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 .
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) based on foreign applications EP20315157.6 and EP20305614.8. The earliest possible effective filing date of the claimed inventions is 04-14-2020 based on the filing date of foreign priority application EP20315157.6.
Information Disclosure Statement
(Previous objection, withdrawn) The Information Disclosure Statement filed 10-14-2022 is acknowledged and has been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
(Previous objection, withdrawn) The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) has been submitted.
Specification
(Previous objection, withdrawn) The abstract of the disclosure was objected to because it uses the legal term “said” in the last line.
Applicant has made appropriate changes.
(Previous objection, withdrawn) The specification was objected to because it is missing reference to the foreign priority applications.
The foreign priority application is included.
(Previous objection, withdrawn) The disclosure was objected to because it contains embedded hyperlinks and/or other form of browser-executable code in the listing of references beginning on page 35.
Applicant has deleted the embedded hyperlink and/or other form of browser-executable code.
Claim Objections
(Previous objection, withdrawn) Claim 28 recites the phrase “coronaviral polypeptide" in lines 5 and 6.
Applicant has made appropriate corrections.
(Previous objection, withdrawn) Claim 29 currently reads “one of the first and second viral polypeptides derives from the nucleoprotein (N) protein and the other SARS-CoV-2 polypeptide derives from the spike (S) protein or from the S1, S2 or S2' protein”.
Applicant has amended the claim.
(Previous objection, withdrawn) Claim 30 currently reads “one of the first and second viral polypeptides derives from the N protein and the other SARS-CoV-2 polypeptide derives from the S1 protein”.
Applicant has amended the claim.
(Previous objection, withdrawn) Claims 31 and 32 currently read “at least 90% of identity”. Please amend the claims to read “"at least 90% identity" (i.e., delete "of") to place the claims in better form.
Applicant has cancelled claims 31 and 32.
(Previous objection, withdrawn) Claim 35 currently reads “a plurality of secondary antibodies, each secondary antibody having specificity for a particular immunoglobulin”.
Applicant has amended the claim.
(Previous objection, withdrawn) Claim 40 currently reads “the method of claim 37, for simultaneously detecting…”.
Applicant has amended the claim.
(Previous objection, withdrawn) Claim 43 recites the phrase “achieves a protection with a vaccine or a vaccine candidate” in lines 1 and 4.
Applicant has cancelled claim 43.
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.
(Previous rejection, withdrawn) Claims 41-43 were rejected under 35 U.S.C. 101 because the claimed inventions are directed to a judicial exception without significantly more.
Applicant has canceled claims 41 – 43.
Claim Rejections - 35 USC § 112(b)
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.
(Previous rejection, withdrawn) Claims 28-44 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.
(Previous rejection, withdrawn) Claim 28 recites the limitations "the immunoglobulins" in line 9, “step b)” in lines 10 and 12, and “step d)” in line 15. Claim 35 recites the limitations "step d)" and “step b)” in line 1. Claim 36 recites the limitation “step f)” in line 3. Claim 37 recites the limitations "the immunoglobulins" in line 6, “step g)” in line 7, “step h)” in line 9, and “step j)” in 11 There is insufficient antecedent basis for these “step” limitations in the claims. Please note that dependent claim 38 also recites the limitation “step g)”. Please amend claim 38 as well to avoid further antecedent basis issues.
Applicant has amended the claim.
(Previous rejection, withdrawn) Claim 29 recites the limitation "the S1, S2, or S2’ protein" in line 3. There is insufficient antecedent basis for this limitation in the claim. Note that this rejection may be overcome by amending the claim as suggested in the claim 29 objection above.
Applicant has amended the claim.
(Previous rejection, withdrawn) Claim 36 recites the limitation “the groups of antibodies” in line 1, and "the type of SARS-CoV-2-specific antibodies" in line 2. There is insufficient antecedent basis for these limitations in the claim.
Applicant has amended the claim.
(Previous rejection, withdrawn) Claim 39 has been amended.
