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 .
Status of the Application
The Amendment filed November 26, 2025, and the Request for Continued Examination filed December 26, 2025, are each acknowledged.
Claims 1-20 were pending. Claims 1-17, 20 and new claim 21 are being examined on the merits. Claim 18 remains withdrawn. Claim 19 is canceled.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on November 26, 2025 has been entered.
Response to Arguments
Applicant’s arguments filed November 26, 2025 have been fully considered.
The following rejections are WITHDRAWN in view of Applicant’s arguments and amendments to the claims:
Rejection of claims under 35 USC § 112(b), indefiniteness, in part
The following rejections are MAINTAINED or MODIFIED:
Rejection of claims under 35 USC § 112(b), in part
Prior art rejections
Response to arguments regarding indefiniteness rejections
Applicant argues that the rejections of claims 5, 9 and 11 should be withdrawn because the claims have been amended to indicate trademarks and generic terminology (Remarks, p. 10).
The Examiner disagrees and reiterates the comments in the Final Office Action mailed August 27, 2025. Specifically, the MPEP 2173.05(u) states that “[if] the trademark … is used in a claim limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 USC 112(b)”. It also states that “[t]he value of a trademark would be lost to the extent that it became the generic name of a product, rather than used as an identification of a source or origin of a product. Thus, the use of a trademark … in a claim to describe a material or product would not only render a claim indefinite, but would also constitute an improper use of the trademark ….” The Examiner suggests amending claims 5, 9 and 11 to replace the trademarks with corresponding generic names/chemical names.
Response to arguments regarding prior art rejections
Applicant argues that the anticipation rejection of claims 1, 2 and 12-17 should be withdrawn in view of the instant amendment to claim 1 requiring that the primers consist of those that amplify the recited genes (Remarks, pp. 11-12).
The Examiner agrees. The anticipation rejection is withdrawn.
Applicant argues that the obviousness rejections should be withdrawn because the Reijns primers differ from the instant primers in structural and functional ways, including, e.g., that the Reijns primers contain degenerate nucleotides, which could affect the specificity and sensitivity of the reaction (Remarks, p. 12). Applicant additionally argues that primer compatibility is an issue in multiplex reactions to avoid misamplification that leads to false-positive or false-negative results and that inventors’ primers were carefully chosen and proven successful as to such considerations (Remarks, pp. 12-14, 16).
However, MPEP 2112.01(II) states that if the composition is physically the same, it must have the same properties, thus, if the prior art teaches the identical chemical structure, the properties Applicant claims are necessarily present. Further, claim 1 does not specify any primer/probe sequences, and none of the dependent claims consist of the entire set of specific primers/probes (identified by their SEQ ID NOs). Thus, if a particular set of primers/probes is required to achieve the sensitivity and specificity in a multiplex reaction identified by Applicant, none of the instant claims are actually limited to that particular set. For example, if a multiplex assay with the desired sensitivity and specificity can only be achieved with the collection of the instant SEQ ID NOs: 1-15 primers/probes and no other primers/probes may be present, then none of the claims require such an embodiment.
Applicant argues that the rejections based on Reijns cannot be sustained because instant claim 1 now requires excluding one of the Reijns primers – specifically, the PhHV primer (Remarks, pp. 15-17).
The Examiner agrees that claim 1 now excludes the Reijns PhHV primer, but disagrees that Reijns does not at least suggest embodiments that do not comprise that primer.
These arguments are not persuasive. The rejections are modified in view of the instant claim amendments.
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 5, 9 and 11 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Indefiniteness rejections
Claim 5 contains the trademark/trade name “Triton”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe the source of a laboratory reagent and, accordingly, the identification/description is indefinite.
Claims 9 and 11 contain the trademarks/trade names “BHQ1”, “BHQ2”, “FAM”, “HEX” and “ROX”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademarks/trade names are used to identify/describe the source of PCR reagents and, accordingly, the identification/description is indefinite.
