DETAILED ACTION
Election/Restrictions
Applicant’s election of various species of primers, probes and target regions, filed March 30, 2026, is acknowledged and entered. The claims have been amended to recite only the elected species. Claims 1-20 are under examination.
Drawings
The drawings are objected to because Figure 3 has nucleotide sequences for primers, probes and amplification products that are not represented by sequence identifiers. These sequences require sequence identifiers.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
In lieu of filing a corrected drawing sheet, Applicant may amend the specification’s description of Figure 3 to recite the sequence identifiers.
Claims Summary
Claim 1 is directed to a method for detecting one or more nucleic acid target regions in a sample. The method comprises:
Forming a reaction mixture, the mixture comprising:
At least a portion of the sample;
A first forward primer and a first reverse primer, both configured to generate a first amplification product of a first target region if present in the sample;
A second forward primer and a second reverse primer, both configured to generate a second amplification product of a second target region if present in the sample;
A third forward primer and a third reverse primer, both configured to generate a third amplification product of a third target region if present in the sample;
A fourth forward primer and a fourth reverse primer, both configured to generate a fourth amplification product of a fourth target region if present in the sample;
Optionally (claim 2), the mixture further comprises one or more of a first, second, third or fourth probe configured to associate with a first, second, third or fourth binding sequence with the first, second, third or fourth target region;
Subjecting the reaction mixture to nucleic acid amplification conditions; and
Forming at least one of the first, second, third or fourth amplification products;
(Claims 15 and 19) The method further comprises detecting formation of the first or second amplification product by detecting a first or second signal from a first or second label in a first detection channel, indicating formation of the first or second amplification product, and detecting an amount of the product (claims 16 and 20); the first label is attached to, or associated with, the first forward or first reverse primer (claim 17) or first probe (claim 18).
(Claims 19-20) The method further comprises detecting formation of the second amplification
The first, second, third or fourth forward primers are SEQ ID NOs: 1, 2, 3 and 5 (claim 3), or independently selected from SEQ ID NOs: 1, 2, 3 and 5 (claim 4). According to Figure 3: SEQ ID NO: 1 is a forward primer for Orf1a; SEQ ID NO: 2 is a forward primer for Orf1a; SEQ ID NO: 3 is a forward primer for N; and SEQ ID NO: 5 is a forward primer for Orf1b.
The first, second, third or fourth reverse primers are SEQ ID NOs: 11, 12, 13 and 15 (claim 5), or independently selected from SEQ ID NOs: 11, 12, 13 and 15 (claim 6). According to Figure 3: SEQ ID NO: 11 is a reverse primer for Orf1a; SEQ ID NO: 12 is a reverse primer for Orf1a; SEQ ID NO: 13 is a reverse primer for N; and SEQ ID NO: 15 is a reverse primer for Orf1b.
The first, second, third or fourth probes are SEQ ID NOs: 21, 22, 23 and 25 (claim 7), or independently selected from SEQ ID NOs: 21, 22, 23 and 25 (claim 8). According to Figure 3: SEQ ID NO: 21 is a probe for Orf1a; SEQ ID NO: 22 is a probe for Orf1a; SEQ ID NO: 13 is a probe for N; and SEQ ID NO: 25 is a probe for Orf1b.
The first, second, third or fourth forward primers are selected from SEQ ID NO: 1, 2, 3 and 5 (claim 9), or independently selected from SEQ ID NO: 1, 2, 3 and 5 (claim 10).
The first, second, third or fourth reverse primers are selected from SEQ ID NO: 11, 12, 13 and 15 (claim 9), or independently selected from SEQ ID NO: 11, 12, 13 and 15 (claim 10).
The first, second, third or fourth probes are selected from SEQ ID NO: 21, 22, 23 and 25 (claim 9), or independently selected from SEQ ID NO: 21, 22, 23 and 25 (claim 10).
Based on the claim language, it is understood that the primer and probe sequences that are represented as SEQ ID NO: 1, 2, 3, 5, 11, 12, 13, 15, 21, 22, 23 and 25 are exactly those sequences in length and content, without any extra nucleotides on either end of each sequence.
The first and second target regions are present within the same gene (claim 11), specifically the Orf1a gene (claim 12). The third and fourth target region is present within a second target gene (claim 13), specifically the N gene (claim 14).
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 3, 5, 7, 12 and 14 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.
Claims 12 and 14 recite “the Orf1a gene” and “the N gene”, respectively, without identifying the source of the genes. It appears from the specification that these two genes are from SARS-CoV-2, however, the claims should identify the source of the two genes so that the metes and bounds of the claims can be determined.
Claim 3 is directed to an embodiment wherein the first, second third or fourth forward primers are SEQ ID NO: 1, 2, 3 and 5. It is not clear what this embodiment is directed to because the combination of underlined words does not seem to agree. The same applies to claims 5 and 7. Clarification and/or correction is required.
Claim Rejections - 35 USC § 102
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 1, 2, 11 and 15-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Cummings et al. (US 2014/0080130 A1, “Cummings”). The claims are summarized above and correlated with the teachings of the prior art in bold font below.