(Previous rejection, withdrawn) Claim 40 currently reads "simultaneously detecting IgG and IgM, or IgA SARS-CoV-2-specific antibodies". As worded, it is unclear which simultaneous detection groupings are claimed.
Applicant has amended the claim.
Claim Rejections - 35 USC § 112(a)
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.
(Previous rejection, withdrawn) Claim 43 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Applicant has cancelled claim 43.
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.
(Previous rejection, maintained and modified as necessitated by amendments) Claims 28, 29, 39, and 44 are rejected under 35 U.S.C. 103 as being unpatentable over Cai et al (medRxiv February 2020- included on IDS) in view of Tcherniaeva et al (Journal of Immunological Methods 2018- see attached form 892).
Claim 28 is drawn to a method for detecting the presence of SARS-CoV-2 specific antibodies in a subject comprising contacting a sample from the subject with at least two groups of particles which are conjugated to distinct SARS-CoV-2 polypeptides then detecting the formation of immunocomplexes between the sample and the particles.
Claim 39 is drawn to simultaneous detection of immunoglobulins specific for N and S or any of its fragments.
Cai et al teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Specifically, SARS-CoV-2 peptides, including those from the spike and nucleocapsid proteins, were synthesized, biotinylated, and conjugated to streptavidin-coated beads. The conjugated beads were mixed with patient sera, washed to remove unbound immunoglobulins, incubated with a secondary antibody (i.e., “antibody conjugate”), washed to remove unbound secondary antibody, then detection was performed with a luminescence reader (Synthetic peptide-based luminescent immunoassay). Although Cai et al teaches the immunoassay with different SARS-CoV-2 peptides, Cai et al does not teach simultaneous detection using at least two different peptides.
However, Tcherniaeva et al teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (abstract). Specifically, Tcherniaeva et al teaches that antigens from both viruses are conjugated to beads (section 2.3). Tcherniaeva et al teaches that there was very strong correlation in results from a CMV-EBV triplex antigen assay versus monoplex assays (Figure 3). Tcherniaeva et al also teaches that the multiplex assay reduces sample input and improves throughput and range of quantification compared to ELISA, making the multiplex assay “especially useful for large-scale surveillance studies" (abstract).
It would have been prima facie obvious to a person with ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Cai et al and Tcherniaeva et al to arrive at a method of simultaneously detecting SARS-CoV-2 antibodies specific to multiple viral antigens. One would have been motivated to do so for the advantage of reducing sample input, improving throughput and range of quantification, and performing large-scale surveillance studies as taught by Tcherniaeva et al. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Thus, the inventions of claims 28 and 39 as a whole were prima facie obvious to one of ordinary skill in the art before the effective filing date of the invention, especially in the absence of evidence to the contrary.
Claim 29 is drawn to the method of claim 28 wherein one of the viral polypeptides derives from the SARS-CoV-2 N protein and the other viral polypeptide derives from the SARS-CoV-2 spike protein or its S1, S2, or S2’ subunits. The examiner has interpreted the phrase “is derived” to indicate that the polypeptide comprises a fragment of the indicated viral protein (e.g., a polypeptide derived from spike would be the S1 subunit or the RBD of spike). Cai et al teaches testing the assay with spike (S) and nucleocapsid (N) proteins (Synthetic peptide-based luminescent immunoassay).
Claim 44 is drawn to a kit comprising the particles and secondary antibodies of claim 28. MPEP 2112.01(III) states that nonfunctional matter does not distinguish a claimed product from an otherwise identical prior art product. The broadest reasonable interpretation of “a kit” includes a box comprising instructions and the particles and secondary antibodies of claim 28. A box and instructions are nonfunctional matter. Thus, the kit of claim 44 is indistinguishable from the particles and secondary antibodies taught by Cai et al.
(Previous rejection, maintained and modified as necessitated by the amendments) Claims 30, 33, 35, 37, 38, and 40 are rejected under 35 U.S.C. 103 as being unpatentable over Cai et al and Tcherniaeva et al as applied to claims 28 and 29 above and further in combination with Liu et al (medRxiv March 2020- see attached form 892).