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, 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.
Claims 1-4 and 12-17 are rejected under 35 U.S.C. 103 as being unpatentable over Reijns (A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection, PLoS Biol, 18:12, 1-20, December 15, 2020), as evidenced by ThermoFisher Scientific (TaqPath 1-Step Multiplex Master Mix User Guide, April 2020).
Regarding independent claim 1, Reijns teaches or suggests …
A multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) method for detecting SARS-CoV-2 virus in a sample suspected to contain SARS-CoV-2 virus comprising: contacting the sample with a reaction mixture comprising primers consisting of those that amplify human RP, viral RdRP, and viral E genes, dNTPs, and a DNA polymerase under conditions suitable for amplification of the SARS-CoV-2 RNA into cDNA (Fig. 1; abstract; p. 12, para. 3; p. 13, para. 3; p. 4, paras. 2-3; p. 13, para. 3 through p. 14, para. 1);
contacting the sample with fluorescent detection probes that bind to amplified human RP, viral RdRP, and viral E genes cDNA, and measuring fluorescence as an indicator of amounts of at least one amplified SARS-CoV-2 cDNA, thereby detecting SARS-CoV-2 RNA and SARS-CoV virus in the sample when fluorescence is detected by a Ct value ≤ 37 with a sigmoidal amplification curve i (Tables 1, 3; Fig. 2).
Regarding the human RP + viral RdRP + viral E gene embodiment:
Regarding the target genes, Reijns teaches the human RP plus viral RdRP plus viral E gene embodiment. Specifically, Reijns teaches RdRP, and the E gene as nucleic acid targets (p. 4, para. 2), and teaches comparing the combination of RdRP and E (p. 4, para. 2) with the combination of RdRP and N (p. 4, para. 3). Reijns also teaches that human RP (i.e., RPP30) is used as an internal control (p. 4, para. 2; Fig. 1; Table 1). Reijns additionally teaches using fluorescent detection probes, each labeled with a different fluorophore (Table 3).
Regarding the human RP + viral RdRP + viral N2 gene embodiment:
Regarding the target genes, Reijns suggests the human RP plus viral RdRP plus viral N2 gene embodiment. Specifically, Reijns teaches RdRP, and the N2 gene as nucleic acid targets (p. 4, para. 2), and teaches comparing the combination of RdRP and E (p. 4, para. 2) with the combination of RdRP and N (p. 4, para. 3). Reijns also teaches that human RP (i.e., RPP30) is used as an internal control (p. 4, para. 2; Fig. 1; Table 1). Reijns additionally teaches using fluorescent detection probes, each labeled with a different fluorophore (Table 3).
Reijns does not, however, explicitly teach an embodiment where all of the human RP plus viral RdRP plus viral N2 gene target genes are multiplexed in a single reaction volume.
Further, Reijns suggests the limitation “primers consisting of those that amplify human RP, viral RdRP and viral E or N2 genes”. Specifically, Reijns teaches that their initial assays focused on human RP, viral RdRP and viral E or N2 genes, but later versions of their assay additionally incorporated PhHV-1 as an extraction control (p. 2, paras. 3-4). Thus, Reijns at least suggests that their initial assays consisted of primers directed human RP, viral RdRP and viral E or N2 genes.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to modify the Reijns method to optimize the selection of targets and controls, and their corresponding primers and probes. Reijns teaches the need for sensitive and specific tests to diagnose SARS-CoV-2 infections in individuals, and teaches that each of the human RP, viral RdRP and viral E or N2 genes are useful targets for such a purpose. The ordinary artisan would have been motivated to combine all of the targets and desired controls into a single multiplex assay to achieve the expected advantage of an assay with increased specificity. The ordinary artisan would have had an expectation of success as the design and modification of multiplex assays that can detect a small number of target nucleic acids is well-known in the art.
