Detailed Office 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 Claims
Acknowledgement is hereby made of receipt and entry of the communication filed 23 April, 2026. Claims 1, 4-9, 13, 21, 23, 25-27, 30-33, 37, 39, 47, 51, and 52 are pending in the instant application. Claims 25-27, 30-33, 37, 39, 47, 51, and 52 stand withdrawn from further consideration by the Examiner, pursuant to 37 C.F.R. § 1.142(b), as being drawn to a non-elected invention.
Joint Inventors, Common Ownership Presumed
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 at the time any inventions covered therein were effectively filed absent any evidence to the contrary. Applicant is advised of the obligation under 37 C.F.R. § 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned at the time a later invention was effectively filed 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.
35 U.S.C. § 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.
Graham v. Deere
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 U.S.P.Q. 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1, 4-9, 13, 21, and 23 stand rejected under 35 U.S.C. § 103 as being unpatentable over the combined teachings of Mokkapati et al. (U.S. Pub. No. 2017/0275712 A1, published 28 September, 2017), Chen et al. (U.S. Pub. No. 2009/0181360 A1, published 16 July, 2009), Nalla et al. (2020), and Yan et al. (2020). The claims are directed toward a method of detecting influenza A, influenza B, RSV, and SARS-CoV-2 in a biological sample comprising the following steps:
a) amplifying nucleic acid from the biological sample with sets of primers that detect an influenza A gene, an influenza B gene, an RSV gene, and a SARS-CoV-2 gene by conducting one or more polymerase chain reactions (PCR) using a set of primers that detects the presence or absence of SARS-CoV-2 and comprises a set of primers that detect SARS-CoV-2 E, N2, and RdRP, wherein the set of primers that detects the presence or absence of SARS-CoV-2 comprises at least one of:
i) a set of primers that detects SARS-CoV-2 E gene comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 90% identical to at least 15 contiguous nucleotides of SEQ ID NO: 79 or SEQ ID NO: 66, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 90% identical to at least 15 contiguous nucleotides of SEQ ID NO: 79 or SEQ ID NO: 66, ii) a set of primers that detects SARS-CoV-2 N2 gene comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 90% identical to at least 15 contiguous nucleotides of SEQ ID NO: 47, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 90% identical to at least 15 contiguous nucleotides of SEQ ID NO: 47, and,
iii) a set of primers that detects SARS-CoV-2 RdRP gene comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 90% identical to at least 15 contiguous nucleotides of SEQ ID NO: 81 or SEQ ID NO: 80, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 90% identical to at least 15 contiguous nucleotides of SEQ ID NO: 81 or SEQ ID NO: 80; and,
b) detecting an amplicon that is produced by the PCR using a detection probe (claim 1).
Claims 4 and 5 reference various primer sets that amplify the influenza A PB2, PA, and MP, avian MP, influenza B MP and NS, RSV A and B, SARS-CoV-2 E, N2, RdRP, and ORF1ab genes. Specifically, claim 4 is directed toward a set of primers comprising the following:
a) a set of primers that detects the presence or absence of influenza A comprises at least one of:
i) 1) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 1, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% complementary to at least 15 contiguous nucleotides of SEQ ID NO: 1; and 2) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 17, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 18;
ii) a set of primers that detects influenza A PA selected from: 1) 1) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 2, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% complementary to at least 15 contiguous nucleotides of SEQ ID NO: 2; and 2) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 20, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 21;
iii) a set of primers that detects influenza A MP selected from: 1) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 3, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% complementary to at least 15 contiguous nucleotides of SEQ ID NO: 3; and 2) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 23, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 24;
iv) a set of primers that detects avian influenza MP selected from: 1) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 4, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% complementary to at least 15 contiguous nucleotides of SEQ ID NO: 4; and 2) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 26, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 27;
b) wherein the set of primers that detects the presence or absence of influenza B comprises at least one of:
i) a set of primers that detects influenza B MP selected from: 1) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 6, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% complementary to at least 15 contiguous nucleotides of SEQ ID NO: 6; and 2) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 32, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 33;
ii) a set of primers that detects influenza B NS selected from: 1) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 7, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% complementary to at least 15 contiguous nucleotides of SEQ ID NO: 7; and 2) a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 35, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 36;
c) wherein the set of primers that detects the presence or absence of RSV comprises at least one of:
i) a set of primers that detects RSV A selected from: at least one forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 38 and/or SEQ ID NO: 67, and at least one reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 39, SEQ ID NO: 68, and/or SEQ ID NO: 69; and
ii) a set of primers that detects RSV B selected from: a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 41, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 42.
