DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims Status
Claims 1-4, 7-16, and 21-26 are pending and under examination on the merits.
Election/Restrictions
Applicant’s election of the required species, (a) IFI6, (b) GBP5, (c), a SARS-CoV-2 Nucleocapsid (N) gene in the reply filed on 7/7/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 1-4, 7-16, and 21-26 are pending and under examination on the merits.
Information Disclosure Statement
The Information Disclosure Statement (IDS) submitted on 1/1/2024 is in compliance with 37 CFR 1.97. Accordingly, the references listed in the IDS are being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Interpretation
The specification (para. [0074]) indicates that “classification” refers to any number(s) or characters that are associated with a particular property of a subject.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on pp. 13, 40, 49, and 50. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http://, www., or other browser-executable code. See MPEP § 608.01.
The disclosure is objected to because of the following informalities: the specification refers to the drawings having color features (para. [0035]), but no petition for use of colored drawings has been granted. The application contains black and white drawings, so the specification should be corrected to not refer to color features.
Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4, 7-16, 21-23, and 25-26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claims recite determining whether a human subject is infected with SARS-CoV-2 (or diagnosing COVID-19 in a human subject) based on differences in gene expression levels. The courts have identified the following concepts and products as examples of laws of nature or natural phenomena:
iii. a correlation between variations in non-coding regions of DNA and allele presence in coding regions of DNA, Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1375, 118 USPQ2d 1541, 1545 (Fed. Cir. 2016);
iv. a correlation that is the consequence of how a certain compound is metabolized by the body, Mayo Collaborative Servs. v. Prometheus Labs., 566 U.S. 66, 75-77, 101 USPQ2d 1961, 1967-68 (2012);
v. a correlation between the presence of myeloperoxidase in a bodily sample (such as blood or plasma) and cardiovascular disease risk, Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1361, 123 USPQ2d 1081, 1087 (Fed. Cir. 2017). See MPEP 2106.04(b)(I).
Accordingly, the claims’ correlation of gene expression with SARS-CoV-2 infection or COVID-19 is clearly directed to a natural phenomenon.
This judicial exception is not integrated into a practical application because the claims breadth would monopolize correlating the expression of particular genes (such as IFI6 and GBP5) with SARS-CoV-2 infection or COVID-19. Because abstract ideas, laws of nature, and natural phenomenon "are the basic tools of scientific and technological work", the Supreme Court has expressed concern that monopolizing these tools by granting patent rights may impede innovation rather than promote it. See Alice Corp., 573 U.S. at 216, 110 USPQ2d at 1980; Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 71, 101 USPQ2d 1961, 1965 (2012). MPEP §2106(I). A claim having broad applicability across many fields of endeavor may not provide meaningful limitations that integrate a judicial exception into a practical application or amount to significantly more. For instance, a claim that generically recites an effect of the judicial exception or claims every mode of accomplishing that effect, amounts to a claim that is merely adding the words "apply it" to the judicial exception. See Internet Patents Corporation v. Active Network, Inc., 790 F.3d 1343, 1348, 115 USPQ2d 1414, 1418 (Fed. Cir. 2015) (The recitation of maintaining the state of data in an online form without restriction on how the state is maintained and with no description of the mechanism for maintaining the state describes "the effect or result dissociated from any method by which maintaining the state is accomplished" and does not provide a meaningful limitation because it merely states that the abstract idea should be applied to achieve a desired result). See also O’Reilly v. Morse, 56 U.S. 62 (1854) (finding ineligible a claim for "the use of electromagnetism for transmitting signals at a distance"); The Telephone Cases, 126 U.S. 1, 209 (1888) (finding a method of "transmitting vocal or other sound telegraphically ... by causing electrical undulations, similar in form to the vibrations of the air accompanying the said vocal or other sounds," to be ineligible, because it "monopolize[d] a natural force" and "the right to avail of that law by any means whatever."). MPEP §2106.05(f). Even if the claims were strictly limited to measuring transcript levels, the claims would still represent a monopoly, because RNA levels may not necessarily correlate with protein levels, for example. Until the claims are limited to use of particular probes or methodologies to do the measuring, they represent a monopoly and the judicial exception is not integrated into a practical application. Notably, claim 22 requires particular methodologies for measuring the gene expression levels, but is so broad such that it encompasses every way of measuring transcript levels, so it also does not integrate the judicial exception into a practical application.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because measuring gene expression is well-understood, routine, and conventional activity in the life science arts. Along those lines, the courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity:
i. Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
ii. Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015). See MPEP § 2106.05(d).