Regarding dependent claim 2, Reijns additionally teaches that the cDNA is produced by isolating RNA from a sample and reverse transcribing SARS-CoV-2 RNA (p. 12, para. 5; p. 2, para. 2; p. 10, para. 2).
Regarding dependent claim 3, Reijns additionally teaches that the cDNA is reverse transcribed from purified or isolated SARS-CoV-2 RNA (p. 12, para. 5). Reijns also teaches or suggests that the reverse transcription is performed using an M-MLV reverse transcriptase, which is reactive at 42°C, which has RNase H activity, but which has no detectable 3’ to 5’ exonuclease activity. Specifically, Reijns teaches using a TaqPath kit (p. 13, para. 3 through p. 14, para. 1). ThermoFisher Scientific teaches that the TaqPath master mix comprises an MMLV reverse transcriptase (p. 23, para. 3), and that the reverse transcriptase is reactive at 42°C (i.e. it can be used at temperatures as high as 53°C – p. 13, Tables). ThermoFisher Scientific does not specifically teach that the MMLV has RNase H activity, but has not detectable 3’ to 5’ exonuclease activity, however, it is generally understood in the art that MMLV reverse transcriptases have these characteristics and the ordinary artisan would be able to optimize to arrive at an enzyme with an appropriate functionality.
Regarding dependent claim 4, Reijns teaches that the DNA polymerase is a Taq DNA polymerase. Specifically, Reijns teaches using a TaqPath kit (p. 13, para. 3 through p. 14, para. 1). ThermoFisher Scientific teaches that the TaqPath master mix comprises a Taq polymerase (p. 20). Reijns suggests that the Taq polymerase has 5’ to 3’ exonuclease activity, as ThermoFisher Scientific teaches that the polymerase is useful for real-time PCR (p. 10) using a FRET-labeled probe (p. 27). It is understood in the art that a polymerase must have 5’ to 3’ exonuclease activity to degrade the FRET-labeled probe. Reijns does not teach that the polymerase has a fidelity of 1X Taq, that it has a 1 min/kb reaction speed, that it exhibits a 3’-A product overhang, that is has undetectable 3’ to 5’ proofreading activity, and that is has undetectable endonuclease activity. However, it is generally understood in the art that Taq polymerases have these characteristics and the ordinary artisan would be able to optimize to arrive at an enzyme with an appropriate functionality.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to modify the Reijns method to include enzymes with the recited functionalities. The ordinary artisan would have been motivated to do so to customize the assay as desired through routine optimization. Further, the selection of a known material based on its suitability for its intended use supports an obviousness determination. MPEP 2144.07. The ordinary artisan would have had an expectation of success as the design and optimization of reagents for real-time PCR assays is well-known in the art.
Regarding dependent claim 12, Reijns additionally teaches a running time of 45 minutes or less (p. 14, para. 2: approximately 30 minutes)
Regarding dependent claims 13-17, each claim recites additional limitations that are not active method steps. Since the prior art teaches all of the active steps of the instant claims, the prior art also inherently meets these limitations. MPEP 2112 III. If there is some particular step or element or structure that is required to achieve the result, then the claims would be unpatentable due to the omission of essential elements or steps. MPEP 2172.01.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Reijns (A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection, PLoS Biol, 18:12, 1-20, December 15, 2020), as evidenced by ThermoFisher Scientific (TaqPath 1-Step Multiplex Master Mix User Guide, April 2020), as applied to claim 1 above, and further in view of GeneLink (PCR Additives & Enhancers, Certification of Analysis & Product Manual, 2014).
Regarding dependent claim 5, Reijns teaches that the PCR reaction mixture comprises a
uracil-DNA glycosylase. Specifically, Reijns teaches using a TaqPath kit (p. 13, para. 3 through p. 14, para. 1). ThermoFisher Scientific teaches that the TaqPath master mix comprises a uracil-DNA glycosylase (ThermoFisher, p. 20).