Claim 5 references specific primer pairs as follows:
a) a set of primers that detects the presence or absence of influenza A comprises at least one of:
i) a set of primers that detects influenza A PB2 comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 17, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 18;
ii) a set of primers that detects influenza A PA comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 20, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 21;
iii) a set of primers that detects influenza A MP comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 23, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 24; and
iv) a set of primers that detects avian influenza MP comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 26, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 27;
b) wherein the set of primers that detects the presence or absence of influenza B comprises at least one of:
i) a set of primers that detects influenza B MP comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 32, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 33; and
ii) a set of primers that detects influenza B NS comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 35, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 36;
c) wherein the set of primers that detects the presence or absence of RSV comprises at least one of:
i) a set of primers that detects RSV A comprising at least one forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 38 and/or SEQ ID NO: 67, and at least one reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 39, SEQ ID NO: 68, and/or SEQ ID NO: 69; and
ii) a set of primers that detects RSV B comprising a forward primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 41, and a reverse primer comprising a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical to at least 15 contiguous nucleotides of SEQ ID NO: 42.
Claim 6 recites the following amplicons:
a) the influenza A PA amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 9;
b) the influenza A PB2 amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 8;
c) the influenza A MP amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 10;
d) the avian influenza MP amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 11;
e) the influenza B MP amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 13;
f) the influenza B NS amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 14;
g) the RSV A amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 15;
h) the RSV B amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 16;
i) the SARS-CoV-2 E amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 462 or SEQ ID NO: 79, or SEQ ID NO: 66;
j) the SARS-CoV-2 N2 amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 47; and/or
k) the SARS-CoV-2 RdRP amplicon comprises a sequence that is at least 85% identical to SEQ ID NO: 80 and/or SEQ ID NO: 81.
Claims 7 and 8 are directed toward the particular probes employed to detect different amplicons (claim 7, influenza A PA probe, an influenza A PB2 probe, an influenza A MP probe, an avian influenza MP probe, an influenza B MP probe, an influenza B NS probe, an RSV A probe, an RSV B probe, a SARS-CoV-2 E probe, a SARS-CoV-2 N2 probe, and a SARS-CoV-2 RdRP probe; claim 8,
a) the influenza A PA probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 22;
b) the influenza A PB2 probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 19;
c) the influenza A MP probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 25;
d) the avian influenza MP probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 28;
e) the influenza B MP probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 34;
f) the influenza B NS probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 37;
g) the RSV A probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 40;
h) the RSV B probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 43;
i) the SARS-CoV-2 E probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 72, SEQ ID NO: 50 or SEQ ID NO: 56;
j) the SARS-CoV-2 N2 probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 74, SEQ ID NO: 75, and/or SEQ ID NO: 53, or SEQ ID NO: 59; and/or
k) the SARS-CoV-2 RdRP probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 77 or SEQ ID NO: 62; and/or
1) the SARS-CoV-2 ORF lab probe comprises a region of at least 15 contiguous nucleotides having a sequence that is at least 85% identical or complementary to at least 15 contiguous nucleotides of SEQ ID NO: 65.