The examiner wishes to note that approaches to overcome this rejection include (i) amending the claims to be limited to a particular methodology of measuring gene expression (e.g., specific probe sequences or approaches to detection), or (ii) requiring a treatment step, as long as there is written support for those amendments in the disclosure.
Claim Rejections - 35 USC § 112 - Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-4, 7-16, and 21-26 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
MPEP 2173.05(s) states:
Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience." Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993; citations omitted).
Reference characters corresponding to elements recited in the detailed description and the drawings may be used in conjunction with the recitation of the same element or group of elements in the claims. Generally, the presence or absence of such reference characters does not affect the scope of a claim. See MPEP § 608.01(m) for information pertaining to the treatment of reference characters in a claim. Presently, the claimed information of Tables 12A, 12B, 12C, 13A, 13B, or 13C (as recited in claims 1, 13-16, 25, and 26) do not meet the requirements of “exceptional circumstances where there is no practical way to define the invention in words.” Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993; citations omitted).
Claims 2-4, 7-12, 14, 16 and 21-26 are also rejected since they depend on claims 1, 13, or 15, but do not remedy this deficiency.
Claims 13-16 and 23-24 require a “known COVID-19 classification”. However, the specification does not define “known COVID-19 classification.” The specification (para. [0074]) indicates that “classification” refers to any number(s) or characters that are associated with a particular property of a subject. However, when applying the broadest reasonable interpretation to the term “COVID 19 classification”, there are multiple reasonable interpretations, either (i) classification of the subject as having COVID 19, or (ii) the taxonomy of SARS-CoV-2 virus with which the subject is infected. Along those lines, claims 23 and 24 require “a cutoff value that discriminates between different COVID-19 classifications” (lines 2-3). Since the term “COVID 19 classification” is indefinite, “a cutoff value that differentiates between different COVID-19 classifications” is also indefinite.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Scope of Enablement
Claims 1-4, 7-16, and 21-26 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for methods of determining whether or not a human subject is infected with SARS-CoV-2, or diagnosing COVID-19 disease in a human subject, for biological samples from tissues known to exhibit expression changes of a first or first and second gene, in which the presence of SARS-CoV-2 is confirmed by detection of SARS-CoV-2 viral RNA, wherein differences in the first or first and second gene expression levels are the same as a positive control, or higher than a negative, does not reasonably provide enablement for similar methods using any biological sample that includes RNA from cells, without proper directionality of a positive and/or negative control, or wherein SARS-CoV-2 RNA is not also detected. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
The breadth of the claims is found in claims 1, 13, and 15.
The nature of the invention is a method of determining whether or not a human subject is infected with SARS-CoV-2, the method comprising (a) receiving biological sample collected from the human subject, the biological sample including human RNA from cells of the subject; (b) measuring, in the biological sample, (i) a first gene expression level of a first human gene IFI6; ii) a second gene expression level of a second human gene GBP5; (c) detecting differences, if any, in the first gene expression level and the second gene expression level relative to reference expression levels characteristic of another human subject who is not infected with SARS-CoV-2; and (d) determining whether the human subject is infected with SARS-CoV-2 based on the differences, if any, determined in (c). The claims also encompass embodiments where only one human gene expression level is determined, and also where the method further detects SARS-CoV-2 viral RNA.
The level of skill of one skilled in this art is high.
The specification teaches that IFI6 and GBP5 transcript levels are increased in oropharyngeal or nasopharyngeal swabs from a cohort of patients having COVID-19 (para. [0079]). However, the specification does not measure expression of these genes in other tissues.