In addition, GeneLink teaches using Triton-X 100 or DMSO as PCR additives (p. 4, Table).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to modify the Reijns method to incorporate the PCR additives of GeneLink. The ordinary artisan would have been motivated to do so to customize the assay as desired through routine optimization. Further, the selection of a known material based on its suitability for its intended use supports an obviousness determination. MPEP 2144.07. The ordinary artisan would have had an expectation of success as the design and optimization of reagents for real-time PCR assays is well-known in the art.
Claims 6-11 and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Reijns (A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection, PLoS Biol, 18:12, 1-20, December 15, 2020) as evidenced by ThermoFisher Scientific (TaqPath 1-Step Multiplex Master Mix User Guide, April 2020 as applied to claim 1 above, and further in view of GenBank Accession No. MT903416.11 (Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/IRN/qom/2020 envelope protein (E) gene, partial cds, August 20, 2020), GenBank Accession No. MT042773.12 (Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/CHN/Tongji-01/2020 orf1ab polyprotein, RNA-dependent RNA polymerase region, gene, partial cds, 2020), GenBank Accession No. MT503099.13 (Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/THA/UDC302519/2020 nucleocapsid phosphoprotein (N) and ORF10 protein (ORF10) genes, partial cds, 2020) and GenBank Accession No. U77665.14 (Human RNaseP protein p30 (RPP30) mRNA, complete cds, 1997) and An (US Patent App. Pub. No. 2003/0050470).
Regarding dependent claims 6-11 and 21, Reijns teaches primers and probes for
detecting the various target genes (Table 3), but does not teach the specific sequences recited in claims 6-11 and 21.
GenBank Accession No. U77665.1 teaches sequences which correspond to RP SEQ ID NOs: 1-3, with 100% homology (SEQ ID NO: 1 nucleotides 1 to 19 correspond to U77665.1 nucleotides 42 to 60 with 100% homology; SEQ ID NO: 2 nucleotides 1 to 25 correspond to the reverse complement of U77665.1 nucleotides 107 to 132 with 100% homology; SEQ ID NO: 3 nucleotides 1 to 23 correspond to U77665.1 nucleotides 63 to 85 with 100% homology).
GenBank Accession No. MT042773.1 teaches sequences which correspond to RdRP SEQ ID NOs: 4-6, with 100% homology (SEQ ID NO: 4 nucleotides 1 to 20 correspond to MT042773.1 nucleotides 61 to 80 with 100% homology; SEQ ID NO: 5 nucleotides 1 to 25 correspond to the reverse complement of MT042773.1 nucleotides 118 to 141 with 100% homology; SEQ ID NO: 6 nucleotides 1 to 25 correspond to MT042773.1 nucleotides 92 to 116 with 100% homology).
GenBank Accession No. MT903416 teaches sequences which correspond to E gene SEQ ID NOs: 10-12, with 100% homology (SEQ ID NO: 10 nucleotides 1 to 22 correspond to MT903416.1 nucleotides 8 to 29 with 100% homology; SEQ ID NO: 11 nucleotides 1 to 21 correspond to the reverse complement of MT903416.1 nucleotides 100 to 120 with 100% homology; SEQ ID NO: 12 nucleotides 1 to 26 correspond to MT903416.1 nucleotides 78 to 103 with 100% homology).
GenBank Accession No. MT503099.1 teaches sequences which correspond to N gene SEQ ID NOs: 13-15, with 100% homology (SEQ ID NO: 13 nucleotides 1 to 19 correspond to MT503099.1 nucleotides 673 to 691 with 100% homology; SEQ ID NO: 14 nucleotides 1 to 20 correspond to the reverse complement of MT503099.1 nucleotides 816 to 835 with 100% homology; SEQ ID NO: 15 nucleotides 1 to 19 correspond to MT503099.1 nucleotides 768 to 786 with 100% homology).