Claims 9 and 13 are further directed toward multiplex detection methods and the utilization of suitable controls. Claims 21 and 23 reference the clinical state of the subject and sample origin.
Applicant is reminded that claim 1 does not reference any specific multiplex PCR primer pairs, but rather references different amplicons (e.g., SARS-CoV-2 E SEQ ID NOS.: 66 (115 nt) and 79 (66 nt); SARS-CoV-2 N2 SEQ ID NO.: 47 (67 nt); and SARS-CoV-2 RdRP SEQ ID NOS.: 80 (187 nt) and 81 (71 nt). Claim 4 also fails to recite any specific primer pairs (with the exception of RSVA/B), amplicons, or probes. Influenza PB2 (IAV), PA (IAV), MP (IAV), MP (avian), MP (IBV), and NS (IBV) primers can be prepared from SEQ ID NOS.: 1 (3,151 nt), 2 (2,587 nt), 3 (982 nt), 4 (931 nt), 6 (1,139 nt), and 7 (1,054 nt), respectively. Moreover, the claim language is not limited to specific sequences because of the comprising limitation. It is suggested Applicant amend the claims to recite sequences that consist of the specific primer pairs, probes, and amplicons. Applicant’s representative is invited to contact the Examiner to discuss suggested claim language.
As previously set forth, Mokkapati et al. (2017) disclose the generation of PCR primer pairs for the detection of influenza A and B. Specifically, primer pairs were generated that are capable amplifying the influenza virus A PB2, PA, and MP regions, and the influenza B virus MP and NS regions. Multiplex RT-PCR was utilized to detect influenza A and B and various subtypes. In particular, suitable gene fragments for the design of primers and probes were identified by first generating sequence alignments of RNA segments using the European Molecular Biology Laboratory (EMBL)-European Bioinformatics Institute (EBI) sequence alignment software, ClustalW. ClustalW is a general purpose multiple sequence alignment program for nucleic acids or proteins that calculates the best match for the selected sequences and aligns them such that the identities, similarities, and differences can be compared. For each potential target, sequence regions, 100-200 nt in length, were chosen that differentiated the targets (see ¶ [0222]).
Design of primers and probes for amplification of RNA fragments in the selected regions was performed using DNA Software, Inc.’s Visual OMP (Oligonucleotide Modeling Platform). Visual OMP models, in silico, the folding and hybridization of single-stranded nucleic acids by incorporating all public domain thermodynamic parameters as well as proprietary nearest-neighbor and multi-state thermodynamic parameters for DNA, RNA, PNA, and Inosine. This enables the effective design of primers and probes for complex assays such as microarrays, microfluidics applications and multiplex PCR (see ¶ [0224]). This is the same approach utilized by Applicant. Specific primer/probe combinations were set forth in Tables A/B.
This assay provided good results with nasal aspirate/wash (NA/W) and nasopharyngeal (NP) swab specimens (see 5.2 Example 2: Clinical Performance; ¶s [0238-0251]). Moreover, the primers, amplicons, and probes appear to be identical to those disclosed in the instant application. This teaching does not disclose a detection method for the detection of influenza A, influenza B, RSV, and SARS-CoV-2.
Chen et al. (2009) disclose a multiplex detection assay for the detection of both influenza and RSV viruses. The diagnostic panel in this example was designed to detect any of Influenza A, Influenza B, RSV A, or RSV B DNA in a singleplex or multiplex reaction. Specifically, it was designed to detect the M gene of each pathogen. The assay includes reagents and primers for the detection of nucleic acid from the target sequence of each species. The assay may further include an internal control (IC) to Verify adequate processing of the target viruses and to monitor the presence of inhibition in the amplification assay to avoid false negative results. The diagnostic test involved a two-step procedure: (1) the extraction of nucleic acid from, for example, the Subject’s nasal cavity for use as the testing template and (2) one-step RT-PCR using reverse transcription to convert target RNA to cDNA followed by the amplification and detection of the target template(s) (see ¶s [0122-0123]). Preferred RSV targets for primer selection and amplification included the RSV A and B M genes. See Table 1 for exemplary primers and probes. This teaching does not disclose a detection method for the detection of influenza A, influenza B, RSV, and SARS-CoV-2.
