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 .
Response to Amendment
The Amendment filed 08/13/2026 has been entered. Claims 1-2, 4-5, 7-8, 11-20, 22, 28, 29, 42-44 remain pending in the application. Applicant’s amendments to the claims have overcome each and every objection and 101 and 112(b) rejections previously set forth in the Non-Final Office Action mailed 05/13/2026. New grounds of rejections necessitated by amendments are discussed below.
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.
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 7-8 and 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.
Regarding claims 7 and 8, claims 7 and 8 recite “method of claim 6”. However, claim 6 has been cancelled. Therefore, it is unclear which claim that claims 7 and 8 are dependent upon. It is suggested to recite “method of claim 6” as “method of claim 1”. For examination purposes, claims 7-8 are interpreted as dependent upon claim 1.
Regarding claim 44, claim 44 recites “an infectious agent” in line 5. It is unclear if the infectious agent of line 5 is the same or different from the infectious agent established in line 2. It is suggested to recite “an infectious agent” as “the infectious agent” in line 5 if referring to the same element.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 15 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 15 recites wherein the memory T-cells are CD4+ and/or CD8+ T cells. Amended claim 1 already recites wherein the memory T-cells are CD4+ and/or CD8+ T cells. Therefore, claim 15 fails to further limit the subject matter of the claim upon which it depends. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 1-2, 4, 7-8, 12, 15, 19-20, 22, 29, 42-44 are rejected under 35 U.S.C. 103 as being unpatentable over in view of Sette et al. (US 20240409587 A; effectively filed 04/12/2021) in view of Invitrogen (Invitrogen, "Assays for cell viability, proliferation and function", Invitrogen, Molecular Probes TM Handbook, 11th Edition, Chapter 15, 89 pages (2010); cited in the IDS filed 02/12/2024) and Wang (US 20210302434 A1; effectively filed 03/25/2020).
Regarding claim 1, Sette teaches a method to identify presence of SARS CoV-2-specific T cells in a sample from a subject to ascertain prior exposure to, or vaccination with, SARS CoV-2 virus (abstract and [0015]-[0017] teaches identifying or determining presence of SARS-CoV-2 T cells which indicates an immune response relevant to SARS-CoV-2 infection or exposure in a subject), comprising:
exposing a biological sample comprising memory T-cells from the subject to one or more peptide antigens specific for SARS CoV-2 ([0015]-[0017] teaches contacting a biological sample from a subject with a composition of composition of one or more proteins, peptides or multimers, wherein the sample includes T cells, and the protein or peptide is of SARS-CoV-2, i.e. peptide antigens specific for SARS-CoV-2);
contacting the exposed memory T-cells with an indicator compound ([0015]-[0017] teaches detecting an amount and/or the activity of, and/or the state of SARS-CoV-2-specific T-cells in the biological sample, which includes assays, which imply the contacting the T cells with an indicator; [0193] teaches T cell responses were measured with Activation Induced Marker (AIM) assays, wherein AIM assays would imply contacting the T cells with an indicator; [0139] and [0229] teaches dyes, labels, and indicators as diagnostic agents for generating detectable signals), wherein the contacting is simultaneous with or sequential to the exposing ([0015]-[0017] teaches contacting a biological sample having SARS-CoV-2-specific T-cells to one or more proteins or peptides for detection and then detecting an amount of, and/or the activity of, and/or the state of antigen-specific T cells; therefore, it is implied that the T cells are contacted with an indicator compound with or sequential to the exposing in order to properly mix and react the T cells of interest with an indicator for proper detection);
analyzing the memory T-cells for the indicator compound ([0015]-[0017] teaches detection and then detecting an amount of, and/or the activity of, and/or the state of antigen-specific T cells; [0193] teaches T cell responses were measured with Activation Induced Marker (AIM) assays, wherein AIM assays would imply contacting the T cells with an indicator; [0139] and [0229] teaches dyes, labels, and indicators as diagnostic agents for generating detectable signals; therefore, detection and analysis of the T cell response or activity includes analysis of the indicator compound for proper detection and measuring the T cells);
wherein the memory T-cells are CD4+ and/or CD8+ T cells ([0015]-[0017] teaches the T cells are CD4+ or CD8+ cells); and
where the biological sample is a blood sample or a fraction thereof ([0125] teaches the biological sample is blood or blood fractions; [0090] teaches “blood or PBMC sample”; [0030],[0190],[0192] teaches PBMC samples).
Sette fails to explicitly teach:
wherein the one or more peptide antigens specific for SARS CoV-2 comprise at least one peptide identified as SEQ ID NO: 1 and/or SEQ ID NO: 12;
contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both;
exposing a second biological sample comprising memory T-cells to a control reagent that (i) lacks the one or more peptide antigens specific for SARS CoV-2 and (ii) comprises a control indicator compound that associates with RNA, DNA, or both, to thereby generate a control sample;
wherein said analyzing comprises (i) measuring signal of indicator compound associated with memory T-cells in the biological sample and measuring signal of control indicator compound associated with memory T-cells in the control sample or (ii) measuring signal of indicator compound associated with RNA in the biological sample and measuring signal of control indicator compound associated with RNA in the second biological sample.
Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]). Sette teaches fluorescent and oligonucleotide labels ([0058]). Sette teaches multimer staining does not kill the labelled cells, thus, cell integrity is maintained for further analysis; and isolating and/or identifying a population of CD8+ T cells having specificity for the peptide in a flow cytometry assay ([0089]). Sette teaches cells can be identified by well-known methods, including staining by a dye ([0127]). Sette a label can include a nucleic acid label comprising DNA and/or RNA, and the label can include fluorescent labels ([0231]).
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of contacting the exposed memory T-cells with the indicator compound of Sette to incorporate Sette’s teachings of assays for T-cells, fluorescent and nucleic acid labels, staining live cells for identification of T-cells in a flow cytometry assay ([0015], [0058], [0089], [0127], [0231]) and Invitrogen’s teachings of dyes and stains for DNA or RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both. Doing so would have a reasonable expectation of successfully allowing for rapid penetration of a stain, i.e. indicator, in the T-cells for further analysis.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. contacting the exposed memory T-cells with an indicator compound and an indicator compound that associates with RNA, DNA, or both) by known methods with no change in their respective functions (i.e. detection and analysis of T-cells), and the combinations yielded nothing more than predictable results (i.e. contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both would yield nothing more than the obvious and predictable result of enabling rapid penetration of a stain in the T-cells for further analysis). See MPEP 2143(A).
