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
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office Action has been withdrawn pursuant to 37 CFR 1.114.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 August 20, 2026 has been entered.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Status of Claims
Claims 109, 110, 116 and 142-157 are currently pending in the instant application. Claims 109, 110 and 116 have been amended by Applicants’ amendment filed 08-20-2026. Claims 111, 112 and 114-129 have been canceled by Applicant’s amendment filed 08-20-2026. Claims 142-157 have been added by Applicants’ amendment filed 08-20-2026.
Applicant's election of Group I with traverse of claims 109-113, 116, 125 and 130, directed to a quality control composition used to assess the functionality of a Nucleic Acid Test (NAT); and the election with traverse of Species as follows:
Species (A): wherein the protecting vehicle is an organism that has the same or similar nucleic acid sequence protection properties when processed through NAT; and wherein the second target nucleic acid sequence is characteristic of some members of the species or genus of the organism to be tested (claim 111), in the reply filed October 23, 2023 was previously acknowledged.
Regarding newly submitted claims 150-154, 156 and 157, the claims are directed to an invention that is independent or distinct from the invention originally claimed for the following reasons: Newly submitted claim 150 is directed to a quality control composition for assessing the functionality of a NAT, comprising (a) at least one first protecting vehicle comprising at least one first protected nucleic acid sequence characteristic of a first target nucleic acid sequence; (b) at least one second protecting vehicle comprising at least one second protected nucleic acid sequence characteristic of a second target nucleic acid sequence; and the second nucleic acid sequence being an exogenous nucleic acid sequence not natively present in the at least one second protecting vehicle, and encodes a resistance gene selected from the group consisting of an antibiotic resistance gene and a drug resistance gene…characteristic of an organism in a test article (claim 150). Newly submitted claim 156 is directed to a composition consisting of (a) at least one first protecting vehicle; and (b) at least one second protecting vehicle; and optionally other non-nucleic acid sequence components. Newly submitted claim 157 is directed to a non-pathogenic quality control composition for assessing the functionality of the NAT to detect a pathogenic organism in a test article, the composition comprising: (a) at least one first protecting vehicle comprising at least one first protected nucleic acid sequence comprising a first nucleic acid sequence, which is characteristic of the pathogenic organism; and (b) at least one second protecting vehicle comprising at least one second protected nucleic acid sequence comprising a second nucleic acid sequence which is characteristic of the pathogenic organism, the second nucleic acid sequence being an exogenous nucleic acid sequence not natively present in the at least one second protecting vehicle, and wherein the at least one second protecting vehicle is a recombinant or otherwise engineered vehicle into which the exogenous second nucleic acid sequence has been introduced… wherein the at least one first protecting vehicle and the at least one second protecting vehicle together comprise the non-pathogenic quality control composition (claim 157). Claim 109 of the claims filed September 1, 2021 was directed to a quality control composition used to assess the functionality of a NAT, wherein the NAT can be used to detect at least one of the presence and/or characteristics of an organism by detecting target nucleic acid sequences in a test article, the quality control composition comprising: (a) at least one first protected nucleic acid sequence comprising a first nucleic acid sequence the presence of which is characteristic of the presence in the test article of a first target nucleic acid sequence being tested in the NAT; and (b) at least one second protected nucleic acid sequence comprising a second nucleic acid sequence the presence of which is characteristic of the presence in the test article of a second target nucleic acid sequence being tested in the NAT, wherein the first and second protected nucleic acid sequences are in more than one protecting vehicle, wherein the protecting vehicles are: (i) any enclosing or associating substance or barrier, protecting the nucleic acid sequences by their containment within or their association with the protecting vehicle; (ii) the same or different type of protecting vehicle; and (iii) protective of their respective nucleic acid sequences of the at least one second protected nucleic acid sequence is not natively present in its protecting vehicle (claim 109). Thus, newly submitted claims 150-154, 156 and 157 require a search and examination beyond the claims as originally presented, and constructively elected. The different species of method and composition would require a different field of search; the prior art applicable to one species would not likely be applicable to another species; and/or the species are likely to raise different non-prior art issues under 35 U.S.C. 101 and/or 35 U.S.C. 112(a). For example, the limitations of newly submitted claims 150-154, 156 and 157 recite different quality control compositions as compared to instant claim 1 of the claims filed September 1, 2021.
As noted in MPEP 818.02(a), wherein subsequently presented claims to an invention other than that acted upon should be treated as provided in MPEP § 821.03. As recited in MPEP 821.04 (¶ 8.04), since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits.
Accordingly, newly submitted claims 150-157 are withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
Please Note: claim 145 recites a second protecting vehicle genetically engineered to contain an exogenous second nucleic acid sequence contain a second exogenous sequence; claim 146 recites an exogenous second sequence integrated into the genome of the second protecting vehicle; and claim 147 recites an exogenous sequence not integrated into the genome of the second protecting vehicle. In the reply filed October 23, 2023, Applicant elected Species (A), which recites that the protecting vehicle is an organism, and the second sequence is characteristic of some members of the species or genus of the organism to be tested. Thus, claims 145-147 are withdrawn as being directed to a non-elected species.
Claims 114-115, 117-122, 124, 126-129 and 131-139 were previously withdrawn, and claims 150-154m 156 and 157 are newly withdrawn, from further consideration pursuant to 37 CFR 1.142(b) in the reply filed October 23, 2023 as being drawn to a non-elected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on October 23, 2023.
Claims 112 and 125 were previously withdrawn, and claims 145-147 are newly withdrawn, from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim.
The restriction requirement was deemed proper and was made FINAL.
The claims will be examined insofar as they read on the elected species.
Therefore, claims 109, 110, 116, 142-144, 148, 149 and 155 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed November 18, 2020 is a 35 U.S.C. 371 national stage filing of International Application No. PCT/CA2019/050689, filed May 21, 2019, which claims the benefit of US Provisional Patent Application 62/673,480, filed May 18, 2018.
Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 120 as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of the first paragraph of 35 U.S.C. 112. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Provisional Patent Application 62673480, filed May 18, 2018, fails to provide adequate support or enablement in the manner provided by the first paragraph of 35 U.S.C. 112 for one or more claims of this application. The specific method steps recited in independent claim 109 does not have support for: at least one first protecting vehicle; at least one second protecting vehicle; enclosing barrier that protects against loss and degradation of the first nucleic acid sequence or second nucleic acid sequence; and allows for extraction of the first nucleic acid sequence and/or the second nucleic acid sequence. Therefore, the priority date for the presently claimed invention is May 21, 2019, the filing date of International Application WO2019218093.