Both Nalla et al. (2020) and Yan et al. (2020) identified suitable SARS-CoV-2 primers and probes for the detection of SARS-CoV-2. Yan and colleagues generated suitable orf1ab and S gene primers by aligning 103 complete genomes of SARS-CoV-2 obtained from four databases, GenBank, GISAID, GWH and NMDC (https://bigd.big.ac.cn/ncov), to confirm the conservation of the selected sequence. Homology analysis was conducted using BLAST (National Centre for Biotechnology Information). Five sets of primers specific to the orf1ab and S genes were designed using the software PRIMEREXPLORER V5 at the website: http://primerexplorer.jp/e/. The primers included an outer forward primer (F3), an outer backward primer (B3), a forward inner primer (FIP) and a backward inner primer (BIP). A loop forward primer (LF) and/or a loop backward primer (LB) were also designed to accelerate the reaction. Two additional primers were also designed primers to amplify the two regions by conventional PCR assay (orf1ab-F: 5ʹ-CAGACCTCGTCTATGCTTTAAGGC-3ʹ; orf1ab-R: 5ʹ-CCCTGGTCAAGGTTAATATAGGCA-3ʹ; SeF: 5ʹ-CTTCCCTCAGTCAGCACCTC-3ʹ; S-R: 5ʹ-AACCAGTGTGTGCCATTTGA-3ʹ) (see Materials and methods, Primer design, p. 774). The specificity of the assay was tested against a number of respiratory pathogens including human coronavirus HcoV-229E, HcoV-NL63, HcoV-OC43, HcoV-HKU1, SARS-CoV (pseudo-virus) and Middle East respiratory syndrome-CoV (pseudo-virus); influenza A-H3N2, H1N1, influenza B, parainfluenza viruses types 1/2/3/4, adenoviruses types 1/2/3/4/5/6/7, respiratory syncytial virus types A/B, human metapneumovirus, human bocavirus, rhinovirus types A/B/C, as well as respiratory pathogens such as Mycoplasma pneumoniae strains M129/FH, Haemophilus influenzae ATCC 49247, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae and Pseudomonas aeruginosa (see Materials and methods, Viruses and bacterial strains, p. 774). This teaching does not disclose a detection method for the detection of influenza A, influenza B, RSV, and SARS-CoV-2.
Nalla and coworkers disclose the generation of a total of 7 different primer-probe sets to be utilized SARS-CoV-2 detection assays (see Table S1 in the supplemental material). The University of Washington (UW) RdRp primer-probe set was designed by the UW Virology Lab. Three additional primer-probe sets were designed as described in the work of Corman et al. (8); these will be referred to as the Corman N-gene, RdRp, and E-gene primer-probe sets. The Centers for Disease Control and Prevention (CDC) N1, N2, and N3 sets were developed by the CDC and have been published on the CDC website (see MATERIALS AND METHODS, SARS-CoV-2 detection assays, p. 2). These primer sets were extremely sensitive and specific for SARS-CoV-2. This teaching does not disclose a detection method for the detection of influenza A, influenza B, RSV, and SARS-CoV-2.
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to perform a multiplex RT-PCR assay for the simultaneous detection of influenza A, influenza B, RSV, and SARS-CoV-2. Mokkapati et al. (2017) provided a detailed description of primer algorithms that are available for the identification of suitable PCR primer and probe sets. This teaching also provided multiple influenza A and B primers/probes. Chen et al. (2009) provide a detailed description about the selection and preparation of suitable influenza and RSV primers/probes. Finally, both Nalla et al. (2020) and Yan et al. (2020) provided a detailed description of suitable PCR primers/probes for the detection of SARS-CoV-2. These teachings provided specific probes and primers derived from the influenza A PB, PA, and MP genes, influenza B MP and NS genes, RSV A and B genes, and SARS-CoV-2 E/S, N2, RdRP, and ORF1ab genes.