As discussed above, claims 28, 29, 39 and 44 were rendered prima facie obvious by the teachings of Cai et al and Tcherniaeva et al. These references do not teach that one of the viral polypeptides is derived from the spike S1 subunit, the specificities of the secondary antibodies, or diagnosing SARS-CoV-2 infection through the detection of antibodies.
However, Liu et al teaches these limitations as detailed below:
Claim 30 is drawn to the method of claim 29 wherein the first SARS-CoV-2 polypeptide is derived from SARS-CoV-2 nucleoprotein (N) protein and the second SARS-CoV-2 polypeptide is derived from the S1 subunit of the SARS-CoV-2 spike protein.
Liu et al teaches an ELISA (i.e., an immunoassay) using the RBD (i.e., portion of the S1 subunit) of a recombinant spike polypeptide (rS-based ELISA).
Claim 33 is drawn to the method of claim 28 wherein the secondary antibody is anti-human IgG. Claim 35 is drawn to the method of claim 28 wherein each secondary antibody is specific for a particular immunoglobulin. Claim 37 is drawn to the method of claim 33 further comprising the same steps set forth in claim 28 except the secondary antibody is anti-IgM. Claim 38 is drawn to the method of claim 37 wherein the SARS-CoV-2 polypeptide derives from the N protein. Claim 40 is drawn to the method of claim 37 comprising simultaneous detection of IgG and IgM or IgG and IgA antibodies against the N, S or PL-Pro proteins.
Liu et al teaches ELISAs to detect both IgG and IgM antibodies against the N and S proteins of SARS-CoV-2 (introduction paragraph 4). Liu et al teaches using anti-human IgG secondary antibody for detection of IgG antibodies and using anti-human IgM secondary antibody for detection of IgM antibodies (rS-based ELISA).
Liu et al teaches the evaluation of S and N protein-based ELISAs to diagnose SARS-CoV-2 infections (discussion paragraph 2).
It would have been prima facie obvious to a person with ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Cai et al, Tcherniaeva et al, and Liu et al to arrive at a method of simultaneously detecting IgG and IgM antibodies against peptides derived from the SARS-CoV-2 S and N proteins and use the results to diagnose SARS-CoV-2 infection. One would have been motivated to do so for the advantage of higher sensitivity simultaneous detection of an antigen that elicits an early antibody response (i.e., S protein) and a later antibody response (i.e., N protein) combined with temporal antibody class dynamics (i.e., IgM antibodies peak early then wane compared to IgG) as taught by Liu et al (discussion paragraph 2). There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Thus, the invention of claims 30, 33, 35, 37, 38, and 40 as a whole were prima facie obvious to one of ordinary skill in the art before the effective filing date of the invention, especially in the absence of evidence to the contrary.
(Previous rejection, withdrawn) Claims 31 and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Cai et al, Tcherniaeva et al, and Liu et al as applied to claim 30 above and further in combination with Zhang et al (GenBank accession number MN908947.1 January 2020- see attached form 892).
Applicant has cancelled claims 31 and 32.
(Previous rejection, maintained) Claim 34 is rejected under 35 U.S.C. 103 as being unpatentable over Cai et al and Tcherniaeva et al as applied to claim 28 above and further in combination with Albon et al 2011 (Journal of Immunological Methods 2011- see attached form 892).
Claim 34 is drawn to the method of claim 28 wherein the groups of particles differ from one another by their “identity codes”. Based on the specification page 23 line 2, the examiner has interpreted the limitation identity codes to be equivalent to any molecule or substance that can be differentially detected (e.g., a fluorophore or luminescent material).
As discussed above, claim 28 was rendered prima facie obvious by the teachings of Cai et al and Tcherniaeva et al. These references do not teach groups of particles differing from one another based on a detectable moiety.
However, Albon et al teaches the multiplex ALBIA method to detect several different antibodies within the same sample (abstract). Specifically, Albon et al teaches that the ALBIA method uses antigens covalently coupled to color-coded microspheres (i.e., particles with different “identity codes”) and a secondary antibody conjugated to a fluorophore. The color of the antigen-conjugated microsphere distinguishes the different antigens, and fluorescent intensity of the secondary antibody measures primary antibody concentration (section 2.3).