Additionally, since Invitrogen teach labeling of cells with an indicator compound that associates with RNA, DNA, or both, which has the same functional capability of labeling cells of Sette, it would have been obvious to have substituted one known element (Sette’s indicator compound) for another (Invitrogen’s indicator compound that associates with RNA, DNA, or both), and the results of the substitution would have been predictable (allowing for rapid penetration of a stain, i.e. indicator, in the T-cells for further analysis). See MPEP 2143(I)(B).
Modified Sette fails to teach:
wherein the one or more peptide antigens specific for SARS CoV-2 comprise at least one peptide identified as SEQ ID NO: 1 and/or SEQ ID NO: 12;
exposing a second biological sample comprising memory T-cells to a control reagent that (i) lacks the one or more peptide antigens specific for SARS CoV-2 and (ii) comprises a control indicator compound that associates with RNA, DNA, or both, to thereby generate a control sample;
wherein said analyzing comprises (i) measuring signal of indicator compound associated with memory T-cells in the biological sample and measuring signal of control indicator compound associated with memory T-cells in the control sample or (ii) measuring signal of indicator compound associated with RNA in the biological sample and measuring signal of control indicator compound associated with RNA in the second biological sample.
Sette teaches a control sample serves as a reference, usually a known reference, for comparison to a test sample; a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control); and controls are also valuable for determining the significance of data ([0129]). Sette teaches investing T cell reactivity against VOCs in cohorts of COVID-19 convalescent, vaccinees and unexposed controls ([0190]). Sette teaches the method for detecting an immune response to RARS-CoV-2 infections, vaccines, or therapies includes T cell response when contacting a biological sample with T cells with proteins or peptides for detection ([0015]-[0017]). Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]). Sette teaches fluorescent and oligonucleotide labels ([0058]). Sette teaches multimer staining does not kill the labelled cells, thus, cell integrity is maintained for further analysis; and isolating and/or identifying a population of CD8+ T cells having specificity for the peptide in a flow cytometry assay ([0089]). Sette teaches cells can be identified by well-known methods, including staining by a dye ([0127]). Sette a label can include a nucleic acid label comprising DNA and/or RNA, and the label can include fluorescent labels ([0231]).
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Sette to incorporate Sette’s teachings of assays for T-cells, fluorescent and nucleic acid labels, staining live cells for identification of T-cells in a flow cytometry assay ([0015], [0058], [0089], [0127], [0231]) and controls for COVID-19 ([0129],[0190]) and Invitrogen’s teachings of dyes and stains for DNA or RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: exposing a second biological sample comprising memory T-cells to a control reagent that (i) lacks the one or more peptide antigens specific for SARS CoV-2 and (ii) comprises a control indicator compound that associates with RNA, DNA, or both, to thereby generate a control sample. Doing so would have a reasonable expectation of successfully improving determining the significance of the test data by comparison of a biological sample with a control reagent as a negative control (e.g. without peptide antigens for SARS-CoV-2).
Modified Sette fails to teach:
wherein the one or more peptide antigens specific for SARS CoV-2 comprise at least one peptide identified as SEQ ID NO: 1 and/or SEQ ID NO: 12;
wherein said analyzing comprises (i) measuring signal of indicator compound associated with memory T-cells in the biological sample and measuring signal of control indicator compound associated with memory T-cells in the control sample or (ii) measuring signal of indicator compound associated with RNA in the biological sample and measuring signal of control indicator compound associated with RNA in the second biological sample.
Sette teaches a control sample serves as a reference, usually a known reference, for comparison to a test sample; a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control); and controls are also valuable for determining the significance of data ([0129]). Sette teaches investing T cell reactivity against VOCs in cohorts of COVID-19 convalescent, vaccinees and unexposed controls ([0190]). Sette teaches the method for detecting an immune response to RARS-CoV-2 infections, vaccines, or therapies includes T cell response when contacting a biological sample with T cells with proteins or peptides for detection ([0015]-[0017]). Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]).
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified said analyzing of modified Sette to incorporate Sette’s teachings of control samples and controls for COVID-19 ([0129],[0190]) and detecting and analyzing T cells with assays ([0015]-[0017]) and Invitrogen’s teachings of dyes and stains for DNA or RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: wherein said analyzing comprises (i) measuring signal of indicator compound associated with memory T-cells in the biological sample and measuring signal of control indicator compound associated with memory T-cells in the control sample or (ii) measuring signal of indicator compound associated with RNA in the biological sample and measuring signal of control indicator compound associated with RNA in the second biological sample. Doing so would have a reasonable expectation of successfully allowing for detecting and measuring the T cells and improving determining the significance of the test data by comparison of signal data of the test with a negative control.
While Sette teaches various peptide antigen sequences specific for SARS-CoV-2 (pages 27-36, table 2), modified Sette fails to teach: wherein the one or more peptide antigens specific for SARS CoV-2 comprise at least one peptide identified as SEQ ID NO: 1 and/or SEQ ID NO: 12.
Wang teaches a kit, composition and method for detection of antibodies to severe acute respiratory syndrome related coronavirus (SARSr-CoV), and for diagnosis of SARSr-CoV infection (abstract). Wang teaches an urgent need for reliable and easy-to-use assays for the detection of SARS-CoV-2 ([0007]). Wang teaches a principle of ELISA including an antigen coating, binding of antigen-specific antibody, binding of secondary antibody, and color development (Fig. 1; [0083]). Wang teaches a spike protein or fragment is conjugated to a detectable entity ([0016]-[0017]). Wang teaches an antigen-binding molecule which bind to a target polypeptide/fragment encoded by a SARSr-CoV ([0127]-[0129]). Wang teaches the spike protein or fragment, i.e. peptide antigen, may comprise SEQ ID NO: 1 ([0018] and page 20, i.e. SEQ ID NO: 12, which includes the claimed SEQ ID NO: 1). Wang teaches the nucleocapsid protein, i.e. peptide antigen, of SARS-CoV-2 comprise SEQ ID NO: 12 ([0110] and page 20, i.e. SEQ ID NO: 8, which includes the claimed SEQ ID NO: 12). Wang teaches a polypeptide encoded by a SARSr-CoV is selected from a spike protein, an envelope protein, a membrane protein and a nucleocapsid protein, or a fragment of a spike protein, envelope protein, membrane protein or nucleocapsid protein ([0113]). Wang teaches assays useful for the detection of antibodies to SARS-CoV-2 spike protein S1 subunit or SARS-CoV-2 spike protein RBD ([0205]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the one or more peptide antigens of modified Sette to incorporate known sequences specific for SARS-CoV-2 peptide antigens of Wang ([0018],[0110] and page 20, SEQ ID Nos: 12 and 8, which includes the claimed SEQ ID Nos: 1 and 12 respectively) to provide: wherein the one or more peptide antigens specific for SARS CoV-2 comprise at least one peptide identified as SEQ ID NO: 1 and/or SEQ ID NO: 12. Doing so would have a reasonable expectation of successfully improving analysis of T cell interaction with specific peptide antigens for SARS CoV-2.