The state of the prior art is shows that IFI6 and GBP5 are induced by additional viruses to SARS-CoV-2. Sajid, et al. (Front Immunol. 2021 Apr 1;12:634937. PMID: 33868257) teaches that upon viral infection, type I interferon is induced, which activates a signaling pathway, leading to induction of about 300 IFN-stimulated genes in the host, and IFI 6 is an IFN-stimulated gene (p. 2, col. 1, paras. 3-4). As shown by Feng, et al. (J Innate Immun. 2017;9(4):419-435, Epub 2017 Apr 5. PMID: 28376501), GBP5 transcript levels are elevated in throat swabs of patients infected with influenza A virus (IAV; p. 422, col. 2, paras. 1-3; Fig. 1).
Biomarkers for a disease must be experimentally shown to function in the context of the samples in which they are used (e.g., urine). Micallef (US9222937, priority to 09/01/2011) teaches that a variety of non-cancer causes raise circulating nucleosome level, and in some cancers, their level varies greatly, encompassing levels of healthy patients (Column 2, last para.). Therefore, circulating nucleosome level cannot be used predictably to prognose any condition barring experimental validation. In short, no one of ordinary skill in this art assumes any protein, nucleotide, or metabolite is a functional biomarker. They need experimental support for use as a biomarker in the specific tissue that is analyzed. In this case, there is insufficient data to show that IFI6 or GBP5 are generic biomarkers for any and all tissues in diagnosing SARS-CoV-2 or COVID-19. To further highlight the unpredictability of the art, increased IFI6 and/or GBP5 transcript levels are associated with infection of viruses other than SARS-CoV-2, so it is not predictable that differences in their expression levels would enable determining whether or not a human subject is infected with SARS-CoV-2 or has COVID-19.
The specification only relates to data generated from oropharyngeal or nasopharyngeal swabs from a cohort of patients having COVID-19, other viral, or non-viral acute respiratory illnesses (para. [0079]), but the claims encompass any sample type that includes human RNA from cells of a human subject. The specification does not enable use of any human tissue source, because it is not clear that the first and second gene expression levels would be affected by SARS-CoV-2 infection, particularly if the tissues are distant from the site of SARS-CoV-2 infection in the subject. Additionally, because IFI6 and GBP5 are increased due to infection with other viruses, their induction alone is not sufficient to diagnose SARS-CoV-2 specifically, as their induction could be due to other viruses. Regarding the control, the breadth of the claims allow for any directionality of changes, however the disclosure makes clear that you only see increases in expression of IFI6 and GBP5 levels due to SARS-CoV-2 infection, and so to be enabled, the method must reflect the necessary increase in their expression relative to an uninfected sample.
Thus, the state of the art recognized that it would be highly unpredictable that IFI6 and/or GPB5 could be used to determine whether a human subject is infected with SARS-CoV-2 or diagnose COVID-19 in the subject. One of skill in the art would neither expect nor predict the appropriate functioning of the method as broadly as currently claimed. Specifically, there is insufficient support for the method working for specifically SARS-CoV-2 rather than additional viruses, without adequate controls, or in any sample source (e.g., tissue).
In view of the lack of the predictability of the art to which the invention pertains as evidenced by Sajid, Feng, and Micallef, the lack of guidance and direction provided by applicants, and the absence of working examples, undue experimentation would be required to use the claimed method as claimed for determining whether or not a human subject is infected with SARS-CoV-2 or diagnosing COVID-19, with a reasonable expectation of success, absent a specific and detailed description in applicant’s specification of how to effectively practice this and absent working examples providing evidence which is reasonably predictive that the claimed methods are functional, commensurate in scope with the claimed invention.
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 (i.e., changing from AIA to pre-AIA ) 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.
Claims 13, 15, 23, and 24 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Mick, et al. (medRxiv [Preprint]. 2020 May 19:2020.05.18.20105171. doi: 10.1101/2020.05.18.20105171, on IDS).
The Prior Art
Mick teaches development of an accurate, clinically practical, COVID-19 diagnostic classifier, based on the host transcriptional response to SARS-CoV-2 infection that may help overcome the limitations of direct detection of viral nucleic acid (p. 6, para. 3).