Applicants are invited to specifically indicate the location of the cited phrase pertinent to claim 109 of the instant application.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed August 20, 2026 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below are herein withdrawn.
Claim Rejections - 35 USC § 102
The rejection of claims 109-111, 116, 123, 140 and 141 is withdrawn under 35 U.S.C. 102(a1)/(a2) as being anticipated by Semikhodskii et al. (US Patent Application Publication 20160108467, April 21, 2016; of record) as evidenced by Krupp et al. (hereinafter “Krupp”) (Indian Journal of Sexually Transmitted Diseases and AIDS, 2015, 36(1), 1-6); and CDC (CDC, 2024,
1-2).
Semikhodskii does not specifically exemplify a second protecting vehicle is a recombinant or otherwise engineered vehicle.
In view of the withdrawn rejection, Applicant’s arguments are rendered moot.
The rejection of claims 109-111, 116, 123, 140 and 141 is withdrawn under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Berg et. al. (hereinafter “Berg”) (US Patent Application Publication 20110065092, published March 17, 2011).
Berg does not specifically exemplify a second protecting vehicle is a recombinant or otherwise engineered vehicle.
In view of the withdrawn rejection, Applicant’s arguments are rendered moot.
Claim Rejections - 35 USC § 103
The rejection of claims 109-111, 116, 123, 140 and 141 is withdrawn under 35 U.S.C. 103 as being unpatentable over Berg et. al. (hereinafter “Berg”) (US Patent Application Publication 20110065092, published March 17, 2011) in view of Witt et. al. (hereinafter “Witt”) (Journal of Virological Methods, 1999, 79, 97-111).
The combined references of Berg and Witt do not specifically exemplify a second protecting vehicle is a recombinant or otherwise engineered vehicle.
In view of the withdrawn rejection, Applicant’s arguments are rendered moot.
Maintained Objections/Rejections
Claim Rejections - 35 USC § 112(b)
The rejection of claims 109, 110 and 116 is maintained, and claims 142-144, 148, 149 and 155 are newly 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.
Claim 109 is indefinite for the recitation of the term “the second nucleic acid sequence” such as recited in claim 109, line 11. There is insufficient antecedent basis for the term “the exogenous second nucleic acid sequence” in the claim because claim 109, line 9 recites the term “at least one second nucleic acid sequence.”
Claim 109 is indefinite for the recitation of the term “a recombinant or otherwise engineered vehicle” such as recited in claim 109, line 13. There is insufficient antecedent basis for the term “a recombinant or otherwise engineered vehicle” in the claim because claim 109, line 13 recites the term “at least one second protecting vehicle.” Moreover, the as-filed Specification and the claims as originally filed do not teach and/or recite recombinant protecting vehicles, engineered protecting vehicles and/or engineered vehicles. The as-filed Specification defines the terms “protecting vehicle” and a “vehicle”, separately (See, paragraphs [0133]-[0134]), such that it is unclear what the second nucleic acid sequence comprises and/or whether it comprises a vehicle or whether it comprises a protecting vehicle and, thus, the metes and bounds of the claim cannot be determined.
Claim 109 is indefinite for the recitation of the term “the first nucleic acid sequence or second nucleic acid sequence” such as recited in claim 109, lines 18-19. There is insufficient antecedent basis for the term “the first nucleic acid sequence or second nucleic acid sequence” in the claim because claim 109, lines 6 and 10 recite the terms “a first nucleic acid sequence” and “a second nucleic acid sequence.” The Examiner suggests that Applicant amend the claim to recite, for example, “the first nucleic acid sequence or the second nucleic acid sequence.”
Claim 109 is indefinite for the recitation of the term “allows for extraction” such as recited in claim 109, line 20 because it the instant as-filed Specification and claims as originally filed do not teach that the protecting vehicles allow for extraction of the nucleic acid sequences. The instant as-filed Specification teaches that nucleic acid sequences can be sufficiently, and/or substantially recovered in the nucleic acid extraction steps of the NAT (paragraph [0017]); or to inhibit loss or degradation of sequences up to the nucleic acid extraction process step and/or to enable recovery of the nucleic acid sequences in the extraction steps (paragraph [0134]), such that it is unclear whether the protecting vehicles “allow” for extraction (e.g., are porous, etc.), or whether the protecting vehicles are subsequently removed, whether they protect nucleic acids prior to extraction, and/or they inhibit loss of nucleic acids before the extraction, etc. and, thus, the metes and bounds of the claim cannot be determined.
Claim 110 is indefinite for the recitation of the term “at least one second protecting vehicle is selected from…an inactivated organism, a non-viable or non-pathogenic organism”” such as recited in claim 110, lines 2-5 because the as-filed Specification teaches that a “vehicle” can be an organism, but a “protecting vehicle” is not an organism (See; paragraphs [0133]-[0134]). Additionally, claim 110 depends from instant claim 109, wherein claim 109 does not recite the presence of a vehicle and, thus, the metes and bounds of the claim cannot be determined.
Claim 142 is indefinite for the recitation of the term “neither the at least one first protecting vehicle nor the at least one second protecting vehicle is the same as the organism to be detected” such as recited in claim 142, lines 1-3 because the claims are directed to a composition, and claim 142 depends from instant claim 109, wherein claim 109 does not recite detecting the presence of an organism, a plurality of organisms to be detected, and/or the presence of a test article. The term “to detect an organism in a test article” is only recited in the preamble of claim 109, such that the term has not been given patentable weight. Moreover, claim 109 recites that the second protecting vehicle is a “recombinant or otherwise engineered vehicle”, wherein the as-filed Specification teaches that a “vehicle” can be an organism, but a “protecting vehicle” is not an organism (See; paragraphs [0133]-[0134]) and, thus, the metes and bounds of the claim cannot be determined.
Claims 143 and 144 are indefinite for the recitation of the term “the organism detected by the NAT” such as recited in claim 143, line 1 because no organism is recited to be detected by the NAT. The term “to detect an organism in a test article” is only recited in the preamble of claim 109, such that the term has not been given patentable weight. Additionally, claim 143 depends from instant claim 109, wherein claim 109 does not recite the presence of an organism, a NAT, and/or detecting anything and, thus, the metes and bounds of the claim cannot be determined.