Absent evidence to the contrary, it would have been prima facie obvious to use suitable computer algorithms to identify suitable PCR primers and probes for the detection of influenza A, influenza B, RSV, and SARS-CoV-2. Moreover, Chen et al. (2009) provides a multiplex PCR detection assay to detect multiple respiratory pathogens (e.g., influenza and RSV). Therefore, it would also have been prima facie obvious to combine primers and probes from multiple respiratory viruses into a multiplex diagnostic method.
Applicant again traverses and submits that the rejection fails to adequately address all of the claim limitations. In particular it fails to identify the relevant primers and probes in any given reference. With respect to amended claim 1, no specific primers are cited. The claim simply requires primers that detect an influenza A or B gene, an RSV gene, or the SARS-CoV-2 genes E, N2, and RdRP. As previously set forth, Both Nalla et al. (2020) and Yan et al. (2020) identified suitable SARS-CoV-2 primers and probes for the detection of SARS-CoV-2. Yan and colleagues generated suitable orf1ab and S gene primers by aligning 103 complete genomes of SARS-CoV-2 obtained from four databases. Nalla and coworkers disclose the generation of a total of 7 different primer-probe sets to be utilized SARS-CoV-2 detection assays (see Table S1 in the supplemental material). The University of Washington (UW) RdRp primer-probe set was designed by the UW Virology Lab. Three additional primer-probe sets were designed as described in the work of Corman et al. (8); these will be referred to as the Corman N-gene, RdRp, and E-gene primer-probe sets. The Centers for Disease Control and Prevention (CDC) N1, N2, and N3 sets were developed by the CDC and have been published on the CDC website (see MATERIALS AND METHODS, SARS-CoV-2 detection assays, p. 2). These primer sets were extremely sensitive and specific for SARS-CoV-2.
With respect to the detection of influenza A and B, Mokkapati et al. (2017) disclose the generation of PCR primer pairs for the detection of influenza A and B. Specifically, primer pairs were generated that are capable amplifying the influenza virus A PB2, PA, and MP regions, and the influenza B virus MP and NS regions. Multiplex RT-PCR was utilized to detect influenza A and B and various subtypes. Chen et al. (2009) disclose a multiplex detection assay for the detection of both influenza and RSV viruses. The diagnostic panel in this example was designed to detect any of Influenza A, Influenza B, RSV A, or RSV B DNA in a singleplex or multiplex reaction. Specifically, it was designed to detect the M gene of each pathogen. The assay includes reagents and primers for the detection of nucleic acid from the target sequence of each species. These references all disclose primer and probe sets useful for the detection of influenza A/B, RSV, and SARS-CoV-2 nucleic acids in biological samples. Thus, one of ordinary skill in the art would have had ample motivation to employ these known primers/probes in a multiplex assay to detect multiple infectious respiratory pathogens.
Claim 4 references specific primers directed against influenza A PB2, PA, MP, avian influenza MP, influenza B MP and NS, RSV A, RSV B, and SARS-CoV-2 E, N2, and RdRP. As noted supra, the prior art clearly teaches the generation of specific primers directed against these respiratory pathogens, including the specific targets of the claimed primers. In particular, Mokkapati et al. (2017) disclose suitable gene fragments for the design of primers and probes were identified by first generating sequence alignments of RNA segments using the European Molecular Biology Laboratory (EMBL)-European Bioinformatics Institute (EBI) sequence alignment software, ClustalW. ClustalW is a general purpose multiple sequence alignment program for nucleic acids or proteins that calculates the best match for the selected sequences and aligns them such that the identities, similarities, and differences can be compared. For each potential target, sequence regions, 100-200 nt in length, were chosen that differentiated the targets (see ¶ [0222]).
