Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Acknowledgement is hereby made of receipt and entry of the communication filed on Jul. 6, 2026. Claims 1, 4-7 and 28-29 are pending and currently examined.
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.
(Previous Rejection – Maintained and Modified Necessitated by Amendment) Claims 1, 4-7 and 28-29 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
The base claim 1 recites “A method for detecting in treating a subject in need thereof comprising: detecting the presence of T-cells specific for a particular virus, wherein: for SARS-CoV-2 wherein the detecting consists essentially of: receiving a tissue sample from said subject; stimulating the tissue sample via incubation with at least one polypeptide or polypeptide fragment derived from the SARS-CoV-2 spike protein; diluting the stimulated tissue sample in a ratio from about 1:1 to 1:5 with a diluent that is protease free; performing at least one quantitative PCR (qPCR) assay on said diluted tissue sample; quantifying the relative concentration of CXCL10 mRNA in the sample; comparing said results with a reference standard; and determining from the results of said comparison whether the subject has T-cells specific for SARS-CoV-2; and treating said subject in response to said comparing.” The claim is not clear for at least the following reasons.
A. Neither the claim nor the specification defines the term “relative concentration of CXCL10 mRNA”. It is noted that a concentration of CXCL10 mRNA can be obtained by qPCR as claimed. However, it is not clear how the concentration thus obtained is related to a “relative concentration.”
B. The term “said results” does not have antecedent basis, so it is clear what this term refers to.
C. Neither the claim nor the specification defines the terms “reference standard”, so it is not clear what it can be and how an undefined reference is to be used for comparison with “said results.”
D. By reciting “performing at least one quantitative PCR (qPCR) assay on said diluted tissue sample”, the claim does not make it clear what the qPCR target is or what is amplified by the PCR. Therefore, it is not clear what the qPCR is, why it is performed, how it is performed, and how the qPCR is related to the succeeding “quantifying” and “comparing” steps.
Moreover, the phrase “on said diluted tissue sample” also makes the performing step not clear since it is not clear if the qPCR must be performed directly on the diluted tissue sample, or it also encompasses a qPCR with the diluted tissue sample being processed. To expedite examination, the claims are interpreted as requiring that the qPCR is performed directly on a diluted tissue sample obtained in the prior steps without processing.
E. By reciting “determining from the results of said comparison whether the subject has T-cells specific for SARS-CoV-2”, it is not clear how the determination is to be made. E.g., it is not clear if it requires comparison between “the relative concentration of CXCL10 mRNA” with the “reference standard.” And, if the answer is yes, it is not clear how the comparison leads to the determination of “whether the subject has T-cells specific for SARS-CoV-2.”
In summary, the claim specifies a qPCR assay on a stimulated tissue sample from the subject without specifying what marker or molecule the qPCR assay is to quantify. On the other hand, the claims specify results that quantify the relative concentration of CXCL10 mRNAs in the sample without specifying how the “results” are obtained. It appears that the claimed “results” are obtained by the claimed qPCR assay. If yes, Applicant must clarify and make proper amendments.
Claims 1 and 4-7 use the word “about” in defining the ratio for dilution or range for concentration, which render the claimed ranges unclear. The Specification defines the word about in paragraph 15, shown below:
[015] As used herein, the term "about" or "approximately" means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, "about" can mean within 3 or more than 3 standard deviations, per the practice in the art. Alternatively, "about" can mean a range of up to 20%, preferably up to 10%, more preferably up to 5%, and more preferably still up to 1 % of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, preferably within 5-fold, and more preferably within 2-fold, of a value.
Instead of providing clear and exclusive definition, the teaching above gives examples for what “about” can mean. It is not clear what ranges/deviations the claimed concentration can encompass besides those described ranges/deviations.
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 of this title, 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.
(Previous Rejection – Withdrawn) Claims 1 and 31 were rejected under 35 U.S.C. 103 as being unpatentable over Deml et al. (US 2013/0288229 A1, published on Oct. 31, 2013).
(Previous Rejection – Withdrawn) Claims 2-7, 21-23, 26-30 and 32 were rejected under 35 U.S.C. 103 as being unpatentable over Deml et al. (US 2013/0288229 A1, published on Oct. 31, 2013) in view of Whelan et al. (US 2023/0346919 A1, published Nov. 2, 2023; PCT filed on Apr. 14, 2021).
The above rejections are withdrawn in view of the amendment filed on Jul. 6, 2026.
(New Rejection – Necessitated by Amendment) Claims 1, 4-7 and 28-29 are rejected under 35 U.S.C. 103 as being unpatentable over Deml et al. (US 2013/0288229 A1, published on Oct. 31, 2013) in view of Whelan et al. (US 2023/0346919 A1, published Nov. 2, 2023; PCT filed on Apr. 14, 2021), and further in view of Cai et al. (Sci Rep 8, 3410 (2018)).
The claims are described and discussed in the 112(b) rejection above.