Claim 144 is indefinite for the recitation of the term “two or more of the at least one first protected nucleic acid” such as recited in claim 144, lines 1-2. There is insufficient antecedent basis for the term “two or more of the at least one protected nucleic acid” in the claim because claim 109, lines 5-6 recites the term “at least one first nucleic acid sequence.”
Claim 148 is indefinite for the recitation of the term “the exogenous second nucleic acid sequence” such as recited in claim 148, lines 1-2. There is insufficient antecedent basis for the term “the exogenous second nucleic acid sequence” in the claim because claim 109, line 9 recites the term “at least one second nucleic acid sequence.” The Examiner suggests that Applicant amend the claim to recite, for example, “the at least one second nucleic acid sequence.”
Claim 149 is indefinite for the recitation of the term “at least one protecting vehicle” such as recited in claim 149, lines 1-2. There is insufficient antecedent basis for the term “the at least one protecting vehicle” in the claim because claim 109, lines 5 and 9 recite the terms “at least one first protecting vehicle” and “at least one second protecting vehicle.”
Claim 149 is indefinite for the recitation of the term “another aldehyde” such as recited in claim 149, line 3 because it is unclear whether any aldehyde (e.g., acetaldehyde, prionaldehyde, benzaldehyde, pivaldehyde, etc.) will inactivate any organism (e.g., human, virus, bacteria, etc.) and, thus, the metes and bounds of the claim cannot be determined.
Claim 155 is indefinite for the recitation of the term “optionally” and “test article to be assessed by the NAT” such as recited in claim 155, lines 1-3 because the claims do not particularly point out and distinctly claim the subject matter which the applicant regards as his invention. Moreover, claim 155 depends from claim 109, wherein claim 109 does not recite a “test article” in the body of the claim, such that the term has not been given patentable weight. Additionally, instant claim 109 does not recite that the test article is assessed by the NAT and, thus, the metes and bounds of the claim cannot be determined.
Claim 116 are indefinite insofar as they ultimately depend from claim 109.
Claim Rejections - 35 USC § 101
The rejection of claims 109, 110 and 116 is maintained, and claims 142-144, 148, 149 and 155 are newly rejected, under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. An analysis with respect to the claims as a whole reveals that they do not include additional elements that are sufficient to amount to significantly more than the judicial exception. See Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 134 S. Ct. 2347, 110 U.S.P.Q.2d 1976 (2014); Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107, 2116, 106 U.S.P.Q.2d 1972 (2013); Mayo Collaborative Svcs. v. Prometheus Laboratories, Inc., 132 S. Ct. 1289, 101 U.S.P.Q.2d 1961 (2012). See also 2014 Interim Guidance on Patent Subject Matter Eligibility, available at http://www.gpo.gov/fdsys/pkg/FR-2014-12-16/pdf/2014-29414.pdf (“2014 Interim Guidance”), and the Office’s examples to be considered in conjunction with the 2014 Interim Guidance in examination of nature-based products, available online at http://www.uspto.gov/patents/law/exam/mdc_ examples_nature-based_ products.pdf (“Nature-Based Products Examples”). See also; the 2019 Revised Patent Subject Matter Eligibility Guidance (hereinafter “2019 PEG”) published in January 2019. This rejection is proper. This rejection is proper.
Analysis of subject-matter eligibility under 35 U.S.C. § 101 requires consideration of three issues: (1) whether the claim is directed to one of the four categories recited in §101; (2) whether the claim recites or involves a judicial exception (i.e., a law of nature, natural phenomenon, or natural product); and (3) whether the claim as a whole recites something that amounts to significantly more than the judicial exception. In this case, the claims as a whole are directed to natural products in the form of a composition comprising of at least one first protecting vehicle comprising at least one first protecting vehicle comprising at least one first protected nucleic acid sequence comprising a first nucleic acid sequence that is characteristic of the organism; and at least one second protecting vehicle comprising at least one second protected nucleic acid sequence comprising a second nucleic acid sequence, which is characteristic of the organism, the second nucleic acid sequence being an exogenous nucleic acid sequence not natively present in the at least one second protecting vehicle, and wherein the at least one second protecting vehicle is a recombinant or otherwise engineered vehicle into which the exogenous second nucleic acid sequence has been introduced wherein the at least one first protecting vehicle and the at least one second protecting vehicle are separate protecting vehicles. Therefore, they must each be considered to determine whether, given their broadest reasonable interpretation, they amount to significantly more than the judicial exception.
The claimed invention is not directed to patent eligible subject matter. Based upon an analysis with respect to the claim as a whole, claim(s) 109, 110, 116, 142-144, 148, 149 and 155 do not recite something significantly different than the judicial exception. The rationale for this determination is explained below:
In this case, the claims as a whole are directed to (and encompass) a natural product including naturally occurring nucleic acids in the form of a quality control composition, the quality control composition comprising: (a) at least one first protecting vehicle comprising at least one first protected nucleic acid sequence comprising a first nucleic acid sequence that is characteristic of the organism; and (b) at least one second protecting vehicle comprising at least one second protected nucleic acid sequence comprising a second nucleic acid sequence which is characteristic of the organism, the second nucleic acid sequence being an exogenous nucleic acid sequence not natively present in the at least one second protecting vehicle, and wherein the at least one second protecting vehicle is a recombinant or otherwise engineered vehicle into which the exogenous second nucleic acid sequence has been introduced wherein the at least one first protecting vehicle and the at least one second protecting vehicle are separate protecting vehicles, each of the at least one first protecting vehicle and the at least one second protecting vehicle being an enclosing substance or enclosing barrier that protects against loss and degradation of the first nucleic acid sequence or second nucleic acid sequence while contained within the at least one first protecting vehicle or the at least one second protecting vehicle, respectively, but allows for extraction of the first nucleic acid sequence and/or the second nucleic acid sequence from the at least one first protecting vehicle or the at least one second protecting vehicle in a nucleic acid extraction step of the NAT, and wherein the at least one first protecting vehicle and the at least one second protecting vehicle together comprise the quality control composition.
Beginning with Step I of the analysis, which asks whether the claimed invention falls within a statutory category, such that the instant claims are directed to a composition of matter, thus, the instant claims are directed to a statutory category. Step I: [YES].