Mick utilized nasopharyngeal or pooled nasopharyngeal + oropharyngeal swabs for its methods (Table S1). Mick utilized metagenomic next generation RNA sequencing (mNGS) to evaluate host gene expression and detect the presence of viruses (p. 9, last para.). Mick teaches performance of pairwise differential expression analyses between three patient groups (i. tested positive for SARS-CoV-2 by PCR, ii. Negative for SARS-CoV-2 but had other pathogenic respiratory viruses, and iii. No virus detected but acute respiratory illness; pp. 2-3, bridging para.). Mick further teaches that a host-based diagnostic might have particular utility if it could increase the sensitivity of standard NP/OP swab PCR testing, which may return falsely negative in a significant proportion of patients (p. 6, para. 2), and that transcriptional profiling has been proven for diagnosis of other acute respiratory infections (p. 2, para. 2). Mick also teaches that the predicted probability of SARS-CoV-2 infection had little apparent relationship to the abundance of SARS-CoV-2, suggesting host gene expression has the potential to provide an orthogonal indication of COVID-19 status even when viral abundance is low (p. 6, para. 2).
Mick determined that a sparse 3-gene classifier (IL1B, IFI6, IL1R2) still achieved an AUC of 0.871 (p. 6, para. 1; Figure 2D, Tables S2 & S3). Mick also discloses a larger, 26-gene classifier that also includes IFI6 and differentiates COVID-19 from other acute respiratory illnesses (viral and non-viral; Fig. 2; p. 19, last para.). Mick’s classifiers were built through machine learning, using a combined lasso and random forest approach, with a nested cross-validation within the training set to select the lasso tuning parameter and for the initial input features, used gene counts with a variance-stabilizing transform derived from the training set only (p. 13, last para.). The classifiers were built using a gold standard of COVID-19 diagnosis based on SARS-CoV-2 PCR positivity (Id.). For the 26-count classifier, using a cut-off of 40% predicted out-of-fold probability for COVID-19 to call a patient positive, this translated into a sensitivity of 97% and a specificity of 96% for patients with non-viral ARIs and 83% for patients with other viral ARIs (Fig. 2B).
Mick’s sequencing revealed that IFI6 was among the most significant genes upregulated by SARS-CoV-2 (p. 3, para. 2). The express, implicit, and inherent disclosures of a prior art reference may be relied upon in the rejection of claims under 35 U.S.C. 102 or 103. "The inherent teaching of a prior art reference, a question of fact, arises both in the context of anticipation and obviousness." In re Napier, 55 F.3d 610, 613, 34 USPQ2d 1782, 1784 (Fed. Cir. 1995). See MPEP §2112. Because Mick states that IFI6 is upregulated, at the very least they are inherently comparing it between SARS-CoV-2-infected subjects with respiratory illness and non-infected controls. Accordingly, Mick discloses a method of diagnosing COVID-19 in a human subject, the method comprising: (a) receiving a biological sample obtained from the human subject, the biological sample including RNA of the human subject; (b) measuring, in the biological sample, a gene expression of IFI6; and (c) determining a classification of whether the human subject has COVID-19 using the first gene expression level and one or more reference gene expression levels determined from a plurality of reference samples having a known COVID-19 classification (claim 15).
Mick also teaches testing for COVID-19 carried out using PCR of NP swab or pooled NP + OP swab specimens using primers targeting either two regions of the SARS-CoV-2 N gene, or the E and RNA-dependent RNA polymerase genes, plus human RNAse P as a positive control (p. 9, para. 2). Additionally, Mick’s method utilizes a SARS-CoV-2 reference-based assembly pipeline that involved removing non-SARS-CoV-2 reads, aligning to the SARS-CoV-2 reference genome, and calculating SARS-CoV-2 reads per-million (rpM) using the number of reads that aligned (p. 10, para. 2). Mick performs robust regression of normalized gene counts against log10(rpM) of SARS-CoV-2 for all genes in the differentiate expression analysis of SARS-CoV-2 vs. no virus or SARS-CoV-2 vs. other virus (p. 12, last para.).
Accordingly, Mick discloses the additional elements of claim 13 (relative to claim 15 described above), of (b) measuring, in the biological sample, a viral expression level of a SARS-CoV-2 viral gene; and (c) determining a classification of whether the human subject has COVID-19 using the first gene expression level, the viral expression level, and one or more reference gene expression levels determined from a plurality of reference samples having a known COVID-19 classification.