Additionally, simple substitution of one known equivalent elements (Sette’s one or more peptide antigens) for another (Wang’s sequences for peptide antigens of SARS CoV-2) would achieve the predicable result of analysis of T cell in response to known peptides of SARS-CoV-2 (see MPEP 2144.05 (II), In re Williams, 36 F.2d 436, 438 (CCPA 1929), “…the substitution of equivalents doing the same thing as the original invention, by substantially the same means, is not such an invention as will sustain a patent”).
Regarding claim 2, Sette further teaches where the biological sample is a blood sample ([0125] teaches the biological sample is blood; [0090] teaches “blood or PBMC sample”).
Regarding claim 4, Sette further teaches where the biological sample is a fraction of the blood sample, wherein the fraction is the buffy coat fraction or peripheral blood mononuclear cells (PBMCs) or a mixture of buffy coat fraction and PBMCs ([0125] teaches the biological sample is blood or blood fractions; [0090] teaches “blood or PBMC sample”; [0030],[0190],[0192] teaches PBMC samples).
Regarding claim 7, modified Sette fails to teach: wherein the second biological sample is from a subject, and wherein the biological sample is from the same subject or wherein the second biological sample is a portion of the biological sample.
Sette teaches a control sample serves as a reference, usually a known reference, for comparison to a test sample; a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control); and controls are also valuable for determining the significance of data ([0129]). Sette teaches investing T cell reactivity against VOCs in cohorts of COVID-19 convalescent, vaccinees and unexposed controls ([0190]). Sette teaches the method for detecting an immune response to RARS-CoV-2 infections, vaccines, or therapies includes T cell response when contacting a biological sample with T cells with proteins or peptides for detection ([0015]-[0017]). Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Sette to incorporate Sette’s teachings of control samples and controls for COVID-19 ([0129],[0190]) to provide: wherein the second biological sample is from a subject, and wherein the biological sample is from the same subject or wherein the second biological sample is a portion of the biological sample. Doing so would have a reasonable expectation of successfully improving determining the significance of the test data by using the same biological sample from a subject, that is used for testing, with a control reagent as a negative control test (e.g. without peptide antigens for SARS-CoV-2).
Regarding claim 8, modified Sette fails to teach: wherein the indicator compound and the control indicator compound are the same.
Sette teaches a control sample serves as a reference, usually a known reference, for comparison to a test sample; a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control); and controls are also valuable for determining the significance of data ([0129]). Sette teaches investing T cell reactivity against VOCs in cohorts of COVID-19 convalescent, vaccinees and unexposed controls ([0190]). Sette teaches the method for detecting an immune response to RARS-CoV-2 infections, vaccines, or therapies includes T cell response when contacting a biological sample with T cells with proteins or peptides for detection ([0015]-[0017]). Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Sette to incorporate Sette’s teachings of control samples and controls for COVID-19 ([0129],[0190]) to provide: wherein the indicator compound and the control indicator compound are the same. Doing so would have a reasonable expectation of successfully improving determining the significance of the test data by using the same biological sample from a subject, that is used for testing, with a control reagent as a negative control test (e.g. without peptide antigens for SARS-CoV-2, but with the same indicator compound). I.e. one of ordinary skill in the art would have provided the method including a test sample, which would include the sample, peptide antigens, and indicator compound, and a control sample, which would include the sample, no peptide antigens, and the indicator compound, in order to provide a control sample for referencing and comparing the data from the test sample.
Regarding claim 12, modified Sette fails to teach: wherein the indicator compound is a fluorescent dye that selectively stains RNA.
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of contacting the exposed memory T-cells with the indicator compound of modified Sette to incorporate Invitrogen’s teachings of dyes and stains selective for RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: wherein the indicator compound is a fluorescent dye that selectively stains RNA. Doing so would have a reasonable expectation of successfully improving selectivity of a cell and allowing for rapid penetration of a stain, i.e. indicator, in the T-cells for further analysis.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. contacting the exposed memory T-cells with an indicator compound and the indicator compound is a fluorescent dye that selectively stains RNA) by known methods with no change in their respective functions (i.e. detection and analysis of T-cells), and the combinations yielded nothing more than predictable results (i.e. contacting the exposed memory T-cells with an indicator compound that selectively stains RNA would yield nothing more than the obvious and predictable result of enabling rapid penetration of a stain in the T-cells for further analysis). See MPEP 2143(A).
Additionally, since Invitrogen teach labeling of cells with an indicator compound that selectively stains RNA, which has the same functional capability of labeling cells of Sette, it would have been obvious to have substituted one known element (Sette’s indicator compound) for another (Invitrogen’s indicator compound that selectively stains RNA), and the results of the substitution would have been predictable (allowing for rapid penetration of a stain, i.e. indicator, in the T-cells for further analysis). See MPEP 2143(I)(B).
Regarding claim 15, Sette further teaches wherein the memory T-cells are CD4+ and/or CD8+ T cells ([0015]-[0017] teaches the T cells are CD4+ or CD8+ cells).
Regarding claim 19, Sette further teaches wherein the one or more peptide antigens specific for SARS CoV-2 comprises between 2-20 peptide antigens specific for SARS CoV-2 or between 3-15 peptide antigens specific for SARS CoV-2 ([0015]-[0017] teaches one or more SARS-CoV-2 peptides; therefore, Sette’s teachings of “or more SARS-CoV-2 peptides” would include at least 2 peptide antigens).