Proceeding to Step IIA – Prong One of the analysis, which asks if the claimed invention is directed to a judicial exception, such that claims 109, 110, 116, 142-144, 148, 149 and 155 are directed to (and encompass) a judicial exception in the form of naturally occurring and/or non-naturally occurring quality control compositions which do not possess markedly different characteristics such as different biological or pharmacological functions or activities, chemical or physical properties and/or structure/function and form as naturally occurring quality control compositions, comprising: a first protecting vehicle comprising a first nucleic acid characteristic of an organism; and a second protecting vehicle comprising at least one second nucleic acid characteristic of the organism, wherein the second nucleic acid is an exogenous nucleic acid not natively present in a second protecting vehicle, wherein the protecting vehicle is recombinant or otherwise engineer vehicle into which the exogenous second nucleic acid has been introduced, and wherein the first and second protecting vehicles comprise an enclosing substance or enclosing barrier, wherein protecting vehicles are defined in the Specification as any enclosing or associating substance or barrier, including but not limited to: a bacterium, eukaryotic cell, protein capsid or shell (such as, viral capsids, a protein capsid or shell), microcompartments, engineered protein shells, virus, a virus-like particle, liposome, an anucleated cell, a vesicle, a nanovesicle, an exosome, a micelle, a solid lipid nanoparticle, a lipid-coated particle, a nanotube, a nanocrystal, a polymeric nanoparticle, an inorganic nanoparticle, interpolyelectrolyte complex, (polyplex) or a dendrimer, armored RNA, or other suitable physical boundary. Thus, under the revised Step IIA analysis, the claims are directed to a naturally occurring products and/or non-naturally occurring products. Step IIA: [YES].
Step IIA - Prong Two asks whether the claim recites additional elements that integrate the exception into a practical application of the exception. It is noted that the specific composition, the NAT, specific organisms, test articles, nucleic acid sequences characteristic of the organism, a first protected nucleic acid sequence, a second protected nucleic acid sequence not natively present in its protecting vehicle, the exogenous nucleic acid sequences not natively present in the second protecting vehicle, the recombinant or otherwise engineered vehicle into which the exogenous second nucleic acid sequence has been introduced, etc. are not identified in instant claim 109. The claims do not recite additional elements or a combination of elements beyond the judicial exception to apply, rely on, or use the judicial exception in a manner that imposes meaningful limits on the judicial exceptions. Thus, the claims do not integrate the judicial exception into a practical application of that exception. Step IIA: [NO].
Proceeding to Step IIB of the analysis: the question then becomes what element or what combination of elements is sufficient to amount to significantly more than the judicial exception? The instant independent claim is recited at a high level of generality, such that substantially all practical applications of the judicial exception are covered. For instance, the claims are recited without any specificity as to the specific composition; the functionality of the NAT; the identity of the at least one protecting vehicle; the identity of the at least one first protected nucleic acid sequence comprising a first nucleic acid sequence that is characteristic of the organism; the organism; the identity of the at least one second protecting vehicle comprising at least one second protected nucleic acid sequence comprising a second nucleic acid sequence which is characteristic of the organism, the second nucleic acid sequence; the origin and identity of the exogenous nucleic acid sequence not natively present in the at least one second protecting vehicle; how the protecting vehicles protect against loss and degradation of the first nucleic acid sequence and second nucleic acid sequence; and how they allow for extraction of the first nucleic acid sequence and/or the second nucleic acid sequence; where the protecting vehicles and nucleic acid sequences are located, etc. The claims amount to nothing more than naturally occurring and/or non-naturally occurring protecting vehicles and nucleic acid sequences, wherein the composition as recited is well known, purely conventional or routine in the art.
For example, non-viable particles (and in particular liposome particles, particles which are in the form of a viral protein coat, non-viable genetically modified organisms or particles made of synthetic polymers), comprising an internal control (IC) nucleic acid sequence as an internal control in nucleic acid-based analysis were known in the art, wherein the use of nucleic acid-based analysis in the field of diagnostic testing including for the diagnosis of microbiological pathogens and genetic disorders, the discovery of unknown infectious agents and improved diagnostic tools, wherein nucleic acid-based analysis can be either qualitative or quantitative and can involve nucleic acid-based amplification techniques, such that ideal IC sequence generally comprises a binding region, such as a primer or probe binding region which are substantially identical to the equivalent regions to the primers or probes bind in the target nucleic acid to be detected. Additionally, a NAT comprises the steps of: (i) obtaining a sample to be analyzed (obtaining a test sample); (ii) bringing said sample into contact with non-viable particles comprising an appropriate internal control nucleic acid; (iii) inducing the release of the nucleic acid to be analyzed from within the sample and the release of the internal control nucleic acid from within the non-viable particles (interpreted as a first protecting vehicle and a second protecting vehicle comprising exogenous and endogenous nucleic acids); and (iv) analyzing the released nucleic acids (performing the NAT), such that in step (i) the sample to be analyzed can be any sample on which it is desired to carry out a qualitative or quantitative nucleic acid-based assay (interpreted as a quality control composition), wherein said samples can thus be derived from in vitro sources (such as cultured cells, bacteria or viral particles) or in vivo sources (such as samples derived from human, plant or animal sources) (interpreted as eukaryotic cells as protecting vehicles) or synthesized in the case of samples containing non-naturally occurring target entities, such that other samples might be those that are tested for detection of food pathogens, wherein samples include blood, serum, plasma, saliva, feces, urine, milk and organ, tissue or cellular extracts or secretions, e.g. mucosa! secretions etc. as evidenced by Berg (US20110065092; of record; Abstract; paragraphs [0003]; [0006]; and [0064]-[[0070]). Moreover, methods of detecting, quantifying, and identifying known or novel pathogens including influenza, hepatitis A, hepatitis B, Dengue, pneumonia using nucleic acid biochips including ViroChip, FluChip, BloodChip, and/or TickChip on commercially available platforms comprising a pan-viral microarray with 60,000 70-nt commercial probes which can tolerate several