Regarding claim 23, Mick anticipates the claim because its classification methods include comparing the first gene expression level to a cutoff value that discriminates between different COVID-19 classifications, and wherein the cutoff value is determined using one or more reference gene expression levels.
Regarding claim 24, Mick utilized a machine learning model that discriminates between different COVID-19 classifications to determine the classification of samples, wherein the model is trained using one or more reference gene expression levels and known COVID-19 classification of the plurality of reference samples.
Therefore, claims 13, 15, 23, and 24 are anticipated by Mick.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-4, 7-16, and 21-26 are rejected under 35 U.S.C. 103 as being unpatentable over Mick, et al. (medRxiv [Preprint]. 2020 May 19:2020.05.18.20105171. doi: 10.1101/2020.05.18.20105171) in view of Fang, et al. (Front Physiol. 2021 Jan 22;11:605792. PMID: 33551833, on IDS), Johansson, et al. (JAMA Netw Open. 2021 Jan 4;4(1):e2035057. doi: 10.1001/jamanetworkopen.2020.35057), and Hounkpe, et al. (Nucleic Acids Res. 2021 Jan 8;49(D1):D947-D955. PMID: 32663312, published online 7/14/2020).
The Prior Art
Mick teaches development of an accurate, clinically practical, COVID-19 diagnostic classifier, based on the host transcriptional response to SARS-CoV-2 infection that may help overcome the limitations of direct detection of viral nucleic acid (p. 6, para. 3).
Mick utilized nasopharyngeal or pooled nasopharyngeal + oropharyngeal swabs for its methods (Table S1). Mick utilized metagenomic next generation RNA sequencing (mNGS) to evaluate host gene expression and detect the presence of viruses (p. 9, last para.). Mick teaches performance of pairwise differential expression analyses between three patient groups (i. tested positive for SARS-CoV-2 by PCR, ii. Negative for SARS-CoV-2 but had other pathogenic respiratory viruses, and iii. No virus detected but acute respiratory illness; pp. 2-3, bridging para.). Mick further teaches that a host-based diagnostic might have particular utility if it could increase the sensitivity of standard NP/OP swab PCR testing, which may return falsely negative in a significant proportion of patients (p. 6, para. 2), and that transcriptional profiling has been proven for diagnosis of other acute respiratory infections (p. 2, para. 2). Mick also teaches that the predicted probability of SARS-CoV-2 infection had little apparent relationship to the abundance of SARS-CoV-2, suggesting host gene expression has the potential to provide an orthogonal indication of COVID-19 status even when viral abundance is low (p. 6, para. 2).
Mick determined that a sparse 3-gene classifier (IL1B, IFI6, IL1R2) still achieved an AUC of 0.871 (p. 6, para. 1; Figure 2D, Tables S2 & S3). Mick also discloses a larger, 26-gene classifier that also includes IFI6 and differentiates COVID-19 from other acute respiratory illnesses (viral and non-viral; Fig. 2; p. 19, last para.). Mick’s classifiers were built through machine learning, using a combined lasso and random forest approach, with a nested cross-validation within the training set to select the lasso tuning parameter and for the initial input features, used gene counts with a variance-stabilizing transform derived from the training set only (p. 13, last para.). The classifiers were built using a gold standard of COVID-19 diagnosis based on SARS-CoV-2 PCR positivity (Id.). For the 26-count classifier, using a cut-off of 40% predicted out-of-fold probability for COVID-19 to call a patient positive, this translated into a sensitivity of 97% and a specificity of 96% for patients with non-viral ARIs and 83% for patients with other viral ARIs (Fig. 2B).
Mick’s sequencing revealed that IFI6 was among the most significant genes upregulated by SARS-CoV-2 (p. 3, para. 2). The express, implicit, and inherent disclosures of a prior art reference may be relied upon in the rejection of claims under 35 U.S.C. 102 or 103. "The inherent teaching of a prior art reference, a question of fact, arises both in the context of anticipation and obviousness." In re Napier, 55 F.3d 610, 613, 34 USPQ2d 1782, 1784 (Fed. Cir. 1995). See MPEP §2112. Because Mick states that IFI6 is upregulated, at the very least they are inherently comparing it between SARS-CoV-2-infected subjects with respiratory illness and non-infected controls.
