DETAILED ACTION
Notice of Pre-AIA or AIA Status
Application number 17/639,023, as filed on 28 February 2022 and published on 29 September 2022 (US 2022/0308055 A1), is being examined under the first inventor to file provisions of the AIA (effective 16 March 2013).
Claims Status
Claim 19 is canceled.
Claims 1-18 and 20-21 are under examination on their merits.
Priority
For claims 1-18 and 20-21 in this application, a priority date of 27 August 2019 is applicable because the subject matter of each of said claims is found in 62/892258 filed 08/27/2019.
Drawings
The drawings are objected to because the image of Figure 3 is not clear and this is evident because the size bar in its bottom right corner is not legible.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claim 1 is objected to because the language requires proper punctuation to make sense of three key elements (i, ii and iii) essential to both alternatives of the method. To improve clarity, the examiner suggests adding a) and b) before each alternative (i.e. before each use of contacting lines 3-4).
Claim 14 is also objected to because “cytomegalovirus (CMV)” should be “a cytomegalovirus (CMV)” to improve readability and for consistency with claim 12.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. §112(b):
(b) CONCLUSION.-The specification shall conclude with one or more claims particularly
pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 8-10 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.
Claim 8: Claim 8 sets out “a method for detecting an immune response to a pathogen in a subject” using “a sample from the subject” (8a) and… “wherein the pathogen is detected based on… observed property” (8d): the preamble of claim 8 contradicts its body/function (8d). Therefore, it is not clear how the immune response is detected by only detecting the added pathogen, which renders claim 8 indefinite. Claims 9-10 are rejected for the same reason since they depend on claim 8.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 3 and 5-7 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Stobbs & Barker 1985 (Phytopathology, 75(4): 492-495).
Stobbs & Barker teaches a “simplified” method for diagnosis of “peach rosette mosaic virus (PRMV)” (p. 492) , which specified the following components in a “standard… procedure” (Abstract and p. 493):
Samples derived from plants were tested for PRMV or other viruses (p. 493, 1st para. on the left and Table 1);
Purified, PRMY-specific immunoglobulin (lg) served as a detection reagent (p. 493, 2nd para. on the left);
PRMY lg conjugated with alkaline phosphatase was used as a signaling substance (p. 493, 2nd para. on the left);
Absorbance “measured at 405 nm in a Beckman DU-8 spectrophotometer fitted with… accessory” was a quantifiable property for determining positive or negative results when (p. 493, 2nd para. on the left).
Stobbs & Barker 1985 also “simplified” the method cited above through “simultaneous addition of conjugate and virus” to the detection reagent (PRMY lg) (Abstract and Table 2), “such that only sample addition, incubation and substrate reaction are required to obtain sample diagnosis” (Abstract) based on absorbance “measured at 405 nm” (p. 493). The inclusion of negative control samples helped to verify the specificity of observed results (p. 493 & p. 495).
Therefore, Stobbs & Barker 1985 disclosed each and every element of claims 1, 3 and 5-7, rendering these claims as fully anticipated under 35 U.S.C. 102(a)(1).
Claims 18-21 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Arevalo et al (US 2016/0146809 A1, published 05/26/2016).
Claims 18-21 specify “a kit for detecting a pathogen, or an antibody against the pathogen, in a sample according to a method of claim 1,” comprising a “container“ in the form of “a tube, vial… or cylinder;” “a detection reagent; and an unmodified signaling substance,” with an option of “preloading a container with the detection reagent… prior to use).