mismatches, which can be used for the discovery of viruses such as SARs coronavirus, Human cardioviruses and Avian bornaviruses in combination with next-generation sequencing on commercially available platforms such as Ion Torrent, Roche GS454 Jr., Pacific Biosciences, and Illumina MiSeq using barcoded primers, wherein the FluChip can detect exogenous viruses in humans including H1N1 and H2N2 subject present a variety of symptoms such as diarrhea, headache, sore throat, fever, chills, and cough are known in the art as evidenced by Chiu (Presentation, IPFA/PEI International Workshop, Budapest, Hungary, 2012, 1-43; of record; pgs. 1-10, 26 and 39); and it is known that exogenous viruses including cancer-associated viruses can be found to infect humans and animals as evidenced by Delwart (PLoS Pathogens, 2013, 9(2), 1-4; of record; Abstract; and pg. 3, col 2); and endogenous retroviruses (ERVs) have contributed to more than 8% of the human genome, wherein viral RNA is permanently integrated into the nuclear DNA of the host cell as a provirus are known in the art as evidenced by Wildschutte (PNAS, 2016, 1-9; Abstract; of record; and pg. 1, col 1, first full paragraph), wherein integration of a DNA copy of the viral genome into a host cell chromosome is an essential step in the retroviral replication cycle as evidenced by Craigie (Cold Springs Harbor Perspectives in Medicine, 2012, 1-18; of record; pg. 1, col 1). Additionally, naturally occurring recombinant enterovirus expressing a torovirus deubiquitinase is known in the art, wherein EVs
are implicated in a wide range of diseases in humans and animals, wherein a novel enterovirus (enterovirus species G [EVG]) (EVG 08/NC_USA/2015) was isolated from a diagnostic sample from a neonatal pig diarrhea case as evidenced by Shang (Journal of Virology, Abstract); and genetic recombination is known to occur frequently and in many different cell types as evidenced by Clancy (Nature Education, 2008, 1-6; Abstract). Furthermore, performing spiked-in metagenomic experiments are known in the art including experiments comprising Neisseria meningitidis, S. agalactiae, and C. albicans obtained from the American Type Culture Collection that was subcultured and used with synthetic CSF; as well as, Mycobacterium fortuitum and Mycobacterium abscessus isolates derived from infected patients; and validation of metagenomic next-generation sequencing tests for pathogen detection is known in the art, wherein biological specimens can be analyzed for pathogens in human cells including three patient respiratory specimens positive for representative pathogens tested in triplicate from nucleic acid extraction, such that result were compared qualitatively; and that analytic sensitivity can be determined for a given pathogen (strain) at a given sequencing depth and (1) average specimen, (2) a representative control specimen, or (3) an individual specimen for which sufficient amounts of residual volumes are available as evidenced by Schlaberg (Arch Pathol Lab Med, 2017, 141, 776-786; of record; pg. 778, col 2, last partial paragraph; pg. 779, col 1, first partial paragraph; pg. 779, col 2, last partial paragraph; pg. 780, col 1, first partial paragraph; and Example 1; and pg. 780, col 2, Example 1). Moreover, high throughput testing of biological samples that may or may not comprise microorganisms, and methods including the use of diagnostic multiplexing panel (DMP) specifically designed for simultaneous identification of a plurality of potential microorganisms that can be present in the biological sample via a primer extension reaction directed at highly conserved nucleic acid sequences in the microorganism is under test, wherein the biological sample is immobilized on a solid substrate at a first location before being transferred to a second location for analysis using the DMP for the diagnosis of infection pathogens; the method comprising immobilizing the biological sample; transferring the immobilized biological sample to a second location; performing a nucleic acid amplification step on microorganism DNA; combining target sequences with primer sequences including primers on a microarray; (e) performing a primer extension reaction; and analyzing the reaction product for target sequences including by mass spectrometry, DNA microarray, incorporation of fluorescently labeled nucleotides; as well as, infectious diseases including MRSA, SARS, avian fluid, HIV, malaria and other pathogens that cause death world-wide; as well as, viral, bacterial, fungal and protozoan microorganisms that are pathogenic to an animal host as evidenced by Semikhodskii (US20160108467, published April 21, 2016; of record; Abstract; and paragraphs [0003]; [0011]-[0017]; [0023]; [0035]; and [0036]); and compositions and methods for the simultaneous multiplex detection of biomarkers in an environmental, non-biological or biological sample including multiple pathogens such as viruses, bacteria, fungi, protozoa and helminths present in a sample; and that test options for the presence of a microorganism including in a human host is shown in Figure 1A including antibody-bead capture, DNA-bead capture, PCR, immunoassay, DNA probe amplification, colony counting, and restriction digest mapping, wherein Figure 2 depicts the design of the PathoChip for metagenome 60 nt probes are selected for all viruses and selected human pathogenic microorganisms; and that cancer is associated with papillomavirus, hepatitis B or C, Epstein-Barr virus, human herpesvirus 8, and T-cell leukemia virus type 1), and one bacterium (Helicobacter pylori); as well as, nucleic acid amplification was known in the art as evidenced by Robertson et al. (US10883145, issued January 5, 2021; of record; effective filing date April 10, 2015; Abstract; col 1; and col 8, lines 28-43; and Figures 1A and 2A-B). Step IIB: [NO].
In sum, when the relevant factors are analyzed, the claims as a whole do NOT recite additional elements that amount to significantly more than the judicial exception itself. Accordingly, claims 109 DOES NOT qualify as eligible subject matter.
Dependent claim(s) 110, 116, 142-144, 148, 149 and 155 when analyzed as a whole are held to be patent ineligible under 35 U.S.C. 101 because they do not add anything that makes the natural product in claim 109 significantly different. For example, claim 116 encompasses the method of claim 109, wherein the quality control composition further comprises an additional first protected nucleic acid sequence, but it does not add anything that makes the natural product in claim 109 significantly different.
Thus, the claims as a whole do NOT recite additional elements that amount to significantly more than the judicial exception itself.
In light of the above consideration and the new guidance, claims 109, 110, 116, 142-144, 148, 149 and 155 are non-statutory. This rejection is newly recited as necessitated by the new Guidance set forth in the Memorandum of July 30, 2015 updating the June 25, 2014 guidance (see June 25, 2014 memorandum from Deputy Commissioner for Patent Examination Policy Andrew Hirshfeld titled Preliminary Examination Instructions in view of the Supreme Court Decision in Alice Corporation Pty. Ltd. v. CLS Bank International, et al. (Alice Corp. Preliminary Examination Instructions) and the Revised Patent Subject Matter Eligibility Guidance (See, Federal Register, vol. 84, No. 4, January 7, 2019).