It would have been prima facie obvious to a person with ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Cai et al, Tcherniaeva et al, and Albon et al to arrive at a method of detecting SARS-CoV-2 antibodies wherein antigen-bound particles are differentially color-coded. One would have been motivated to do so for the advantage of detecting antibodies against different antigens within the same assay. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Thus, the invention of claim 34 as a whole was prima facie obvious to one of ordinary skill in the art before the effective filing date of the invention, especially in the absence of evidence to the contrary.
(Previous rejection, maintained and modified as necessitated by the amendments) Claim 36 is rejected under 35 U.S.C. 103 as being unpatentable over Cai et al, Tcherniaeva et al, and Liu et al as applied to claim 35 above and further in combination with ThermoFisher (Fluorescent Western Blotting April 1 2020- see attached form 892).
Claim 36 is drawn to the method of claim 35 wherein the groups of antibodies differ from one another by their indicator reagent so as to discriminate the type of SARS-CoV-2-specific antibodies when step f) is carried out.
ThermoFisher teaches the advantages of using fluorescently labeled secondary antibodies in western blotting (i.e., an immunoassay). Specifically, ThermoFisher teaches that using secondary antibodies labeled with different fluorophores enables a multiplexed western blot assay without needing to strip and re-probe the membrane (advantages of fluorescent western blot detection). ThermoFisher teaches that it is critical to select fluorophores (i.e., indicator reagent) that are detected in different channels/ filters for labeling secondary antibodies to enable accurate differential detection (fluorophore and filter selection).
It would have been prima facie obvious to a person with ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Cai et al, Tcherniaeva et al, Liu et al, and ThermoFisher to arrive at a method of detecting different classes of SARS-CoV-2 antibodies using differentially labeled secondary antibodies. One would have been motivated to do so for the advantage of performing a multiplexed immunoassay as taught by ThermoFisher. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Thus, the invention of claim 36 as a whole was prima facie obvious to one of ordinary skill in the art before the effective filing date of the invention, especially in the absence of evidence to the contrary.
(Previous rejection, withdrawn) Claims 42 and 43 are rejected under 35 U.S.C. 103 as being unpatentable over Cai et al and Tcherniaeva et al as applied to claim 28 above and further in combination with Amanat and Krammer (Immunity, available online April 6 2020- see attached form 892).
Applicant has cancelled claims 42 and 43.
(New rejection as necessitated by the amendments) Claims 45 and 46 are rejected under 35 U.S.C. 103 as being unpatentable over Cai and Tcherniaeva as applied to claims 28, 29, 39, and 44 above, and further in view of Trivedi et al (Scientific reports, 2019, 10.1038/s41598-018-37747-5, hereinafter, “Trivedi”).
As discussed above, claims 28, 29, 39, and 44 were rendered prima facie obvious by Cai and Tcherniaeva. Cai teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Tcherniaeva teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (Abstract). The references fail to teach a secondary antibody coupled to a fluorescent label.
However, Trivedi teaches a multiplexed serological assay for the detection and surveillance of human coronaviruses (Abstract). Trivedi teaches a multiplexed magnetic microsphere immunoassay to simultaneously detect IgG antibodies specific for recombinant nucleocapsid proteins from hCoVs 229E, NL63, OC43, HKU1, SARS-CoV, and MERS-CoV (Abstract). Regarding claims 45 and 46, Trivedi teaches adding beads conjugated to viral antigens before adding sera to the beads (Section: recN Monoplex Immunoassay). Trivedi teaches the beads are then separated using a magnetic plate separator (Section: recN Monoplex Immunoassay). Trivedi teaches the beads are washed and then placed in solution with - Phycoerythrin (R-PE) conjugated goat anti-human IgG before detection of fluorescence (Section: recN Monoplex Immunoassay). Trivedi also teaches that this protocol was applied to a multiplexed assay (Section: recN Multiplex Immunoassay).