Key teachings in Arevalo et al 2016:
An ELISA-based method for detecting peptide-antibody complexes used “a mixture of suitable peptides” as the capture reagent, plus “reagents for detecting peptide-antibody complexes” (¶[0032], as intended for “specific measurement of human IgG” (¶[0079]) against “a South American Leishmania strain (claim 1);
“Anti-human IgG labelled with a signal generator (substrate chromogen or colloidal gold)” provided signals (¶[0029]) for “detecting the presence or absence of… immune complex” (claim 1);
Results are based on “absorbance at 490 nm” (¶[0088]);
“An optical density greater than cut-off 0.3” was considered “as positive” (¶[0088]);
A “diagnostic kit” comprising “ELISA plates… pre-coated” with peptides, as well as “positive control, negative control, acceptable diluents, enzyme conjugated anti-human IgG, substrate chromogen, substrate buffer and an instruction manual to use the kit” (claim 6);
“Other components of a kit can easily be determined by one of skill in the art. Such components may include coating reagents, polyclonal or monoclonal capture antibodies specific for a peptide of the invention, or a cocktail of two or more of the antibodies, purified or semi-purified extracts of these antigens as standards… indicator charts for colorimetric comparisons, disposable gloves, decontamination instructions, applicator sticks or containers, a sample preparatory cup, etc.” (¶[0036]).
With respect to claim 18, the diagnostic kit above contains holders for the sample on the ELISA plate. The detection reagent includes the peptides as well as anti-human IgG conjugate. The unmodified signaling substance is the substrate chromogen. Thus, Arevalo teaches a kit for detecting the Leishmania above that meets all the limitations of claim 18.
In essence, Arevalo et al 2016 taught the design and use of a clinically oriented diagnostic kit for pathogen detection in a plate format (equivalent to a dish or cylinder which the wells of the ELISA plate can be called), and their use of substrate chromogen as a substrate did not require prior labeling. Thus, Arevalo clearly anticipates claim 20 also. With respect to claim 21, a kit containing all the contents above is immediately visualized as packaged by one of ordinary skill in this art. Otherwise the kit components are not together in one product, the kit. These teachings from a single prior art effectively render claims 18-21 as fully anticipated under 35 U.S.C. 102(a)(1).
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.
Claims 1-2 and 4 are rejected under 35 U.S.C. 103 as being unpatentable over Stobbs & Barker 1985 (Phytopathology, 75(4): 492-495), in view of Q. Huo 2013 (US PGPub 2013/0052661 A1, published 03/07/2013).
As dependents of claim 1, Claims 2 and 4 recite the measurement of signals in intermediate steps, “wherein observing a property of the signaling substance before the signaling substance contacts the sample and/or unlabeled detection reagent and again after the signaling substance contacts the sample and/or unlabeled detection reagent” (claim 2) and “wherein the signaling substance comprises nanoparticles, microparticles, magnetic particles, silica particles, polymer beads, quantum dots, electrodes, graphene, carbon nanotubes, or gold thin films, or a combination thereof” (claim 4).
Stobbs & Barker 1985 taught a “simplified” method (a sandwich ELISA assay) for diagnosis of “peach rosette mosaic virus (PRMV)” (p. 492), which specified the following components in a “standard… procedure” (Abstract and p. 493) and a modified version (Table 2):
Samples derived from plants were tested for PRMV or other viruses (p. 493, 1st para. on the left and Table 1);
Purified, PRMY-specific immunoglobulin (lg) served as a detection reagent (p. 493, 2nd para. on the left);
PRMY lg conjugated with alkaline phosphatase was used as a signaling substance upon addition of its substrate (p. 493, 2nd para. on the left);
Absorbance “measured at 405 nm in a Beckman DU-8 spectrophotometer fitted with… accessory” was a quantifiable property for determining positive or negative results when (p. 493, 2nd para. on the left).
A modified assay allowed “simultaneous addition of conjugate and virus to specific antibody-coated plates” (Pg. 494), and the absorbance was recorded for testing samples with or without the target pathogen (a virus), and for wells with “buffer only” (the equivalent of no detection reagent, Table 2). This buffer only sample will not retain much of the antibody-alkaline phosphatase conjugate since no virus is present but would clearly contain substrate. Therefore, this condition would be understood by a PHOSITA to read absorbance of the substrate before it contacts a sample while the test conditions of Table 2 observe a property after the signaling substance contacts a sample.
In essence, Stobbs & Barker 1985 taught the use of a sandwich ELISA-based method for virus detection, wherein virus-specific antibody served as a detection reagent and alkaline phosphatase/substrate as signaling substances to facilitate the measurement of a quantifiable readout (absorbance at 405 nm) (Table 1 & Table 2). Although they did not propose the use of nanoparticles as detection signals, but these deficiencies are remedied by Huo 2013.