Response to Arguments
Applicant’s arguments filed August 20, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) Applicant submits that the claims are not directed to natural products, or non-natural products that are not markedly different than their function in nature because the composition comprises two or more protecting vehicles, wherein at least one vehicle is a recombinant or otherwise engineered vehicle into which an exogenous nucleic acid sequence, not natively present in that vehicle, has been introduced (pg. 15 through pg. 16, first full paragraph); (b) the composition possesses markedly different structural characteristics from any natural material: it is an assembly of separately produced vehicles, at least one of them a recombinant construct not found as such in nature (Applicant Remarks, pg. 16, last full paragraph); (c) the amended composition requires a separate engineered assembly of protecting vehicles, at least one of which is by the man-made introduction of an exogenous sequence, such as a manufactured control for methicillin-resistant S. aureus (Applicant Remarks, pg. 17 first and second full paragraphs); (d) the claim recites more than the judicial exception, wherein the unmodified natural component is not performing its natural role; it is a separately produced marker-source within an engineered control reagent the combination of protecting vehicles possesses a utility that none of its components possesses individually and that no natural product possesses: and permits a laboratory to validate a man-made assay for a target, e.g., a dangerous or infections target, without handling that target (Applicant Remarks, pg. 17, last partial paragraph); and (e) the claims are still patent eligible as having a practical application of the judicial exception contrary to the Examiner's assertion (Applicant Remarks, pg. 18, first full paragraph).
Regarding (a) and (b), Applicant’s assertion that the composition comprises two or more protecting vehicles, wherein at least one vehicle is a recombinant or otherwise engineered vehicle into which an exogenous nucleic acid sequence, not natively present in that vehicle, wherein at least the recombinant construct is not found in nature, has been introduced, is not found persuasive. As an initial matter, please see the 35 USC 112(b) rejection regarding the term “a recombinant or otherwise engineered vehicle” including that the as-filed Specification does not teach an engineer vehicle or an engineered protecting vehicle. Additionally, the instant rejection includes both naturally occurring and/or non-naturally occurring nucleic acid sequences and/or protecting vehicles which do not possess markedly different characteristics such as different biological or pharmacological functions or activities, chemical or physical properties and/or structure/function and form as naturally occurring and/or non-naturally occurring organisms and/or nucleic acid sequences. Moreover, it is known that there are naturally occurring recombinant viruses including an enterovirus that expresses a torovirus deubiquitinase as evidenced by Shang; and naturally occurring recombination in bacteria is known in the art, wherein bacteria take up foreign DNA molecules and stably integrate them into the host genome as independent plasmids as evidenced by Abcam (pg. 1, first full paragraph).
It is noted that the instant claims are very broadly recited, such that they clearly encompass any nucleic acid sequences that are characteristic of an organism and/or any protecting vehicles, where protecting vehicles are defined as any enclosing or associating substance or barrier, including but not limited to: a bacterium, eukaryotic cell, protein capsid or shell, microcompartments, virus, a virus-like particle, liposome, an anucleated cell, a vesicle, an exosome, a micelle, an armored RNA, or other suitable physical boundary (e.g., the body of a human, a mammal, etc.). Humans can undergo natural genetic rearrangement and recombination, such that a patient can comprise a mixed population of normal cells and cells that have undergone recombination with retroviral sequences. Thus, the claims remain rejected.
Regarding (c), Applicant’s assertion that the amended composition requires a separate engineered assembly of protecting vehicles, at least one of which is by the man-made introduction of an exogenous sequence, such as a manufactured control for methicillin-resistant S. aureus, is not found persuasive. Please see the discussion supra regarding the 35 USC 112(b) rejection. The as-filed Specification does not teach “a recombinant or otherwise engineered protecting vehicle;” and the instant claims do not recite how the vehicle is engineered e.g., (by nature, in the laboratory, horizontal gene transfer, natural vectors, biotechnologically modifying organisms, etc.). Instead, the as-filed Specification teaches:
Recombinant nucleic acids, recombinant plasmids, recombinant viral vectors, recombinant or natural viruses, and recombinant bacterium.
Engineered fluids, engineered protein shells, engineered mecA gene, engineered viral vector, and a liposome engineered to contain a mecA gene.
Separate definitions for an “organism”, a “whole organism”, a “vehicle” and a “protecting vehicle”. The definitions for a “vehicle” and a “protecting vehicle” do not include a recombinant vehicle, a recombinant protecting vehicle, an engineered vehicle and/or an engineered protecting vehicle (except for, engineered protein shells).
Instant claim 109 does not recite what Applicant asserts, e.g., “an engineered assembly of protecting vehicles, at least one of which is by the man-made introduction of an exogenous sequence.” Instead,
instant claim 109 recites:
“wherein the at least one second protecting vehicle is a recombinant or otherwise engineered vehicle into which the exogenous second nucleic acid sequence has been introduced”
As noted supra, recombination and/or engineering can occur naturally. Additionally, the rejection allows for naturally occurring and non-naturally occurring nucleic acid sequences and/or protecting vehicles which do not possess markedly different characteristics such as different biological or pharmacological functions or activities, chemical or physical properties and/or structure/function and form as naturally occurring and/or non-naturally occurring organisms and/or nucleic acid sequences. Thus, the claims remain rejected.
Regarding (d), Applicant’s assertion that the unmodified natural component is not performing its natural role; it is a separately produced marker-source within an engineered control reagent the combination of protecting vehicles possesses a utility that none of its components possesses individually and that no natural product possesses: and the QC composition permits a laboratory to validate a man-made assay for a target, e.g., a dangerous or infections target, without handling that target, is not found persuasive. It is noted that the instant claims are directed to a composition, and not to a method of using the composition, such as in an assay. Contrary to Applicant’s assertion of the composition possessing a utility, the composition recited in claim 109 does not comprise a marker-source, an engineered control agent, a nucleic acid test, a laboratory, a man-made assay, a target including a dangerous target or an infections target, and/or the steps of performing, validating, handling, etc. The composition recited in claim 109 simply comprises at least two protecting vehicles (as recited), wherein each comprises a nucleic acid characteristic of an organism. The claims as a whole do not recite anything that amounts to significantly more than the judicial exception. Thus, the claims remain rejected.