Regarding claim 20, modified Sette fails to explicitly teach: wherein exposing further comprising exposing the biological sample to one or more peptide antigens non-specific for SARS CoV-2.
Sette teaches methods, uses and medicaments include modulating immune activity of a cell against a pathogen, for example, a bacteria or virus ([0044]). Sette teaches examples of non-limiting examples of coronaviruses (CoV) from which T cell epitopes can be identified include, e.g., SARS-CoV (SARS-CoV-1), MERS-CoV, and SARS-CoV-2, but also betacoronaviruses, e.g., HCoV-OC43, HCoVHKU1, HCoV-229E and alphacoronaviruses such as HCoV-NL63, and/or other coronaviruses endemic in humans ([0126]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of exposing of modified Sette to incorporate Sette’s teachings of methods involving pathogens such as bacteria or virus, and examples of coronaviruses from which T cells can be identified include viruses other than SARS-CoV2 ([0044],[0126]) to provide: wherein exposing further comprising exposing the biological sample to one or more peptide antigens non-specific for SARS CoV-2. Doing so would have a reasonable expectation of successfully improving analysis of a subject’s exposure to or vaccination with pathogens other than SARS CoV-2.
Regarding claim 22, Sette teaches a method to ascertain prior exposure of a subject to an infectious pathogen (abstract and [0015]-[0017] teaches identifying or determining presence of SARS-CoV-2 T cells which indicates an immune response relevant to SARS-CoV-2 infection or exposure in a subject), comprising:
exposing a biological sample comprising memory T-cells from the subject to one or more peptide antigens specific for the pathogen ([0015]-[0017] teaches contacting a biological sample from a subject with a composition of one or more proteins, peptides or multimers, wherein the sample includes T cells, and the protein or peptide is of SARS-CoV-2, i.e. peptide antigens specific for SARS-CoV-2);
contacting the exposed memory T-cells with an indicator compound ([0015]-[0017] teaches detecting an amount and/or the activity of, and/or the state of SARS-CoV-2-specific T-cells in the biological sample, which includes assays, which imply the contacting the T cells with an indicator; [0193] teaches T cell responses were measured with Activation Induced Marker (AIM) assays, wherein AIM assays would imply contacting the T cells with an indicator; [0139] and [0229] teaches dyes, labels, and indicators as diagnostic agents for generating detectable signals), wherein the contacting is simultaneous with or sequential to the exposing ([0015]-[0017] teaches contacting a biological sample having SARS-CoV-2-specific T-cells to one or more proteins or peptides for detection and then detecting an amount of, and/or the activity of, and/or the state of antigen-specific T cells; therefore, it is implied that the T cells are contacted with an indicator compound with or sequential to the exposing in order to properly mix and react the T cells of interest with an indicator for proper detection);
analyzing the memory T-cells for the indicator compound (]0015]-[0017] teaches detection and then detecting an amount of, and/or the activity of, and/or the state of antigen-specific T cells; [0193] teaches T cell responses were measured with Activation Induced Marker (AIM) assays, wherein AIM assays would imply contacting the T cells with an indicator; [0139] and [0229] teaches dyes, labels, and indicators as diagnostic agents for generating detectable signals; therefore, detection and analysis of the T cell response or activity includes analysis of the indicator compound for proper detection and measuring the T cells).
Sette fails to explicitly teach: contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both; and wherein said analyzing comprises measuring signal of indicator compound and measuring signal of indicator in a control sample.
Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]). Sette teaches fluorescent and oligonucleotide labels ([0058]). Sette teaches multimer staining does not kill the labelled cells, thus, cell integrity is maintained for further analysis; and isolating and/or identifying a population of CD8+ T cells having specificity for the peptide in a flow cytometry assay ([0089]). Sette teaches cells can be identified by well-known methods, including staining by a dye ([0127]). Sette a label can include a nucleic acid label comprising DNA and/or RNA, and the label can include fluorescent labels ([0231]).
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of contacting the exposed memory T-cells with the indicator compound of Sette to incorporate Sette’s teachings of assays for T-cells, fluorescent and nucleic acid labels, staining live cells for identification of T-cells in a flow cytometry assay ([0015], [0058], [0089], [0127], [0231]) and Invitrogen’s teachings of dyes and stains for DNA or RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both. Doing so would have a reasonable expectation of successfully allowing for rapid penetration of a stain, i.e. indicator, in the T-cells for further analysis.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. contacting the exposed memory T-cells with an indicator compound and an indicator compound that associates with RNA, DNA, or both) by known methods with no change in their respective functions (i.e. detection and analysis of T-cells), and the combinations yielded nothing more than predictable results (i.e. contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both would yield nothing more than the obvious and predictable result of enabling rapid penetration of a stain in the T-cells for further analysis). See MPEP 2143(A).
Additionally, since Invitrogen teach labeling of cells with an indicator compound that associates with RNA, DNA, or both, which has the same functional capability of labeling cells of Sette, it would have been obvious to have substituted one known element (Sette’s indicator compound) for another (Invitrogen’s indicator compound that associates with RNA, DNA, or both), and the results of the substitution would have been predictable (allowing for rapid penetration of a stain, i.e. indicator, in the T-cells for further analysis). See MPEP 2143(I)(B).
Modified Sette fails to teach: wherein said analyzing comprises measuring signal of indicator compound and measuring signal of indicator in a control sample.
Sette teaches a control sample serves as a reference, usually a known reference, for comparison to a test sample; a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control); and controls are also valuable for determining the significance of data ([0129]). Sette teaches investing T cell reactivity against VOCs in cohorts of COVID-19 convalescent, vaccinees and unexposed controls ([0190]). Sette teaches the method for detecting an immune response to RARS-CoV-2 infections, vaccines, or therapies includes T cell response when contacting a biological sample with T cells with proteins or peptides for detection ([0015]-[0017]). Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]).