Cai, Tcherniaeva, and Trivedi are considered to be analogous to the claim invention because they aim to detect viral antigens using an immunoassay. Cai teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Tcherniaeva teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (Abstract). Trivedi teaches a multiplexed immunoassay using antibodies conjugated to a fluorescent label (Section: recN Multiplex Immunoassay).
Together, the prior art teaches that multiple viral antigens from SARS-CoV-2 can be detected using a multiplexed immunoassay where the secondary antibodies are coupled to a fluorescent label. Therefore, it would have been prima facie obvious before the effective filing date of the claimed invention to use a multiplexed immunoassay with a secondary antibody that is coupled to a fluorescent label for SARS-CoV-2 because doing so would enable higher sensitivity using less material, thereby increasing the chance of positively identifying a SARS-CoV-2 infection. One of ordinary skill in the art would have had a reasonable expectation of success in using a multiplexed immunoassay with a fluorescent coupled secondary antibody given that the method is well known, has been successfully demonstrated, and commonly used in the prior art.
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill in the art at the time of filing especially in the absence of evidence to the contrary.
(New rejection as necessitated by the amendments) Claims 47 and 48 are rejected under 35 U.S.C. 103 as being unpatentable over Cai and Tcherniaeva as applied to claims 28, 29, 39, and 44 above, and further in view of Milliplex et al (HUMAN ADIPOKINE MAGNETIC BEAD PANEL 2 96-Well Plate Assay, 2017, Cat. # HADK2MAG-61K, hereinafter, “Milliplex”).
As discussed above, claims 28, 29, 39, and 44 were rendered prima facie obvious by Cai and Tcherniaeva. Cai teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Tcherniaeva teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (Abstract). The references fail to teach a secondary antibody coupled to a biotin label and a fluorescent signal is generated once streptavidin-R-PE is added.
However, Milliplex teaches a multiplexed immune assay to detect cytokines (Introduction). Milliplex teaches using a Luminex multiplex bead immunoassay to achieves this goal (Introduction). Importantly, Milliplex teaches the principle of the Luminex multiplex bead immunoassay (Section: Principle of the Luminex multiplex bead immunoassay). Milliplex teaches analytes are bound to capture antibodies on beads. Analytes are then introduced to analyte-specific biotinylated antibodies (Section: Principle of the Luminex multiplex bead immunoassay). Excess biotinylated detector antibodies are washed and streptavidin conjugated to the fluorescent protein, R-Phycoerythrin (streptavidin-RPE), is added and incubated forming a four-member solid phase sandwich (Section: Principle of the Luminex multiplex bead immunoassay). The beads are analyzed with the Luminex 100/200™ instrument (Section: Principle of the Luminex multiplex bead immunoassay). By monitoring the spectral properties of the beads and the amount of associated R-Phycoerythrin (RPE) fluorescence, the concentration of one or more analytes can be determined (Section: Principle of the Luminex multiplex bead immunoassay).
Regarding claim 47, Milliplex teaches a secondary antibody that is coupled to a biotin label (Section: Principle of the Luminex multiplex bead immunoassay).
Regarding claim 48, Milliplex teaches a fluorescent signal is generated and detected after the addition of streptavidin-RPE (Section: Principle of the Luminex multiplex bead immunoassay).
Cai, Tcherniaeva, and Milliplex are considered to be analogous to the claim invention because they aim to detect analytes using an immunoassay. Cai teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Tcherniaeva teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (Abstract). Milliplex teaches a multiplexed immunoassay using biotinylated secondary antibodies and the conjugation of the antibodies with streptavidin-RPE (Section: Principle of the Luminex multiplex bead immunoassay).
Together, the prior art teaches that multiple viral antigens from SARS-CoV-2 can be detected using a multiplexed immunoassay with biotinylated secondary antibodies where a fluorescence signal is generated after the addition of streptavidin-RPE. Therefore, it would have been prima facie obvious before the effective filing date of the claimed invention to use a multiplexed immunoassay with biotinylated secondary antibodies where a fluorescence signal is generated after the addition of streptavidin-RPE for SARS-CoV-2 because doing so would enable higher sensitivity using less material, thereby increasing the chance of positively identifying a SARS-CoV-2 infection. One of ordinary skill in the art would have had a reasonable expectation of success in using a multiplexed immunoassay with biotinylated secondary antibodies where a fluorescence signal is generated after the addition of streptavidin-RPE given that the method is well known, has been successfully demonstrated, and commonly used in the prior art.