Cummings discloses multiplex amplification for the detection of various species of S. enterica (see abstract). The method comprises at least two primer sets for simultaneous use, each having a forward and reverse primer, to hybridize and amplify target one or more target regions in one or more species from a sample (see paragraphs [0016]-[0017], [0020], [0029], [0051], [0052] and [0058]) (claim 1). Cummings discloses a kit comprising four primer sets and accompanying probes, all having different attached labels, wherein amplified products are visualized on gels and quantified/measured (see paragraphs [0033], [0046], [0054] and [0063]) (claims 1, 2 and 15-20). In paragraph [0023], the detection of one amplification product is accomplished with at least two primer sets (claim 11, aspect of two primer sets for one gene). Therefore, the claims are anticipated by the prior art.
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 12-14 are rejected under 35 U.S.C. 103 as being unpatentable over Cummings et al. (US 2014/0080130 A1, “Cummings”) as applied to claims 1 and 11 above, and further in view of Linnen et al. (US 2006/0134609A1, “Linnen”). The claims are summarized above and correlated with the teachings of the prior art in bold font below.
The teachings of Cummings are outlined above. Cummings does not disclose primers/probes for Orf1a, nor nucleocapsid. It would have been obvious to have applied Cumming’s multiplex amplification assay to any pathogen of interest, such as coronaviruses, for the purpose of distinguishing between different types (see Linnen, paragraphs [0003] and [0005]). Linnen discloses primer/probe sequences for Orf1a and nucleocapsid from various types of coronaviruses (see paragraph [0146]). It would have been obvious to have used Linnen’s primers/probes in Cummings’ multiplex amplification method to identify multiple targets in samples with a reasonable expectation of success, since Linnen also uses the primers/probes in an amplification assay (claims 12 and 14). As for the use of two primer sets for Orf1a, and two primer sets for nucleocapsid, one would have been motivated to choose any genes taught by Linnen, with a reasonable expectation of success given Cumming’s suggestion to use more than one primer set for one gene, in addition to Cumming’s suggestion to detect more than one gene (claim 13). Therefore, the claimed embodiments would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1 and 2 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 11 and 12 of U.S. Patent No. 12,065,707 B2. Although the claims at issue are not identical, they are not patentably distinct from each other. The patented claims are directed to a method for detecting SARS-CoV-2 in a biological sample, comprising providing a sample in a reaction mixture that includes three sets of primers for N, S and Orf1ab, respectively, and one or more sets of primers to amplify a target within a non-SARS-CoV-2 respiratory pathogen, such as influenza A/B or RSV, followed by amplification and detection of amplification products. Instant claims 1 and 2 are directed to a similar method wherein the target regions are generic. Thus, the patented claims are directed to a species of the instantly claimed genus. A species anticipates a genus.
Claims 15-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 12,065,707 B2 in view of Cummings et al. (US 2014/0080130 A1, “Cummings”). Although the claims at issue are not identical, they are not patentably distinct from each other.
Instant claims 15-20 are directed to embodiments wherein the amplification products are detected via the use of signals/labels. The patented claims do not recite labels/signals, however, it would have been obvious to have claimed these embodiments. Cummings discloses a multiplex amplification assay using four primer sets and accompanying probes, all having different attached labels, wherein amplified products are visualized on gels and quantified/measured (see paragraphs [0033], [0046], [0054] and [0063]). It would have been obvious to have claimed these embodiments with a reasonable expectation of success since visualization of the amplified products is a means for detection.
Conclusion
No claim is allowed.
Claims 4, 6 and 8-10 are objected to for being dependent on a rejected claim. Claims 4, 6 and 8-10 are free of the prior art because the primers/probes are limited to sequences selected from groupings of sequences that include SEQ ID NO: 2, 5, 15, 22 and 25, which are free of the prior art of record.
SEQ ID NO: 12 (reverse primer for Orf1a) is disclosed in US2023/0340624A1 as SEQ ID NO: 21. US2023/0340624A1 has priority to CN202010814021.2, filed August 13, 2020. The sequence is found in CN202010814021.2 on page 11, the ninth sequence from the top of the first table, ACTGCCGTTGCCACATAGAT. Also, CN112094944 (published version of CN202010814021.2) published 12/18/2020. US2023/0340624A1 is not relied upon in an art rejection over claim 5 because the claim is indefinite (see rejection under 35 U.S.C. 112(b) above). If claim 5 is amended to overcome the indefiniteness rejection, then this reference may be applied as prior art depending on the claim limitations.
SEQ ID NO: 23 (probed for N) is disclosed in WO2021/152181 A1, filed February 1, 2021, (priority to SE 2050090-6, filed January 30, 2020) as SEQ ID NO: 1837. The sequence is found in SE 2050090-6 as SEQ ID NO: 19436. WO2021/152181 A1 is not relied upon in an art rejection over claim 7 because the claim is indefinite (see rejection under 35 U.S.C. 112(b) above). If claim 7 is amended to overcome the indefiniteness rejection, then this reference may be applied as prior art depending on the claim limitations.
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.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Stacy B. Chen whose telephone number is 571-272-0896. The examiner can normally be reached on M-F (7:00-4:30). 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.
/STACY B CHEN/Primary Examiner, Art Unit 1672
Prosecution Insights