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified said analyzing of modified Sette to incorporate Sette’s teachings of control samples and controls for COVID-19 ([0129],[0190]) and detecting and analyzing T cells with assays ([0015]-[0017]) and Invitrogen’s teachings of dyes and stains for DNA or RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: wherein said analyzing comprises measuring signal of indicator compound and measuring signal of indicator in a control sample. Doing so would have a reasonable expectation of successfully allowing for detecting and measuring the T cells and improving determining the significance of the test data by comparison of signal data of the test with a negative control.
Regarding claim 29, modified Sette fails to explicitly teach: wherein the method further comprises exposing a second biological sample comprising memory T-cells to a control reagent that (i) lacks the one or more peptide antigens specific for the pathogen and (ii) comprises a control indicator compound that associates with RNA, DNA, or both, to thereby generate the control sample.
Sette teaches a control sample serves as a reference, usually a known reference, for comparison to a test sample; a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control); and controls are also valuable for determining the significance of data ([0129]). Sette teaches investing T cell reactivity against VOCs in cohorts of COVID-19 convalescent, vaccinees and unexposed controls ([0190]). Sette teaches the method for detecting an immune response to RARS-CoV-2 infections, vaccines, or therapies includes T cell response when contacting a biological sample with T cells with proteins or peptides for detection ([0015]-[0017]). Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]). Sette teaches fluorescent and oligonucleotide labels ([0058]). Sette teaches multimer staining does not kill the labelled cells, thus, cell integrity is maintained for further analysis; and isolating and/or identifying a population of CD8+ T cells having specificity for the peptide in a flow cytometry assay ([0089]). Sette teaches cells can be identified by well-known methods, including staining by a dye ([0127]). Sette a label can include a nucleic acid label comprising DNA and/or RNA, and the label can include fluorescent labels ([0231]).
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Sette to incorporate Sette’s teachings of assays for T-cells, fluorescent and nucleic acid labels, staining live cells for identification of T-cells in a flow cytometry assay ([0015], [0058], [0089], [0127], [0231]) and controls for COVID-19 ([0129],[0190]) and Invitrogen’s teachings of dyes and stains for DNA or RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: wherein the method further comprises exposing a second biological sample comprising memory T-cells to a control reagent that (i) lacks the one or more peptide antigens specific for the pathogen and (ii) comprises a control indicator compound that associates with RNA, DNA, or both, to thereby generate the control sample. Doing so would have a reasonable expectation of successfully improving determining the significance of the test data by comparison of a biological sample with a control reagent as a negative control (e.g. without peptide antigens for SARS-CoV-2).
Regarding claim 42, Sette further teaches wherein the one or more peptide antigens specific for the pathogen comprises between 2-20 peptide antigens specific for the pathogen or between 3-15 peptide antigens specific for the pathogen ([0015]-[0017] teaches one or more SARS-CoV-2 peptides; therefore, Sette’s teachings of “or more SARS-CoV-2 peptides” would include at least 2 peptide antigens).
Regarding claim 43, modified Sette fails to explicitly teach: wherein exposing further comprising exposing the biological sample to one or more peptide antigens non-specific for the pathogen.
Sette teaches methods, uses and medicaments include modulating immune activity of a cell against a pathogen, for example, a bacteria or virus ([0044]). Sette teaches examples of non-limiting examples of coronaviruses (CoV) from which T cell epitopes can be identified include, e.g., SARS-CoV (SARS-CoV-1), MERS-CoV, and SARS-CoV-2, but also betacoronaviruses, e.g., HCoV-OC43, HCoVHKU1, HCoV-229E and alphacoronaviruses such as HCoV-NL63, and/or other coronaviruses endemic in humans ([0126]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of exposing of modified Sette to incorporate Sette’s teachings of methods involving pathogens such as bacteria or virus, and examples of coronaviruses from which T cells can be identified include viruses other than SARS-CoV2 ([0044],[0126]) to provide: wherein exposing further comprising exposing the biological sample to one or more peptide antigens non-specific for SARS CoV-2. Doing so would have a reasonable expectation of successfully improving analysis of a subject’s exposure to or vaccination with pathogens other than SARS CoV-2.
Regarding claim 44, Sette teaches a method to identify presence of T cells specific for an infectious agent in a sample from a subject to ascertain prior exposure to, or vaccination with, the infectious agent (abstract and [0015]-[0017] teaches identifying or determining presence of SARS-CoV-2 T cells which indicates an immune response relevant to SARS-CoV-2 infection or exposure in a subject), comprising:
exposing a biological sample comprising memory T-cells from the subject to one or more peptide antigens specific for an infectious agent ([0015]-[0017] teaches contacting a biological sample from a subject with a composition of composition of one or more proteins, peptides or multimers, wherein the sample includes T cells, and the protein or peptide is of SARS-CoV-2, i.e. peptide antigens specific for SARS-CoV-2);
contacting the exposed memory T-cells with an indicator compound 0015]-[0017] teaches detecting an amount and/or the activity of, and/or the state of SARS-CoV-2-specific T-cells in the biological sample, which includes assays, which imply the contacting the T cells with an indicator; [0193] teaches T cell responses were measured with Activation Induced Marker (AIM) assays, wherein AIM assays would imply contacting the T cells with an indicator; [0139] and [0229] teaches dyes, labels, and indicators as diagnostic agents for generating detectable signals), wherein the contacting is simultaneous with or sequential to the exposing ([0015]-[0017] teaches contacting a biological sample having SARS-CoV-2-specific T-cells to one or more proteins or peptides for detection and then detecting an amount of, and/or the activity of, and/or the state of antigen-specific T cells; therefore, it is implied that the T cells are contacted with an indicator compound with or sequential to the exposing in order to properly mix and react the T cells of interest with an indicator for proper detection);
analyzing the memory T-cells for the indicator compound ([0015]-[0017] teaches detection and then detecting an amount of, and/or the activity of, and/or the state of antigen-specific T cells; [0193] teaches T cell responses were measured with Activation Induced Marker (AIM) assays, wherein AIM assays would imply contacting the T cells with an indicator; [0139] and [0229] teaches dyes, labels, and indicators as diagnostic agents for generating detectable signals; therefore, detection and analysis of the T cell response or activity includes analysis of the indicator compound for proper detection and measuring the T cells).
Sette fails to explicitly teach: contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both; and wherein said analyzing comprises measuring signal of indicator compound and measuring signal of indicator in a control sample.
Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]). Sette teaches fluorescent and oligonucleotide labels ([0058]). Sette teaches multimer staining does not kill the labelled cells, thus, cell integrity is maintained for further analysis; and isolating and/or identifying a population of CD8+ T cells having specificity for the peptide in a flow cytometry assay ([0089]). Sette teaches cells can be identified by well-known methods, including staining by a dye ([0127]). Sette a label can include a nucleic acid label comprising DNA and/or RNA, and the label can include fluorescent labels ([0231]).
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of contacting the exposed memory T-cells with the indicator compound of Sette to incorporate Sette’s teachings of assays for T-cells, fluorescent and nucleic acid labels, staining live cells for identification of T-cells in a flow cytometry assay ([0015], [0058], [0089], [0127], [0231]) and Invitrogen’s teachings of dyes and stains for DNA or RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both. Doing so would have a reasonable expectation of successfully allowing for rapid penetration of a stain, i.e. indicator, in the T-cells for further analysis.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. contacting the exposed memory T-cells with an indicator compound and an indicator compound that associates with RNA, DNA, or both) by known methods with no change in their respective functions (i.e. detection and analysis of T-cells), and the combinations yielded nothing more than predictable results (i.e. contacting the exposed memory T-cells with an indicator compound that associates with RNA, DNA, or both would yield nothing more than the obvious and predictable result of enabling rapid penetration of a stain in the T-cells for further analysis). See MPEP 2143(A).
Additionally, since Invitrogen teach labeling of cells with an indicator compound that associates with RNA, DNA, or both, which has the same functional capability of labeling cells of Sette, it would have been obvious to have substituted one known element (Sette’s indicator compound) for another (Invitrogen’s indicator compound that associates with RNA, DNA, or both), and the results of the substitution would have been predictable (allowing for rapid penetration of a stain, i.e. indicator, in the T-cells for further analysis). See MPEP 2143(I)(B).
Modified Sette fails to teach: wherein said analyzing comprises measuring signal of indicator compound and measuring signal of indicator in a control sample.
Sette teaches a control sample serves as a reference, usually a known reference, for comparison to a test sample; a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control); and controls are also valuable for determining the significance of data ([0129]). Sette teaches investing T cell reactivity against VOCs in cohorts of COVID-19 convalescent, vaccinees and unexposed controls ([0190]). Sette teaches the method for detecting an immune response to RARS-CoV-2 infections, vaccines, or therapies includes T cell response when contacting a biological sample with T cells with proteins or peptides for detection ([0015]-[0017]). Sette teaches detecting an amount or a relative amount of, and/or the activity of, and/or the state of SARS-CoV-2 antigen-specific T-cells in the biological sample comprises measuring T cell proliferation, and various assays including ELISA, immunofluorescence assay, FACS analysis, and reporter assay ([0015]).
Invitrogen teaches fluorescent dye-based assays for cell viability are reliable and easy to perform (page 655, left column , third paragraph), which includes proliferation assay kits to rapidly monitor presence of newly replicated DNA or total nucleic acid content (page 655, left column, third paragraph). Invitrogen teaches viability assessment of cells include nucleic acid stains (page 660, last paragraph). Invitrogen teaches SYTO nucleic acid stains for live cells(page 664, second paragraph), where SYTO cell stains can be selective for RNA (page 665, paragraphs 1-3). Invitrogen teaches SYTO nucleic acid stains rapidly penetrates the membranes of live cells, which can then be identified by their characteristic morphology, or in the case of flow cytometric applications, by their light-scattering properties (page 700, second paragraph). Invitrogen teaches SYTO can stain DNA or RNA (page 700, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified said analyzing of modified Sette to incorporate Sette’s teachings of control samples and controls for COVID-19 ([0129],[0190]) and detecting and analyzing T cells with assays ([0015]-[0017]) and Invitrogen’s teachings of dyes and stains for DNA or RNA for viability and proliferation assessment of cells (page 655, left column, third paragraph ; page 660, last paragraph ; page 64, second paragraph - page 665, third paragraph; page 700, paragraphs 1-3) to provide: wherein said analyzing comprises measuring signal of indicator compound and measuring signal of indicator in a control sample. Doing so would have a reasonable expectation of successfully allowing for detecting and measuring the T cells and improving determining the significance of the test data by comparison of signal data of the test with a negative control.
Claims 5 and 28 are rejected under 35 U.S.C. 103 as being unpatentable over in view of Invitrogen and Wang as applied to claims 1 and 22 above, and further in view of Wheeler et al. (US 20090203063 A1).
Regarding claim 5, Sette further teaches wherein said exposing to one or more peptide antigens specific for SARS CoV-2 comprises exposing to a solution comprising the one or more peptide antigens ([0015]-[0017] teaches contacting the biological sample with a composition of composition of one or more proteins, peptides or multimers, and the protein or peptide is of SARS-CoV-2, i.e. peptide antigens).
Modified Sette fails to teach: wherein said exposing to one or more peptide antigens specific for SARS CoV-2 comprises exposing to a solution comprising the indicator compound and one or more of a buffer, an energy source for the cells, and a balanced salt solution, thereby simultaneously with said exposing, contacting the T cells with the indicator compound.
Wheeler teaches a method for cell based assays and cell culture (abstract). Wheeler teaches cells can include blood cells ([0118]). Wheeler teaches analysis of cells by staining with viability dyes ([0067]). Wheeler teaches cells were cultured and assayed on a device for viability ([0115]). Wheeler teaches an embodiment of a suspension of cells, and a droplet including a cell assay reagent that include cell culture media, proteins, cell process agonists or antagonists, labeling agents fluorescent dyes, viability dyes, phosphate buffered saline, balanced salt solutions, nutrient mixtures, and any combination thereof ([0117]). Wheeler teaches droplets with cells are manipulated or assayed simultaneously with multiple reagents ([0011]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the step of exposing of modified Sette to incorporate the Wheeler’s teachings of reagents for cells that can include buffers, energy sources, and balanced salt solutions, and simultaneous manipulation or assay of cells with reagents ([0117],[0011]) to provide: wherein said exposing to one or more peptide antigens specific for SARS CoV-2 comprises exposing to a solution comprising the indicator compound and one or more of a buffer, an energy source for the cells, and a balanced salt solution, thereby simultaneously with said exposing, contacting the T cells with the indicator compound. Doing so would have a reasonable expectation of successfully improving efficiency and simplicity of exposing the biological sample to a reagent solution that includes desired and necessary components (e.g. peptide antigen, buffer, energy source, balanced salt solution), which would also ensure optimized environmental conditions for cell processing and analysis.