Regarding (e), Applicant’s assertion that the claims are still patent eligible as having a practical application of the judicial exception, is not found persuasive. Applicant has not identified the practical application asserted to be recited in the instant claims. One of ordinary skill in the art before the effective filing date of the claimed invention could not make and use the quality control composition based on the limitations as recited in the instant claims. The claims do not recite a NAT, identify a specific type of NAT (e.g., PCR, RT-PCR, LAMP, TMA, etc.), the organisms that can be detected, a specific test article (e.g., a urine sample, H1N1 virus, Staphylococcus aureus, food, river water, soil, etc.), a specific first protecting vehicle, a specific nucleic acid sequence that is characteristic of a particular organism, the sequences characteristic of an organism, a specific second protecting vehicle, the identity of a specific recombinant protecting vehicle, the identity of a specific engineered protecting vehicle, specific exogenous second nucleic acid sequence, the identity of a specific enclosing substance and/ specific enclosing barrier (e.g., a protein coat, human body, liposome, cell, a house, etc.).
The very broadly recited claims, when read in light of the as-filed Specification, are difficult to interpret due to the variety of overlapping definitions. For example, a “sample” (or test sample) refers to a sample to be tested, but it can also refer to a “test article” (the terms can be used interchangeably). Additionally, the term “test article” refers to articles suspected of being in the sample (e.g., an organism), or it can be derived from a sample (paragraphs [00130]). The term “organism” refers to a cell or cells of a living being, including viruses, where consistent with the context, wherein an organism includes a eukaryote, eukaryotic cell, prokaryote, prokaryotic cell, bacterium, virus, fungus, fungal cell, archaeon, protist, or parasite (paragraph [00131]). A “vehicle” is any nucleic acid comprising entity or carrier that may encapsidate, encapsulate or comprise a nucleic acid including an organism (paragraph [00133]; however, the term “protecting vehicle” refers to any enclosing or associating substance or barrier (encompassing an organism?) (paragraph [00134]). Thus, a single “organism” can be a sample, a test article, a vehicle, a protecting vehicle, etc. The instant claims do not recite or provide any practical application of the judicial exception. One of ordinary skill in the art has no idea as to the structure of the composition, and/or what structure is useful as a quality control composition to assess the functionality of a NAT to detect an organism in a test article. The claims amount to nothing more than naturally occurring and/or non-naturally occurring protecting vehicles and nucleic acid sequences, wherein the composition as recited is well known, purely conventional or routine in the art. Thus, the claims remain rejected.
New Objections/Rejections
Specification Objection
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (See; paragraph [0007]). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code. See MPEP § 608.01.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 110, 142-144 and 155 are rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 110 recites (in part): “at least one second protecting vehicle is selected from…an inactivated organism, a non-viable or non-pathogenic organism” in lines 2-5 because “vehicles” are defined in the as-filed Specification to include organisms, but “protecting vehicles” are not defined to include organisms (See; paragraphs [0133]-[0134]), such that claim 110 depends from claim 109, wherein claim 109 recites the presence of an “otherwise engineered vehicle.” Thus, claim 110 is an improper dependent claims for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 142 recites (in part): “wherein neither the at least one first protecting vehicle…is the same as the organism to be detected in the test article” in lines 1-3 because the as-filed Specification teaches that a “vehicle” can be an organism, but a “protecting vehicle” is not an organism (See; paragraphs [0133]-[0134]). Additionally, claim 142 depends from claim 109, wherein claim 109 does not recite detecting the presence of an organism, a plurality of organisms, a test article; and/or a vehicle. Thus, claim 142 is an improper dependent claims for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 143 recites (in part): “wherein the organism that is detected by the NAT is a pathogenic organism…is non-pathogenic” in lines 1-3 because claim 143 depends from claim 109, wherein claim 109 recites the term “to detect an organism in a test article” in the preamble of claim 109, such that the body of claim 109 does not recite detecting an organism, or the use of any organism in the quality control composition. Thus, claim 143 is an improper dependent claims for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 144 recites (in part): “wherein two or more of the at least one first protected nucleic acid…genome native to the organism detected by the NAT” in lines 1-4 because claim 144 depends from claim 109, wherein claim 109 recites the term “a NAT to detect an organism in a test article” in the preamble of claim 109, such that the term is not given patentable weight. Moreover, instant claim 109 does not recite detecting an organism, detecting anything by a NAT, or the use of any organism in the quality control composition. Thus, claim 144 is an improper dependent claims for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 155 recites (in part): “further comprising a medium…of a test article to be assessed by the NAT” in lines 1-3 because claim 155 depends from instant claim 109, wherein claim 109 recites the term “test article” only in the preamble of claim 109, such that the term has not been given patentable weight. Moreover, instant claim 109 does not recite that the test article is assessed by the NAT. Thus, claim 155 is an improper dependent claims for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 109, 110, 116, 142-144, 148 and 155 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Antionette van der Kuyl (hereinafter “van der Kuyl”) (Retrovirology, 2012, 9(6), 1-10).
Regarding claims 109, 142, 143 and 144, van der Kuyl teaches that human ERVs (HERVs) belong to the beta-, gamma-, or spuma-retrovirus groups, such that endogenous delta- and lenti- viruses are notably absent in humans, although endogenous lentivirus genomes have been found in lower primates, wherein exogenous retroviruses that currently form a health threat to humans intriguingly belong to those absent groups, wherein the best studied of the two infectious human retroviruses is the lentivirus human immunodeficiency virus (HIV) which has an overwhelming influence on its host by infecting cells of the immune system, such that one HIV-induced change is the induction of HERV transcription, often leading to induced HERV protein expression (interpreting humans or human cells as a first protecting vehicle/enclosing barrier comprising a first protected nucleic acid that is characteristic of the organism; and interpreting human cells that comprise the HIV, the retrovirus or the capsid as a second vehicle comprising a second nucleic acid sequence that is exogenous, not natively present in humans; is recombinant when introduced; naturally engineered; the virus is pathogenic but nucleic acids are non-pathogenic, claims 109, 142 and 143) (Abstract, lines 3-10). van der Kuyl teaches that around 8% of the human genome is of retroviral origin (interpreted as comprising 0.5-100% of a genome native to the organism, claim 144) (pg. 1, col 2, last partial paragraph, lines 1-2). van der Kuyl teaches that retrovirus particles contain, apart from two copies of the viral RNA genome, spliced viral RNA’s, several tRNAs, and varying amounts of cellular mRNAs that are co-packaged in a concentration dependent manner, such that some of the cellular RNAs, such as those coding for ribosomal proteins, are preferentially packaged in HIV virions (also interpreting HIV virion capsid to be second protecting vehicle; comprising exogenous nucleic acids; an enclosing barrier; a recombinant vehicle and a naturally engineered vehicle; pathogenic and non-pathogenic, claims 109, 142 and 143) (pg. 4, col 1, first full paragraph, lines 1-7). van der Kuyl teaches that in vitro HIV-1 infection of either CD4 expressing T-cell lines or stimulated peripheral blood mononuclear cells (PBMC’s) upregulates the production of HERV-K RNA and proteins compared to non-infected cells; and analysis of blood plasma samples from HIV-1 infected patients also showed a significant increase of HERV-K RNA expression, with titers as high as 106-1010 copies/ml, such that in >95% of samples HERV-K pol RNA was found compared to only 5-8% of the control samples, which included hepatitis C virus (HCV) infected patients and healthy individuals (interpreted as healthy individuals and patients; and from 0.5-100% of viral genome, claims 109 and 144) (pg. 4, col 1, last partial paragraph; and col 2, first partial paragraph, lines 1-3). van der Kuyl teaches that HERV-K recombinant genomes were detected in blood plasma from some HIV-1 infected patients but not in breast cancer patients (interpreted as detecting an organism in a patient; and interpreting protecting vehicles including cells, retroviral particles, capsid, etc. as allowing for extraction; and protects against loss and degradation, claim 109) (pg. 4, col 2, first partial paragraph, lines 24-27). van der Kuyl teaches that infection of humans with the retrovirus HIV-1 has profound effects upon the resident, endogenous retro viruses, wherein transcripts and proteins representing diverse classes of endogenous retroviruses are upregulated (pg. 8, col 1, last full paragraph, lines 1-4).
