 103(a) as being unpatentable over Peccia et al. “Peccia” (Nature Biotechnology, September 18, 2020, 38(10, IDS of record dated 06/30/2023):1164-1167, in view of Harb et al. “Harb” (Environmental science and pollution research international, 2016, 24(6):5370-580, IDS of record dated 06/30/2023) and further in view of D’Aoust et al. “D’Aoust” (Water Research, 2020, 188(23):1-13, Available online 23 October 2020, IDS of record dated 06/30/2023).
The claims are directed to a method of detecting a pathogen in an environmental liquid matrix, comprising: a) taking a sample of the environmental liquid matrix, b) extracting nucleic acid without prior purification of the sample, notably without prior clarification of the sample, and c) amplifying at least 2 pathogen sequences in a multiplex digital PCR (dPCR) reaction using the nucleic acid of step b) as a template.
Regarding claims 18-20, 24-26 and 34, Peccia discloses a method to detect SARS-CoV-2 in wastewater sludge samples, which were mixed (homogenized) and used directly for RNA extraction (Abstract) (instant claims 18, 24-26). Peccia utilized two pathogen sequences, N1 and N2, which were amplified by qRT-PCR (page 1167 first column first para. and Fig. 1).
Peccia does not disclose using dPCR.
Harb, however, discloses a method to detect a pathogen in wastewater samples by taking a sample, (e.g. influent samples that are centrifuged) concentrating it by putting it on a filter and using the fraction on the filter (Material and Methods), extracting DNA and performing digital PCR for several bacterial species on the extracted DNA. Additionally, D’Aoust discloses a method to quantify the presence of SARS-CoV-2 in wastewater solid samples which were first settled and the supernatant used (section 2.3). The sample was concentrated by filtering and PEG precipitation. The samples were used to extract RNA which was used in a digital PCR to amplify N1, N2 and N3 (section 2.8) (instant claims 18, 31 and 32).
Accordingly, it would have been obvious to one of ordinary skill in the art to generate a method of detecting a pathogen in an environmental liquid matrix, extracting nucleic acid without prior purification of the sample as disclosed by Peccia, whereby the amplification of wastewater samples are conducted using digital PCR as disclosed by Harb; and given the fact that D’Aoust demonstrates wastewater samples can be utilized by digital PCR for SARS-CoV-2. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success given the knowledge that liquid wastewater samples can be used to detect SARS-CoV-2 using digital PCR and that samples can be detected from liquid samples for the advantage of better quantification of viral presence in samples, not having a delay between specimen collection and the reporting of test results, thus, immediate wastewater results can provide considerable advance notice of infection dynamics.
Regarding claims 21-23, with respect to the supernatant volume, water temperature and molecular weight below 10kDa are separated, it is not inventive and considered routine and obvious to one of ordinary skill in the art as routine experimentation. It has long been settled to be no more than routine experimentation for one of ordinary skill in the art to discover an optimum value of a result effective variable. According to section 2144.05 of the M.P.E.P., "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum of workable ranges by routine experimentation." Application of Aller, 220 F.2d 454, 456, 105 USPQ 233, 235-236 (C.C.P.A. 1955). "No invention is involved in discovering optimum ranges of a process by routine experimentation." Id. at 458, 105 USPQ at 236-237. The "discovery of an optimum value of a result effective variable in a known process is ordinarily within the skill of the art." Application of Boesch, 617 F.2d 272, 276, 205 USPQ 215, 218-219 (C.C.P.A. 1980). It would have been obvious for one of ordinary skill to determine the appropriate desired volume, temperature and molecular weight of the sample in the composition of the methods disclosed by the prior art by routine experimentation procedures known in the art. Therefore, the claimed invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claims 27-33 are rejected under 35 U.S.C. 103(a) as being unpatentable over Peccia et al. “Peccia” (Nature Biotechnology, September 18, 2020, 38(10, IDS of record dated 06/30/2023):1164-1167, in view of Harb et al. “Harb” (Environmental science and pollution research international, 2016, 24(6):5370-580, IDS of record dated 06/30/2023), D’Aoust et al. “D’Aoust” (Water Research, 2020, 188(23):1-13, Available online 23 October 2020, IDS of record dated 06/30/2023) as applied to claim 18 above, and further in view of Sun et al. “Sun” (CN111286558), Peng et al. “Peng” (CN110144364) and An et al. “An” (US PGPUB 2003/0050470). The teachings of Peccia, Harb and D’Aoust are outlined above and incorporated herein.
Regarding claims 27-33, Sun discloses SEQ ID NOs: 1 and 4 (claim 2; page 2 of Sun) for detecting coronavirus 2019-nCoV nucleic acid. Peng discloses designing primers to amplify the target piece of LoxP sequence and target fragment for a Cre-LoxP recombination system for use in virus studies and discloses sequences comprising SEQ ID NOs: 10, 11 and 12 (SEQ ID NO:14 of Peng). Moreover, An teaches "Various probes and primers can be designed around the disclosed nucleotide sequences. Primers may be of any length but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the second residue is 2, etc., an algorithm defining all primers can be proposed: n to n+y where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus one (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 . . . and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 . . . and so on. For a 20-mer, the probes correspond to bases 1 to 20, 2 to 21, 3 to 22 . . . and so on." (paragraphs [0065] – [0067]). Therefore, An not only taught designing primers of any length based on a known sequence, but also taught an algorithm for defining all possible primers of a given length based on a known sequence. In this respect, An taught that all possible subsequences of a known sequence could be considered as a primer for that sequence. While An was discussing in particular sequences having to do with prostate, bladder and breast cancer (see Abstract), one of ordinary skill in the art would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
Accordingly, it would have been obvious to one of ordinary skill in the art to generate primer pairs to the known sequence of SARS CoV-2 as the primers (SEQ ID NOs: 1 and 4 of the instant claims) were known in the prior art as disclosed by Sun; and the sequence disclosed by Peng (SEQ ID NOs: 10, 11 and 12 of the instant claims) for rapid qualitative and quantitative determination of microorganisms by dPCR amplification. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success for the advantage of optimizing the dPCR for having rapid identification as well as accurate, reliable determination of the presence of SARS-CoV2 given the fact that Sun and Peng disclose known primer sequences; and An demonstrates the plain consideration of any subsequence of a known sequence as a primer for that sequence. Therefore, the claimed invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Barry Chestnut whose telephone number is (571)270-3546. The examiner can normally be reached on M-Th 8:00 to 4:00.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Thomas Visone can be reached on 571-270-0684. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BARRY A CHESTNUT/Primary Examiner, Art Unit 1672