Regarding claim 28, Sette further teaches wherein said exposing to one or more peptide antigens specific for SARS CoV-2 comprises exposing to a solution comprising the one or more peptide antigens ([0015]-[0017] teaches contacting the biological sample with a composition of composition of one or more proteins, peptides or multimers, and the protein or peptide is of SARS-CoV-2, i.e. peptide antigens).
Modified Sette fails to teach: wherein said exposing to one or more peptide antigens specific for the pathogen comprises exposing to a solution comprising the indicator compound and one or more of a buffer, an energy source for the cells, and a balanced salt solution, thereby simultaneously with said exposing, contacting the T cells with the indicator compound.
Wheeler teaches a method for cell based assays and cell culture (abstract). Wheeler teaches cells can include blood cells ([0118]). Wheeler teaches analysis of cells by staining with viability dyes ([0067]). Wheeler teaches cells were cultured and assayed on a device for viability ([0115]). Wheeler teaches an embodiment of a suspension of cells, and a droplet including a cell assay reagent that include cell culture media, proteins, cell process agonists or antagonists, labeling agents fluorescent dyes, viability dyes, phosphate buffered saline, balanced salt solutions, nutrient mixtures, and any combination thereof ([0117]). Wheeler teaches droplets with cells are manipulated or assayed simultaneously with multiple reagents ([0011]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the step of exposing of modified Sette to incorporate the Wheeler’s teachings of reagents for cells that can include buffers, energy sources, and balanced salt solutions, and simultaneous manipulation or assay of cells with reagents ([0117],[0011]) to provide: wherein said exposing to one or more peptide antigens specific for the pathogen comprises exposing to a solution comprising the indicator compound and one or more of a buffer, an energy source for the cells, and a balanced salt solution, thereby simultaneously with said exposing, contacting the T cells with the indicator compound. Doing so would have a reasonable expectation of successfully improving efficiency and simplicity of exposing the biological sample to a reagent solution that includes desired and necessary components (e.g. peptide antigen, buffer, energy source, balanced salt solution), which would also ensure optimized environmental conditions for cell processing and analysis.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Sette in view of Invitrogen and Wang as applied to claim 1 above, and further in view of Balin et al. (US 20190117689 A1).
Regarding claim 11, modified Sette fails to teach: wherein said analyzing comprises measuring an RNA signal based on signal of indicator compound associated with RNA, measuring a DNA signal based on signal of indicator compound associated with DNA, and determining a ratio of RNA signal to DNA signal or of DNA signal to RNA signal.
Balin teaches compositions comprising T cells (abstract). Balin teaches T cells were enriched from PBMCs and stained ([0031],[0040]). Balin teaches RNA and DNA was isolated from the target cells and the ratio of bacterial RNA to DNA was calculated to determine alive bacteria; which was used to calculate the percent killing as compared with infected MDMs alone without T cells achieved under each condition ([0034]). Balin teaches determining the RNA to DNA ratio to measure viability ([0106]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of analyzing of modified Sette to incorporate Balin’s teachings of analyzing and determining ratios between RNA and DNA ([0034],[0106]) to provide: wherein said analyzing comprises measuring an RNA signal based on signal of indicator compound associated with RNA, measuring a DNA signal based on signal of indicator compound associated with DNA, and determining a ratio of RNA signal to DNA signal or of DNA signal to RNA signal. Doing so would have a reasonable expectation of successfully improving analysis of a biological sample including T cells as discussed by Balin.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Sette in view of Invitrogen and Wang as applied to claim 1 above, and further in view of Maples et al. (US 20040185447 A1).
Regarding claim 13, modified Sette further teaches wherein said contacting comprises contacting the exposed memory T-cells with a first indicator compound that selectively stains RNA or DNA (see above claim 1). Modified Sette fails to teach wherein said contacting comprises contacting the exposed memory T-cells with a second indicator compound that non-specifically stains RNA and DNA.
Maples teaches a composition for enhancing differential staining of RNA and DNA in a sample comprising cells, a first dye that can bind specific and non-specific binding sites, and a second dye that competes to bind to nonspecific binding sites (abstract). Maples teaches the composition allows for enhanced differential staining of nucleic acids and improved automated analysis ([0026]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the step of contacting of modified Sette to incorporate Maples’ teachings of enhancing differential staining of RNA and DNA using a second dye that bind to nonspecific binding sites (abstract; [0026]) to provide: wherein said contacting comprises contacting the exposed memory T-cells with a second indicator compound that non-specifically stains RNA and DNA. Doing so would have a reasonable expectation of successfully enhancing differential staining of RNA and DNA, and therefore allowing for improved automated analysis of the biological sample.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Sette in view of Invitrogen and Wang as applied to claim 1 above, and further in view of Stern et al. (US 20160047816 A1).
Regarding claim 14, modified Sette fails to teach: wherein the indicator compound has an excitation between about 330-360 nm and an emission between about 500-600 nm.
Stern teaches assay methods for detecting or quantifying analytes in a sample comprising signaling agents (abstract), wherein the signaling agents includes a dye or fluorophore that releases a detectable signal ([0084]). Stern teaches biological samples can include blood ([0181]). Stern teaches a binding agent can include DNA and RNA ([0168]). Stern teaches exemplary indicator compounds ([0154]) that includes indicator compounds that has an excitation between about 330-360 nm and an emission between about 500-600 nm (page 16, table 1A, Dansyl, Dansyl Amine, Dansyl Cadaverine, Dansyl DHPE, Dopamine; page 17, table 1A, Fura-2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the indicator compound of modified Sette to incorporate the teachings of indicator compounds of Stern ([0154]; pages 16-17, table 1A) to provide: wherein the indicator compound has an excitation between about 330-360 nm and an emission between about 500-600 nm. Doing so would have a reasonable expectation of successfully optimizing the excitation and emission of the indicator compound for optical analysis.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. the indicator compound with an excitation between about 330-360 nm and an emission between about 500-600 nm) by known methods with no change in their respective functions (i.e. optical excitation and detection of emission of the indicator compound), and the combinations yielded nothing more than predictable results (i.e. providing the claimed indicator compound with the range of excitation and emission would yield nothing more than the obvious and predictable result of enabling specific excitation and detection of the indicator compound). See MPEP 2143(A).