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill in the art at the time of filing especially in the absence of evidence to the contrary.
(New rejection as necessitated by the amendments) Claims 49 and 50 are rejected under 35 U.S.C. 103 as being unpatentable over Cai, Tcherniaeva, and Liu as applied to claims 30, 33, 35, 37, 38, and 40 above, and further in view of Trivedi.
As discussed above, claims 30, 33, 35, 37, 38, and 40 were rendered prima facie obvious by Cai, Tcherniaeva, and Liu. Cai teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Tcherniaeva teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (Abstract). Liu teaches ELISAs to detect both IgG and IgM antibodies against the N and S proteins of SARS-CoV-2 (introduction paragraph 4). Liu et al teaches using anti-human IgG secondary antibody for detection of IgG antibodies and using anti-human IgM secondary antibody for detection of IgM antibodies (rS-based ELISA). The references fail to teach a secondary antibody coupled to a fluorescent label.
However, Trivedi teaches a multiplexed serological assay for the detection and surveillance of human coronaviruses (Abstract). Trivedi teaches a multiplexed magnetic microsphere immunoassay to simultaneously detect IgG antibodies specific for recombinant nucleocapsid proteins from hCoVs 229E, NL63, OC43, HKU1, SARS-CoV, and MERS-CoV (Abstract). Regarding claims 49 and 50, Trivedi teaches adding beads conjugated to viral antigens before adding sera to the beads (Section: recN Monoplex Immunoassay). Trivedi teaches the beads are then separated using a magnetic plate separator (Section: recN Monoplex Immunoassay). Trivedi teaches the beads are washed and then placed in solution with - Phycoerythrin (R-PE) conjugated goat anti-human IgG before detection of fluorescence (Section: recN Monoplex Immunoassay). Trivedi also teaches that this protocol was applied to a multiplexed assay (Section: recN Multiplex Immunoassay).
Cai, Tcherniaeva, Liu, and Trivedi are considered to be analogous to the claim invention because they aim to detect viral antigens using an immunoassay. Cai teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Tcherniaeva teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (Abstract). Liu teaches ELISAs to detect both IgG and IgM antibodies against the N and S proteins of SARS-CoV-2 (introduction paragraph 4). Liu et al teaches using anti-human IgG secondary antibody for detection of IgG antibodies and using anti-human IgM secondary antibody for detection of IgM antibodies (rS-based ELISA). Trivedi teaches a multiplexed immunoassay using antibodies conjugated to a fluorescent label (Section: recN Multiplex Immunoassay).
Together, the prior art teaches that multiple viral antigens from SARS-CoV-2 can be detected using a multiplexed immunoassay where the secondary antibodies are coupled to a fluorescent label. Therefore, it would have been prima facie obvious before the effective filing date of the claimed invention to use a multiplexed immunoassay with a secondary antibody that is coupled to a fluorescent label for SARS-CoV-2 because doing so would enable higher sensitivity using less material, thereby increasing the chance of positively identifying a SARS-CoV-2 infection. One of ordinary skill in the art would have had a reasonable expectation of success in using a multiplexed immunoassay with a fluorescent coupled secondary antibody given that the method is well known, has been successfully demonstrated, and commonly used in the prior art.
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill in the art at the time of filing especially in the absence of evidence to the contrary.
(New rejection as necessitated by the amendments) Claims 51 and 52 are rejected under 35 U.S.C. 103 as being unpatentable over Cai, Tcherniaeva, and Liu as applied to claims 30, 33, 35, 37, 38, and 40 above, and further in view of Milliplex.