Design of primers and probes for amplification of RNA fragments in the selected regions was performed using DNA Software, Inc.’s Visual OMP (Oligonucleotide Modeling Platform). Visual OMP models, in silico, the folding and hybridization of single-stranded nucleic acids by incorporating all public domain thermodynamic parameters as well as proprietary nearest-neighbor and multi-state thermodynamic parameters for DNA, RNA, PNA, and Inosine. This enables the effective design of primers and probes for complex assays such as microarrays, microfluidics applications and multiplex PCR (see ¶ [0224]). This is the same approach utilized by Applicant. Specific primer/probe combinations were set forth in Tables A/B.
Thus, the prior art clearly identifies suitable targets in influenza A PB2, PA, MP, avian influenza MP, influenza B MP and NS, RSV A, RSV B, and SARS-CoV-2 E, N2, and RdRP that can be targeted for multiplex analysis. Specific primer and probe set were designed using various art-recognized algorithms. Absent evidence to the contrary, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to identify suitable gene targets in influenza, RSV, and SARS-CoV-2, and to use art-recognized algorithms to identify suitable primer pairs and diagnostic probes. Applicant’s reply failed to proffer any evidence demonstrating that the recited probes provided any unexpected results with respect to multiplex amplification. One of ordinary skill in the art would have been sufficiently motivated to perform a multiplex assay on known common respiratory viral pathogens such as influenza, RSV, and SARS-CoV-2.
Applicant also previously provided a declaration under 37 C.F.R. § 1.132 (filed 04 September, 2025) by Dr. Chu. It was noted that the combination of specific primers and probes for SARS-CoV-2, influenza A, influenza B, and RSV genes addresses the challenges associated with genetic drift and shift. Optimizing multiplex assays can be challenging due to factors such as spurious amplification and the inability to predict which primer pairs will provide optimal amplification. Creating multiplexed q-PCR methods also suffer from the inability to detect different nucleic acid sequences in a single sample. It was argued that many of these deficiencies were solved by the approach taken in this application. A multiplex design strategy was employed to screen, optimize, and select suitable primer and oligos. In particular, the original SARS-CoV-2 primer design interfered with cycle threshold (Ct). A new SARS-CoV-2 E gene target was developed to overcome this limitation.
The affidavit/declaration is sufficient/insufficient to overcome the rejection because the showing is not commensurate in scope with the claims. The declaration stated that primer design is critical and often requires empirical testing to ascertain the precise combination of primer pairs. However, the declaration failed to identify the precise primer pairs utilized. With respect to IAV PB2, PA, and MP, avian MP, IBV MP and NS, specific primer pairs were not identified. With respect to the SARS-CoV-2 E, N2, and RdRP targets, once again, specific primer pairs were not provided. Rather, reference was made to primers derived from various amplicons. As previously set forth, claim 1 fails to identify a single IAV, IBV, RSV or avian influenza target and attendant primer pairs/probes. With respect to claim 4, once again, reference was only made to these genes without providing specific primer sequences. Accordingly, the rejection is hereby maintained. Applicant’s representative is invited to contact the Examiner to discuss suggested claim language.
Action Is Final
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 C.F.R. § 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 C.F.R. § 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.
Correspondence
Any inquiry concerning this communication should be directed to Jeffrey S. Parkin, Ph.D., whose telephone number is (571) 272-0908. The Examiner can normally be reached Monday through Friday from 10:00 AM to 6:00 PM. A message may be left on the Examiner's voice mail service. 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 are unsuccessful, the Examiner's supervisor, Janet L. Andres, Ph.D., can be reached at (571) 272-0867. Direct general status inquiries to the Technology Center 1600 receptionist at (571) 272-1600.
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Respectfully,
/JEFFREY S PARKIN/Primary Examiner, Art Unit 1671 28 June, 2026
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