Additionally, since Stern teaches a recognized problem or need of choosing appropriate indicator compounds ([0084],[0154]; table 1A), and Stern provides a finite number of identified predictable potential solutions for indicator compounds ([0154], pages 16-17, table 1A), it would have been obvious to choose wherein the indicator compound has an excitation between about 330-360 nm and an emission between about 500-600 nm from a finite number of identified, predictable indicator compounds in the art of dyeing and staining, i.e. it would have been obvious to try the specific indicator compound with a reasonable expectation of successfully optimizing the excitation and emission of the indicator compound for optical analysis. See MPEP 2143(I)(E).
Claims 16-18 are rejected under 35 U.S.C. 103 as being unpatentable over Sette in view of Invitrogen and Wang as applied to claim 1 above, and further in view of Peng et al. (PENG ET AL., "Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19", Nature Immunology, Vol. 21, No. 11, pp. 1336- 1345 (2020); cited in the IDS filed 02/12/2024).
Regarding claim 16, modified Sette fails to teach: the method of claim 1, further comprising after said contacting and before said analyzing, incubating for a period of time.
Peng teaches analysis of T cell responses in response to SARS-CoV-2 (abstract). Peng teaches PBMCs were labeled and then incubated for 15 minutes at 37° C, therefore allowing sample analysis by flow cytometry (page 10, section “Pentamer phenotyping”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Sette to incorporate Peng’s teachings of analysis of biological samples including PBMCs and incubation of the sample (page 10, section “Pentamer phenotyping”) to provide: the method of claim 1, further comprising after said contacting and before said analyzing, incubating for a period of time (i.e. 15 minutes). Doing so would have a reasonable expectation of successfully improving desired cellular reaction and staining prior to optical analysis.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. after said contacting and before said analyzing, incubating for a period of time) by known methods with no change in their respective functions (i.e. allowing for a biological sample to react with reagents and stains), and the combinations yielded nothing more than predictable results (i.e. providing after said contacting and before said analyzing, incubating for a period of time would yield nothing more than the obvious and predictable result of enabling desired cellular reaction and staining prior to optical analysis). See MPEP 2143(A).
Regarding claim 17, modified Sette fails to teach: wherein said incubating is at a temperature of between about 25-40° C.
Peng teaches analysis of T cell responses in response to SARS-CoV-2 (abstract). Peng teaches PBMCs were labeled and then incubated for 15 minutes at 37° C, therefore allowing sample analysis by flow cytometry (page 10, section “Pentamer phenotyping”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Sette to incorporate Peng’s teachings of analysis of biological samples including PBMCs and incubation of the sample at 37° C (page 10, section “Pentamer phenotyping”) to provide: wherein said incubating is at a temperature of between about 25-40° C. Doing so would have a reasonable expectation of successfully improving desired cellular reaction and staining prior to optical analysis.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. incubating between about 25-40° C) by known methods with no change in their respective functions (i.e. allowing for a biological sample to react with reagents and stains), and the combinations yielded nothing more than predictable results (i.e. providing incubating between about 25-40° C would yield nothing more than the obvious and predictable result of enabling desired cellular reaction and staining prior to optical analysis). See MPEP 2143(A).
Regarding claim 18, modified Sette further teaches wherein said period of time is between about 10-60 minutes or between about 10-30 minutes (see above claim 16; modified Sette in combination of Peng provides incubation for 15 minutes; Peng, “Pentamer phenotyping”, incubation for 15 minutes).
Response to Arguments
Applicant’s arguments, see page 6, filed 08/13/2026, with respect to the claim objections and rejections under 35 U.S.C. 112(b) and 101 have been fully considered and are persuasive. The claim objections and rejections under 35 U.S.C. 112(b) and 101 of 05/13/2026 have been withdrawn.
Applicant’s arguments, see pages 6-8, filed 08/13/2026, with respect to the rejection(s) of the claims under 35 U.S.C. 103, specifically regarding amended claim 1 requiring SEQ ID NO: 1 and/or SEQ ID NO: 12, have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Sette et al. (US 20240409587 A; effectively filed 04/12/2021) in view of Invitrogen (Invitrogen, "Assays for cell viability, proliferation and function", Invitrogen, Molecular Probes TM Handbook, 11th Edition, Chapter 15, 89 pages (2010); cited in the IDS filed 02/12/2024) and Wang (US 20210302434 A1; effectively filed 03/25/2020).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Grifoni et al. (Grifoni et al., “A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2”, Cell Host & Microbe 27, 671–680, April 8, 2020) teaches target candidate targets for immune responses to SARS-CoV-2 (abstract). Grifoni teaches known dominant SARS-CoV B cell epitope regions including SEQ ID NO: 1 (table 4, first sequence).
Ying (US 20220218816 A1; effectively filed 04/16/2020) teaches nucleic acid molecules that can be used for the management, prevention, and treatment of coronavirus infection ([0002]). Ying teaches the non-naturally occurring nucleic acids encode a viral peptide or protein derived from coronavirus SARS-CoV-2 ([0004]). Ying teaches quantification of SARS-CoV-2 protein antigen ([0032]). Ying teaches exemplary SARS-CoV-2 native antigen sequences ([0148]; Table 1). Ying teaches an encoded S protein of coronavirus SARS-CoV-2 comprises an amino acid sequence of SEQ ID NO: 1 ([0177] and Table 4 i.e. SEQ ID NO: 40, which comprises the claimed SEQ ID NO: 1; Table 4 teaches exemplary sequences of signal peptides and SARS-CoV-2 antigens). Ying teaches the viral peptide or protein is the N protein which comprises SEQ ID NO: 12 ([0017] and Table 1, i.e. SEQ ID NO: 18, which comprises the claimed SEQ ID NO: 12).
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to HENRY H NGUYEN whose telephone number is (571)272-2338. The examiner can normally be reached M-F 7:30A-5:00P.
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/HENRY H NGUYEN/Primary Examiner, Art Unit 1758
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