Huo 2013 did disclose a nanoparticle (NP)-based assay (similar to claims 1 and 2), in which a “baiting molecule” and a “binding partner” were used for detecting “biomolecule complex” (Abstract and claim 9). A stepwise “screening analysis” (¶[0018]) of signal properties was done “when the nanoparticles may or may not need to be isolated from the rest of the assay solution” (¶[0018]), while an “alternative” approach allowed “successive exposure of the assay solution to baiting molecule for target” (¶[0019]). The target in this assay is the equivalent of protein complex on a pathogen (the basis for the method in Stobbs & Barker 1985). As can be seen in Figure 2, Huo’s method works similar to sandwich ELISAs in which two detection reagents sandwich a target, in this case XA. Figures 1-2 both show nanoparticle-tagged antibodies yielding increased particle size which can be detected by dynamic light scattering (¶[0014]). Figure 4 and ¶[0007] discuss negative controls which include non-specific gold nanoparticle antibodies. Thus, like Stobbs & Barker above, Huo is concerned with negative controls and nonspecific signals, some of which are discussed at ¶[0027], along with specific signal associated with particle size increases.
Taken together, it would have been obvious before the filing of the instant application that detection of PRMV by Stobbs & Barker could be replaced by the method of Huo when gold nanoparticle is a preferred signaling substance. This change is one type of sandwich immunoassay for another. The new assay based on gold particle size increase would predictably function to detect the virus since all that is needed is use of one or both antibodies of Stobbs & Barker to make the assay of Huo specific for PRMV. Furthermore, it would have been equally obvious to measure negative controls as was done in both Stobbs and Huo to determine the specific signal in test samples. One control could clearly be buffer control, and this would amount to measurement of nanoparticle size before sample contact. Equally obvious is the use of a before- and after-binding particle size comparison that provides supporting data. Particle size or colorimetric parameters as in Huo could be measured before sample addition and after, wherein an increase in particle size equates to presence of virus (PRMV in Stobbs & Barker). The positive samples would produce signals over time like the graph in Figure 1 of Huo. From a starting point (before sample addition) to after sample addition and at different intervals of incubation time, an increase in gold particle size would be predictably observed for positive control samples and test samples containing the viral target. The graph of Huo’s Figure 1 makes very clear that such detection before and after sample addition would have been obvious.
With respect to claim 4, the nanoparticles of Huo 2013 are substances used to produce signals in binding assays. The alkaline phosphatase of Stobbs & Barker 1985 is also a substance used to produce a signal for a binding assay. Therefore, it would have been obvious to one of ordinary skill in this art before the filing of the instant application to substitute one known signaling substance/readout for another as discussed supra. This is application of rationale B of MPEP 2143. Thus, claims 1-2 and 4 are rendered obvious Stobbs & Barker 1985 and Huo 2013 .
Claims 8-10 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al 2018 (Sensors and Actuators B: Chemical 271:24-32) in view of Bonelli et al. 1999 (WO 99/63349, published 12/09/1999).
Claims 8-10: these claims broadly draw “a method of detecting an immune response to a pathogen in a subject,” by allowing “the target pathogen” to bind to “at least one molecular component in the sample,” and the resulting product is allowed to contact “a signaling substance” to produce a signal/property for “observing.”
Key teachings in Liu et al 2018:
A “highly sensitive label-free antibody detection” method was used for the detection of “immunoglobulin M (IgM)” (Abstract, Pg. 24), with a “potential application of clinical point of care” (Abstract);
“Anti-IgM” is used as a capture reagent (Fig. 2, Pg. 26);
“Gold-coated silica nanoparticles” served as a signaling substance (Abstract & Fig. 2);
A CCD spectrometer (Ocean optics, HR4000, UK) was used to measure signals (Fig. 3, Pg. 27);
“Spectra were always measured and then compared with water (blank sample)” to “take into account the signal change caused only by… specific binding (section 3.1 on Pg. 27).