In addition, regarding claims 8-11, Reijns teaches that the fluorescent detection probes are labeled with different fluorescent moieties, as recited in claims 8 and 10. Regarding claims 9 and 11, Reijns teaches BHQ-1 and BHQ-2 as quencher moieties and teaches using those moieties in FRET pairs with various reporter moieties, but does not teach the specific FRET pairs recited in claims 9 and 11. However, FRET pairs are well-known in the art, and the ordinary artisan would be able to optimize the probe design to arrive at the recited FRET pairs.
Further, regarding the differences between the Reijns sequences and the instantly claimed primers and probes, An teaches “[v]arious probes and primers can be designed around the disclosed nucleotide sequences. Primers can 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 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 1 (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” (paras. 65-67).
Therefore, An not only teaches designing primers or probes based on a known sequence, but also teaches an algorithm for defining all possible primers and probes of a given length based on a known sequence. In this respect, An teaches that all possible subsequences of a known sequence could be considered as a primer or probe for that sequence. While An is discussing sequences having to do with prostate, bladder and breast cancer (e.g., abstract), the ordinary artisan 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.
Therefore, while the Reijns primers and probes comprise different sequences than the instantly claimed primers and probes, Reijns directs the ordinary artisan to the specific gene targets, the sequences of which are described in the various GenBank entries. The ordinary artisan would be able to optimize the primer and probe design, as described in An, to arrive at the claimed sequences.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to incorporate the recited primers and probes into the modified Reijns method, discussed above. The ordinary artisan would have been motivated to optimize the sequences of the various primers and probes in order to improve the efficiency of the amplification reaction. The ordinary artisan would also have been motivated to select FRET pairs for the probes that would allow the assay to distinguish between the various targets. The selection of a known material based on its suitability for its intended use supports an obviousness determination. MPEP 2144.07. The ordinary artisan would have had an expectation of success, as optimizing primer and probe sequences and probe labeling is well-known in the art.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Reijns (A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection, PLoS Biol, 18:12, 1-20, December 15, 2020) as evidenced by ThermoFisher Scientific (TaqPath 1-Step Multiplex Master Mix User Guide, April 2020, as applied to claim 1 above, and further in view of Polack (Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine, N Engl J Med, 383:2603-2615, December 10, 2020).
Regarding claim 20, Reijns teaches …
A method for preventing or treating an infection by SARS-CoV-2 comprising selecting a
subject in need of vaccination or treatment for SARS-CoV-2 by detection SARS-CoV-2 RNA in a biological sample from the subject according to the method of claim 1 (see citations for claim 1 above).
In addition, Polack teaches vaccinating the subject when SARS-CoV-2 RNA is not detected (p. 2603, para. 4; p. 2604, right col., para. 1: exclusion criteria included a medical history of Covid-19).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to incorporate an additional treatment/vaccination step into the Reijns or modified Reijns method, discussed above. Reijns teaches that the method is useful for the diagnosis of SARS-CoV-2 infections. It would have been obvious to the ordinary artisan to try using the Reijns method to diagnose SARS-CoV-2 infections in patients, and to provide an appropriate follow-up prophylaxis/treatment, as diagnostic assays are known in the art to be used for such purposes. The ordinary artisan would have had an expectation of success as the use of PCR-based assays for diagnosis is well-known in the art.
Conclusion
Claims 1-17 and 20-21 are being examined, and are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 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, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CAROLYN L GREENE/Primary Examiner, Art Unit 1681
1 GenBank Accession No. MT903416.1 was cited in the PTO-892 Notice of References Cited mailed February 27, 2025.
2 GenBank Accession No. MT042773.1 was cited in the PTO-892 Notice of References Cited mailed February 27, 2025.
3 GenBank Accession No. MT503099.1 was cited in the PTO-892 Notice of References Cited mailed February 27, 2025.
4 GenBank Accession No. U77665.1 was cited in the PTO-892 Notice of References Cited mailed February 27, 2025.
Prosecution Insights