Mick also teaches testing for COVID-19 carried out using PCR of NP swab or pooled NP + OP swab specimens using primers targeting either two regions of the SARS-CoV-2 N gene, or the E and RNA-dependent RNA polymerase genes, plus human RNAse P as a positive control (p. 9, para. 2). Additionally, Mick’s method utilizes a SARS-CoV-2 reference-based assembly pipeline that involved removing non-SARS-CoV-2 reads, aligning to the SARS-CoV-2 reference genome, and calculating SARS-CoV-2 reads per-million (rpM) using the number of reads that aligned (p. 10, para. 2). Mick performs robust regression of normalized gene counts against log10(rpM) of SARS-CoV-2 for all genes in the differentiate expression analysis of SARS-CoV-2 vs. no virus or SARS-CoV-2 vs. other virus (p. 12, last para.).
An explanation of how Mick anticipates claims 13, 15, 23, and 24 is detailed above in the rejection under 35 U.S.C. §102.
However, Mick does not teach measuring and detecting gene expression levels of GBP5 as compared to another human subject who is not infected with SARS-CoV-2.
Fang teaches analysis of high-throughput sequencing data of uninfected human bronchial organoids and SARS-CoV- 2infected human bronchial organoids in the GEO database to explore the effects of SARS-CoV-2 (p. 2, col. 1, para. 4), and identified 456 differentially expressed genes (DEGs; Abstract). IFI6 and GBP5 were among the DEGs up-regulated in SARS-CoV-2 infection (Table 1).
It would have been obvious to one of ordinary skill in the art to modify Mick’s methods to incorporate use of GBP5 as a diagnostic marker for SARS-CoV-2 infection and COVID-19 into the classifiers disclosed by Mick that comprise IFI6 measurement. Fang discloses that GBP5 is induced by SARS-CoV-2 infection, and so one of ordinary skill in the art would look to use its correlation to SARS-CoV-2 infection to help identify infection and disease with the virus. Mick discloses use of multiple gene classifier sets to diagnose SARS-CoV-2 infection or COVID 19. The examiner notes that IFI6 is among the genes in Tables 12A, 13A; GBP5 is among the genes in Tables 12B and 13B; and IFI6 + GBP5 are among the two-gene sets disclosed in Tables 12C and 13C of the specification. Accordingly, claims 1, 12, 13, 15, and 23-26 were prima facie obvious before the priority date of the instant invention.
It would also would have been obvious to test human subjects that have signs or symptoms of COVID-19 disease, as done by Mick, and required by claim 3.
Regarding claim 4, in Mick’s method, the biological sample comprises SARS-CoV-2 viral RNA, and a presence of the SARS-CoV-2 viral RNA is detected. Further, regarding claim 7, which requires the method further comprises detecting a presence or quantity of a SARS-CoV-2 viral gene in the biological sample and determining whether the human subject is infected with SARS-CoV-2 based on the detection of the SARS-CoV-2 viral gene and the differences, if any, determined in step (c), it would be obvious because Mick’s method utilizes both clinical PCR and mNGS to measure and quantify each of the SARS-CoV-2 genes, which would include the SARS-CoV-2 nucleocapsid (N) gene (in the case of mNGS), or the N gene (in the case of clinical PCR, and required by claim 11). Similarly, claims 14 and 16, which require determining the classification of whether the human subject has COVID-19 using the first gene expression level, the second gene expression level, the viral expression level (claim 14), and the one or more reference gene expression levels determined from the plurality of reference samples having the known COVID-19 classification.
Regarding claim 10, which requires the biological sample comprises cells collected from one or more of the subject’s nose, mouth, throat, and lower respiratory tract, and claim 21, wherein the biological sample is obtained using a nasal swab, a nasopharyngeal swab, an oropharyngeal swab, a buccal swab, a broncho-alveolar lavage, or an endotracheal aspirate, each claim would have been obvious because Mick’s methods utilize nasopharyngeal or oropharyngeal and nasopharyngeal swabs. These swabs would inherently possess cells, because host RNAs that are measured in Mick’s methods are in cells.
Regarding claim 22, which requires the first gene expression level and the second gene expression level and measuring the viral expression level comprises next generation sequencing (NGS), that would be obvious because Mick’s method utilizes mNGS.