Regarding claims 110 and 155, van der Kuyl teaches human blood and/or PMBCs, and patients infected with the retrovirus HIV-1 and HIV-2 (interpreted as eukaryotic cells in healthy individuals and HIV infected individuals; virus; and interpreting blood as a medium, claims 110 and 155) (pg. 2, Figure 1; and pg. 4, col 1, last partial paragraph; and col 2, first partial paragraph).
Regarding claims 116 and 148, van der Kuyl teaches other endogenous viruses and exogenous viruses including HIV-1, HIV-2, HTLV-1, HFLV-2, HERV-K, HERV-F, H, I, E,R,W; HERV-L, and SFV; and that in vitro HIV-1 infection of either CD4 expressing T-cell lines or stimulated peripheral blood mononuclear cells (PBMC’s) upregulates the production of HERV-K RNA and proteins compared to non-infected cells; and analysis of blood plasma samples from HIV-1 infected patients also showed a significant increase of HERV-K RNA expression, with titers as high as 106-1010 copies/ml, such that in >95% of samples HERV-K pol RNA was found compared to only 5-8% of the control samples, which included hepatitis C virus (HCV) infected patients and healthy individuals (interpreting cells comprising HERV-K and hepatitis C virus as a third protected nucleic acid characteristic of an organism; and in separate protecting vehicles; and encodes a virus gene; and interpreting blood as a medium, claims 116, 148 and 155) (pg. 2, Figure 1; and pg. 4, col 1, last partial paragraph; and col 2, first partial paragraph, lines 1-3).
Regarding claim 149 (in part), van der Kuyl teaches that vertebrate genomes contain substantial amounts of retroviral sequences in various states of inactivation since their integration (interpreted as inactivated organism, claim 149) (pg. 1, col 1, first partial paragraph, lines 6-8).
van der Kuyl does not specifically exemplify that an organism is inactivated via aldehydes, heat, UV, etc. (claim 149, in part).
van der Kuyl meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and
103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for
the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 109, 110, 116, 142-144, 148, 149 and 155 are rejected under 35 U.S.C. 103 as being unpatentable over Antionette van der Kuyl (hereinafter “van der Kuyl”) (Retrovirology, 2012, 9(6), 1-10) in view of Schmid et. al. (hereinafter “Schmid”) (Communications in Clinical Cytometry, 1999, 38, 195-200).
The teachings of van der Kuyl as applied to claims 109, 110, 116, 142-144, 148 and 155 are described supra.
van der Kuyl does not specifically exemplify that an organism is inactivated via aldehydes, heat, UV, etc. (claim 149, in part).
Regarding claim 149 (in part), Schmid teaches that flow cytometers are utilized frequently in research and clinical laboratories to analyze HIV-infected samples, wherein previous reports about the hazards associated with the use of flow cytometers have focused on cell sorting because flow sorters generate droplets and aerosols during their normal operation and thus can expose operators to toxins or to pathogens contained in the samples to be sorted, such that the Biohazards Working Group of the International Society for Analytical Cytology (ISAC) has generated biosafety guidelines for cell sorting of unfixed, viable cells (pg. 195, col 1, last full paragraph). Schmid teaches that cultures of peripheral blood mononuclear cells obtained from HIV-infected patients can contain infectious virus at concentrations that can exceed HIV concentrations found in peripheral blood, wherein laboratory-adapted strains of HIV, e.g., HTLV-III, LAV, are present in in vitro infected cell cultures; and samples for flow cytometric analysis can also consist of genetically manipulated cells which contain genomic sequences of HIV (pg. 195, col 2, last full paragraph, lines 6-13). Schmid teaches the inactivation of HIV in the laboratory including HIV cells and cell-free HIV including by formaldehyde inactivation, with heat at 37oC, with disinfectant exposure including commercial chlorine, ethyl alcohol, and isopropyl alcohol exposure; and UV inactivation (interpreted as inactivating the organism, claim 149) (pg.197, col 1, first through third full paragraphs). Schmid teaches that biosafety containment includes spill, disposal, in filters, ventilation, public areas, etc. (pg. 196, Table 1).
It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of inactivating HIV as exemplified by Schmid, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of monitoring HIV infections, or monitoring other viral infections such as HCV in patients as compared to healthy individuals as disclosed by van der Kuyl to include the methods of inactivating viruses and/or retroviruses such as HIV including through formaldehyde inactivation, with heat, with disinfectant exposure including commercial chlorine, and/or by UV inactivation as taught by Schmid with a reasonable expectation of success in rendering retrovirus particles safe for biosafety, biosafety containment and/or for disposal.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly
rejected under 35 USC §103(a) as obvious over the art.
Conclusion
Claims 109, 110, 116, 142-144, 148, 149 and 155 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMY M BUNKER whose telephone number is (313) 446-4833. The examiner can normally
be reached on Monday-Friday (6am-2:30pm).
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
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