Liu et al 2018 effectively taught a label-free method for the detection of immune response in a way similar to claims 8-10, although they fell short of applying their method for detecting a pathogen-specific IgM response in a patient sample.
Bonelli et al. 1999, on the other hand, taught a “method for the detection of antibodies and/or antibody isotypes specific for at least two different phases of an infection” (Abstract) in a “sample” (“blood, serum or… therefrom”) (claim 9), including samples from “9 individual patients” after human cytomegalovirus (HCMV) infection (Pg. 22), with HCMV fusion protein serving as a capture reagent (claim 13); their methods were also broadened to test IgM and IgG against hepatitis B virus, Toxoplasma gondii and Borrelia burgdorieri (claim 13) and “can be combined with established prior art analytical techniques) (Pg. 6).
By combining the teaching of Liu et al 2018 and Bonelli et al. 1999, a PHOSITA would have found it obvious before the filing date of the instant application to detect a HCMV-specific IgM using the capture reagents taught by Bonelli et al. 1999 in the method of Liu et al 2018 to readily arrive at a detection method of claims 8-10. Clearly, one must obtain the sample first, contact said sample with the HCMV fusion protein of Bonelli, then contact the sample with the anti-IgM of Liu, and finally contact the sample with nanoparticles (a signaling substance) as taught by Liu. If the immune response (anti-HCMV IgM) is detected, a signal (size or color change) will be observed and compared with the signal from control samples, making a proper diagnosis (presence or absence of HCMV) for the sample and/or the subject from which the sample was taken. Therefore, the subject matter of claims 8-10 would have been Prima Facie obvious over Liu et al 2018 and Bonelli et al. 1999. The combination of the known elements above would have given a PHOSITA a reasonable expectation of success and predictable results.
Claim 11 and its dependent claims 12-17 are rejected under 35 U.S.C. 103 as being unpatentable over Q. Huo 2013 (US PGPub 2013/0052661 A1, published 03/07/2013) in view of van der Bij et al. 1988 (Journal of Medical Virology 25:179-188) and further in view of Goldstein et al. 1982 (Infection and Immunity, 38(1): 273-281).
Claims 11-13 and 15 recite a generic method for detecting pathogen based on “inclusion bodies or protein aggregates” that are indicative of a pathogen “in a subject” (claim 11), “wherein the pathogen is a virus” (claim 12) and “in a human or nonhuman mammal” (claim 13), and the method required “mixing a signaling substance with the sample” (claim 11), “either before or after” the addition of a labeled or unlabeled detection reagent“ (claim 15). “Observing a property of the signaling substance” facilitates pathogen detection (claim 11). Claims 14 and 16-17 then extend claim 11 with three more limitations: “wherein the pathogen is cytomegalovirus (CMV)” (claim 14), and “the inclusion body comprises one or more owl's eye related to cytomegalovirus, Cowdry type B related polio and adenovirus, Warthin-Finkeldey bodies related measles, Negri bodies related to Rabies, Torres bodies related to Yellow fever, Cowdry type A bodies related to Herpes simplex virus and Varicella zoster virus” (claim 16), and “wherein the sample is urine” (claim 17).
Huo 2013 disclosed a nanoparticle (NP)-based assay (similar to claim 11 in this application), in which a “baiting molecule” and a “binding partner” were used for detecting “biomolecule complex” (Huo 2013, Abstract and claim 9) and for “protein aggregate detection and quantitative analysis” (¶[0030] & ¶[0032]) based on “fluorescence signal change” (¶[0031]) and “Rayleigh scattering” (¶[0032]). By “adding a second step to the assay… a solution of baiting molecule that can specifically bind with an interested binding partner molecule… will cause a further increase of the nanoparticle size or nanoparticle cluster formation” (¶[0019]) for observation (the equivalent of claim 15). A stepwise “screening analysis” (¶[0018]) of signal properties was done “when the nanoparticles may or may not need to be isolated from the rest of the assay solution” (¶[0018]), while an “alternative” approach allowed “successive exposure of the assay solution to baiting molecule for target” (¶[0019]). In two “embodiments,” Huo’s method differentiated specific binding of NP-tagged antibodies to protein targets (FIG. 1 and FIG. 2) based on NP property changes detected by dynamic light scattering (¶[0014]), and negative controls included non-specific NP-antibodies (FIG. 4 and ¶[0007]). In one of the “Diagnostic Applications” (¶[0038]), “molecular differences” were noted “between serum samples with and without prostate cancer from both mice models and human donors were tested” for cancer-specific biomarkers ([0035]). These “embodiments” fell short of detecting “protein aggregate” (e.g., inclusion body) associated with pathogens, but the method was believed to be versatile enough to allow “numerous variations, changes and substitutions” (¶[0054]).