One of ordinary skill in the art would have been motivated to diagnose SARS-CoV-2 infection or COVID 19. There would be a reasonable expectation of success because Mick discloses methods of determining whether or not a human subject is infected with SARS-CoV-2 or has COVID-19, and Fang teaches that GBP5 is induced by SARS-CoV-2 infection. Therefore, claims 1, 3-4, 7, 10-16, and 21-26 were prima facie obvious before the priority date of the instant invention.
However, Mick and Fang do not specifically teach a method wherein the human subject does not have signs or symptoms of COVID-19 disease.
Johansson teaches that SARS-CoV-2, the etiology of COVID-19, is readily transmitted person to person, and optimal control of COVID-19 depends on directing resources to mitigation efforts that are most likely to prevent transmission (p. 1; Abstract). Johansson also teaches that SARS-CoV-2, unlike SARS-CoV, is transmitted from persons without symptoms, and transmission from such people can arise from presymptomatic individuals or individuals who never experience symptoms (p. 2, paras. 1-2). Johansson further discloses that successful control of SARS-CoV-2 cannot rely solely on identifying and isolating symptomatic cases, but rather effective control also requires reducing the risk of transmission from people with infection who do not have symptoms, and suggests strategic testing of people who are not ill, such as those who have exposures to known cases or are at high risk of exposing others (p. 7, para. 1).
It would have been obvious to modify the method of determining whether or not a human subject is infected with SARS-CoV-2 rendered obvious by Mick and Fang to test human subjects that do not have signs or symptoms of COVID-19 disease. Johansson discloses that SARS-CoV-2 may be transmitted by persons without symptoms. It also would have been obvious for the method to further comprise detecting a presence or quantity of a SARS-CoV-2 viral gene in the biological sample, and determining whether the human subject has COVID-19 based on the detection of the SARS-CoV-2 viral gene and the differences, if any, determined in step (c), as required by claim 8, because Mick’s methods do so. One of ordinary skill in the art would have been motivated to reduce the risk of SARS-CoV-2 transmission from people with infection who do not have symptoms. There would have been a reasonable expectation of success because the methods of determining whether or not a human subject is infected with SARS-CoV-2 taught by Mick has high accuracy and sensitivity. Therefore, claims 1-4, 7-8, 10-16, and 21-26 were prima facie obvious to one of ordinary skill in the art before the instant filing date.
However, Mick, Fang, and Johansson do not teach wherein the first gene expression level and the second gene expression level in the biological sample are determined by normalizing a measured expression level with an expression of a human normalization gene, as required by claim 9.
Hounkpe teaches that housekeeping genes are constitutively expressed genes in all cell types of the organism in normal physiological conditions (p. 947, first paragraph; abstract). Hounkpe further teaches that due to these characteristics, housekeeping genes are useful as references of gene expression in molecular biology and computational experiments, and these genes are used as internal controls for the calibration of quantitative PCR (qPCR), used to quantitatively estimate the expression of any gene of interest under different experimental conditions (p. 947, col. 2, para. 1). Hounkpe also teaches that conventionally, qPCR normalization used the expression of reference genes to calibrate the expression levels of genes of interest (p. 949, col. 1, last para.). Additionally, Hounkpe discloses a web-based database that offers an accurate database of human housekeeping genes and transcripts (Abstract).
It would have been obvious to modify the method of determining whether or not a human subject is infected with SARS-CoV-2 rendered obvious by Mick and Fang such that the first gene expression level and second gene expression level in the biological sample are determined by normalizing a measured expression level with an expression level of a human normalization gene. One of ordinary skill in the art would have been motivated to determine the first gene expression level and second gene expression level. There would have been a reasonable expectation of success because Hounkpe discloses that housekeeping genes are conventionally to calibrate the expression levels of genes of interest in qPCR. Therefore, claims 1-4, 7-16, and 21-26 were prima facie obvious to one of ordinary skill in the art before the instant filing date.
Conclusion
No claim is allowed.
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/JEFFREY MARK SIFFORD/Examiner, Art Unit 1671 /Michael Allen/Supervisory Patent Examiner, Art Unit 1671