As discussed above, claims 30, 33, 35, 37, 38, and 40 were rendered prima facie obvious by Cai, Tcherniaeva, and Liu. Cai teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Tcherniaeva teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (Abstract). Liu teaches ELISAs to detect both IgG and IgM antibodies against the N and S proteins of SARS-CoV-2 (introduction paragraph 4). Liu et al teaches using anti-human IgG secondary antibody for detection of IgG antibodies and using anti-human IgM secondary antibody for detection of IgM antibodies (rS-based ELISA).
The references fail to teach a secondary antibody coupled to a biotin label and a fluorescent signal is generated once streptavidin-R-PE is added.
However, Milliplex teaches a multiplexed immune assay to detect cytokines (Introduction). Milliplex teaches using a Luminex multiplex bead immunoassay to achieves this goal (Introduction). Importantly, Milliplex teaches the principle of the Luminex multiplex bead immunoassay (Section: Principle of the Luminex multiplex bead immunoassay). Milliplex teaches analytes are bound to capture antibodies on beads. Analytes are then introduced to analyte-specific biotynlated antibodies (Section: Principle of the Luminex multiplex bead immunoassay). Excess biotinylated detector antibodies are washed and streptavidin conjugated to the fluorescent protein, R-Phycoerythrin (streptavidin-RPE), is added and incubated forming a four-member solid phase sandwich (Section: Principle of the Luminex multiplex bead immunoassay). The beads are analyzed with the Luminex 100/200™ instrument (Section: Principle of the Luminex multiplex bead immunoassay). By monitoring the spectral properties of the beads and the amount of associated R-Phycoerythrin (RPE) fluorescence, the concentration of one or more analytes can be determined (Section: Principle of the Luminex multiplex bead immunoassay).
Regarding claim 51, Milliplex teaches a secondary antibody that is coupled to a biotin label (Section: Principle of the Luminex multiplex bead immunoassay).
Regarding claim 52, Milliplex teaches a fluorescent signal is generated and detected after the addition of streptavidin-RPE (Section: Principle of the Luminex multiplex bead immunoassay).
Cai, Tcherniaeva, Liu, and Milliplex are considered to be analogous to the claim invention because they aim to detect analytes using an immunoassay. Cai teaches a bead-based luminescent immunoassay to detect IgG and IgM antibodies in sera from SARS-CoV-2 patients (abstract). Tcherniaeva teaches a bead-based multiplex immunoassay for the simultaneous detection of cytomegalovirus (CMV) and Epstein Barr virus (EBV) antibodies (Abstract). Liu teaches ELISAs to detect both IgG and IgM antibodies against the N and S proteins of SARS-CoV-2 (introduction paragraph 4). Liu teaches using anti-human IgG secondary antibody for detection of IgG antibodies and using anti-human IgM secondary antibody for detection of IgM antibodies (rS-based ELISA). Milliplex teaches a multiplexed immunoassay using biotinylated secondary antibodies and the conjugation of the antibodies with streptavidin-RPE (Section: Principle of the Luminex multiplex bead immunoassay).
Together, the prior art teaches that multiple viral antigens from SARS-CoV-2 can be detected using a multiplexed immunoassay with biotinylated secondary antibodies where a fluorescence signal is generated after the addition of streptavidin-RPE. Therefore, it would have been prima facie obvious before the effective filing date of the claimed invention to use a multiplexed immunoassay with biotinylated secondary antibodies where a fluorescence signal is generated after the addition of streptavidin-RPE for SARS-CoV-2 because doing so would enable higher sensitivity using less material, thereby increasing the chance of positively identifying a SARS-CoV-2 infection. One of ordinary skill in the art would have had a reasonable expectation of success in using a multiplexed immunoassay with biotinylated secondary antibodies where a fluorescence signal is generated after the addition of streptavidin-RPE given that the method is well known, has been successfully demonstrated, and commonly used in the prior art.
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill in the art at the time of filing especially in the absence of evidence to the contrary.
Response to Arguments
Applicant's arguments filed 9/22/2025 have been fully considered but they are not persuasive.
Applicant contends on page 7 of the Remarks: that the Specification and Abstract has been amended to overcome the objections
In response: The objections have been withdrawn.