van der Bij et al. 1988, on the other hand, taught the detection HCMV-specific antigens by “immunological staining” and “microscopic examination” of “peripheral blood leukocytes (3rd para. on Pg. 180), “urine cultures” (Fig. 2 on Pg. 182) and “CMV-infected tissues” (3rd para. on Pg. 181) using a mixture of three monoclonal antibodies that “prominently stained the inclusion-bearing cytomegalic cells” (Pg. 181), and they also taught the use of “CMV-infected fibroblasts and blood cell preparations” as positive controls (“CMV Antigen Staining” on Pg. 182) to prove specificity (“in 34 controls… CMV-Ag+ cells were not detected) (1st para. below TABLE I on Pg. 183). These CMV antigen-specific assays did rely on visual detection/observation, but they fell short of specifically staining inclusion body. This deficiency was overcome by Goldstein et al. 1982, which taught the detection of “cytoplasmic inclusion bodies” (Abstract on Pg. 273) in lung-tissues from HCMV-infected transplant patients (FIG. 4 on Pg. 278) using a monoclonal antibody (6-C5) that “reacts with an 80,000-dalton protein that appears late in infection and remains localized in cytoplasmic inclusion bodies” (Abstract).
For a PHOSITA interested in developing a versatile method for the detection of pathogen-associated protein aggregates, including human CMV antigen/inclusion body in a urine sample, several straightforward substitutions for the methods of Huo 2013 would suffice. First, the 6-C5 monoclonal antibodies of Goldstein et al. 1982 can be used directly as a source of specific detection reagent (“baiting molecule”) for CMV-associated protein aggregate/inclusion body because it is known to bind “cytoplasmic inclusion bodies” (Goldstein et al. 1982, Abstract & FIG. 4). Second, the signaling molecules (gold nanoparticles/AuNP) adopted by Huo 2013 for the detection of protein aggregate-antibody complex replace the immunofluorescence method of Goldstein et al. 1982 such that the observation of AuNP-associated binding signals not only detects color change but also allows the assessment of binding dynamics (e.g., fast versus slow binding) or changes in AuNP size. Third, other antibodies developed by van der Bij et al. 1988 can be used as additional detection reagents for confirmation if needed. Fourth, urine sample (“urine cultures”) taught by van der Bij et al. 1988 (Fig. 1 on Pg. 184) can replace lung tissue samples used by Goldstein et al. 1982. Mixing a urine sample with AuNP-coated HCMV antibody will lead to a change in either AuNP size or a change in color for observation before arriving at a proper diagnosis, while assay specificity can be validated using a panel of negative and positive control samples, as indicated by Huo 2013 and van der Bij et al. 1988. Fifth, a second antibody with or without a signaling substance (AuNP) can be used to further increase the chance of detection or simply to increase the size of AuNP (signals) bound to protein aggregates for alternative observation (as disclosed by Huo 2013). These simple substitutions of one reagent for another in an immunoassay would facilitate the detection of virus-associated protein aggregates (as in claim 16) with highly predictable results. Therefore, the subject matter of claims 11-17 is another obvious application of rationale B of MPEP 2143.
Conclusion
No claim is allowed.
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/JIANMING TANG/
Examiner, Art Unit 1671 /Michael Allen/Supervisory Patent Examiner, Art Unit 1671