Applicant contends on page 9 of the Remarks: that the novelty of the instant application is the use of differently labeled particles carrying different SARS-CoV-2 polypeptides in a single receptacle. The Applicant argues that Cai and Liu teach the separate receptacles for SARS-CoV-2 polypeptides.
In response: As discussed above and previously, it would have been prima facie obvious to a person with ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Cai et al, Tcherniaeva et al, and Liu et al to arrive at a method of simultaneously detecting IgG and IgM antibodies against peptides derived from the SARS-CoV-2 S and N proteins and use the results to diagnose SARS-CoV-2 infection. One would have been motivated to do so for the advantage of higher sensitivity simultaneous detection of an antigen that elicits an early antibody response (i.e., S protein) and a later antibody response (i.e., N protein) combined with temporal antibody class dynamics (i.e., IgM antibodies peak early then wane compared to IgG) as taught by Liu et al (discussion paragraph 2). There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Additionally, Cai states “We detected both IgM and IgG in the same sera from the 276 infection-confirmed patients. IgG was detected in 71.4% (197/276) of all the sera, higher than the detection rate of IgM (57.2%, 158/276). A combination the two antibodies enhanced the detection rate to 81.5% (225/276)” (Discussion ¶2). Therefore, while Cai does not teach differently labeled particles carrying different SARS-CoV-2 polypeptides in a single receptacle, Cai does provide a clear motivation that the detection of multiple antibodies would result in a higher fidelity readout. Furthermore, as discussed above, Trivedi and Milliplex teach bead-based multiplex immunoassay methods for the detection of several polypeptides, including those of viruses, in a single receptacle. Therefore, while the prior art does not teach the use of differently labeled particles carrying different SARS-CoV-2 polypeptides in a single receptacle it would be obvious to one of ordinary skill in the art to detect SARS-CoV-2 polypeptides in a single receptacle using differently labels particles.
Applicant contends on page 10 of the Remarks: The particular invention of the instant application results in in surprising sensitivity, peaking at 97.7% for anti-S1 IgG and 100% for anti-N IgG and 74.8% for anti-S1 IgM.
In response: The sensitivity and performance of the claimed method can be largely attributed to the recombinant proteins used to detect antibodies. The performance of the assay would differ if only the recombinant protein used were changed and all other aspects of the method remained the same. Solely to rebut Applicant’s argument, Frank (Immunology and Evolution of Infectious Disease, 2002) evidences that the specificity and cross-reactivity of antibodies and epitopes in immune recognition of parasite molecules (Section: Chapter 4, ¶1). Frank evidences that the antibodies and different epitopes bind at different strengths and that single substitutions can affect binding strength (Section: 4.1. Antigens and Antibody Epitopes). As such, the current claims of the instant application would not guarantee high performance of the claimed method because the performance of the method is dependent on the binding strength of the recombinant proteins used to detect antibodies. As a singular amino acid can affect binding strength, the sensitivity is due to the used recombinant proteins and not by using a single receptacle to detect different antibodies.
Applicant contends on page 12 of the Remarks: The skilled person had no reasonable expectation of successfully increasing the performance of the tests by simultaneously detecting immunoglobins against two different SARS-CoV-2 proteins in the same receptacle.
In response: As discussed above and previously, Cai provides a clear teaching, suggestion, and motivation that the detection of multiple antibodies would result in a higher fidelity readout (Discussion, ¶2). Trivedi and Milliplex teach bead-based multiplex immunoassay methods for the detection of several polypeptides, including those of viruses, in a single receptacle. Therefore, a person of ordinary skill in the art would have the reasonable expectation of being able to detect multiple antibodies in a single receptacle to increase the fidelity of the readout because detecting multiple SARS-CoV-2 antibodies is known to increase the detection rate and using a single receptacle was well known in the art.
Conclusion
NO CLAIMS ARE ALLOWED.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/DANYAL HASSAN ALAM/ Examiner, Art Unit 1672
/THOMAS J. VISONE/ Supervisory Patent Examiner, Art Unit 1672
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