Deml teaches an invention relating to a method for detection, differentiation and quantification of T cell populations, comprising the steps of: a) contacting a first aliquot of a body fluid of an individual with at least one antigen, wherein the body fluid contains antigen presenting cells (APC) and T cells, b) incubating the first aliquot with at least one antigen for a certain period of time, c) detection and differentiation of the T cell population by detecting in the first aliquot and in a second aliquot of the body fluid of the individual, which has not been incubated with the at least one antigen, at least a first marker of the APC induced by T cells in a specific T cell population using reverse transcription quantitative real time polymerase chain reaction (RT-qPCR), and d) detection and quantification of the T cell population by determining the ratio of the detected marker of the APC of the first aliquot to the second aliquot as well as a kit for performing the method. See Abstract.
Fig. 1B of Deml presents a schematic of the invention. See below:
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It shows that the mRNA of a marker gene is detected by RT-qPCR, showing an increased expression of the marker when an APC is stimulated by a disease pathogen-specific polypeptide (i.e., a disease antigen) in presence of an activated Th cell.
Deml teaches that the antigen can be an antigen from a bacteria, virus, plant, animal, fungi or parasite (see [0108], and that, more specifically, the antigen can be a polypeptide of the cytomegalovirus (CMV), Epstein-Barr Virus (EBY), Hepatitis B virus (HBV), Hepatitis C virus (HCV), human immunodeficiency virus (HIV), parvovirus B19, Varicella Zoster virus (VZV), vaccinia virus, adenovirus, JC- and BK-virus, A, B, C type influenza virus, Mycobacterium tuberculosis, borrelia, Toxoplasma gondii or aspergilli or a tumour or auto antigen (see [0109]). Deml further teaches that the marker of the APC can be a member of the CXCL family e.g. CXCL9, CXCL10, or CXCL11, among others. See [0135].
FIG. 19 of Deml shows the relative increase in expression of the genes FCGRlABC, CXCL9, CXCL10, CXCL11 in samples of a healthy volunteer and of a patient with a latent TB after stimulation with tuberculin PPD in comparison to the respective unstimulated samples. The real time qPCR was performed using the SYBR green system. On the x-axis the genes and individuals, respectively, are plotted. The y-axis shows the relative increase in expression (2DCq). See [0055].
Accordingly, Deml teaches a method of detecting and/or differentiating T-cells from a subject specific for a disease antigen, including a virus antigen, comprising stimulating a tissue sample (here, a body fluid) from the subject with an antigen, including a virus antigen, performing at least one quantitative PCR (qPCR) assay on mRNA of markers, including the marker CXCL10, from a stimulated tissue sample, obtaining results that quantify the relative concentration of CXCL10 mRNAs in the sample, and comparing said results with a reference standard (which may be results obtained from a healthy subject or a unstimulated aliquot of tissue sample, see Fig. 19). Such a detection/differentiation of T-cells in a sample from a subject can also be considered as “gauging the immune status of a subject with respect to a specific virus”.
However, even if Deml teaches that various different viruses, bacteria and other pathogens may be included in the disclosed invention, it is silent on SARS-CoV-2; Deml is also silent on performing a qPCR assay directly on a diluted tissue sample, instead, it teaches that RT-PCR analysis is performed on RNA isolated from samples. See [0148].
Whelan teaches an invention relating to compositions and methods useful for vaccinating for or preventing a Coronavinus infection, antibody screening, and
variant prediction. The disclosure also provides for compositions and methods useful for sera diagnostics, treatment screening, and methods of making the compositions. See Abstract. Whelan teaches that among the various aspects of the disclosure is the provision of compositions and methods for using and making Coronavirus (SARS CoV-2) vaccines and screening assays. 1. A recombinant vesicular stomatitis virus (rVSV) comprising at least a portion of a coronavirus spike protein (S) or a functional fragment or a functional variant thereof. An aspect of the disclosure provides for a recombinant vesicular stomatitis virus (rVSV) construct or vaccine platform comprising: at least a portion of a vesicular stomatitis virus (VSV); and/or at least a portion of, a functional fragment of, or functional variant of the spike (S) of SARS-CoV-2 (SEQ ID NO: 1) and/or at least about 80% identical to SEQ ID NO: 1. Another aspect of the disclosure provides for a recombinant vesicular stomatitis virus (rVSV) comprising in its genome a nucleic acid sequence encoding at least a portion of, a functional fragment of, or functional variant of the spike (S) of SARS-CoV-2 (SEQ ID NO: 1) and/or at least about 80% identical to a functional portion or fragment of SEQ ID NO: 1. See [0005].
Whelan further teaches that animals immunized with one or two doses of VSV-eGFP-SARS-CoV-2 had significantly lower levels of pro-inflammatory cytokine and chemokine mRNA than did VSV-eGFP vaccinated mice. Specifically, type I and Ill interferons (IFN-g and IFN-l) were decreased early during infection in both one-dose and two-dose groups of mice immunized with VSV-eGFP-SARS-CoV-2. Although there were no detectable differences in IFN-b or TNF-a levels between groups, IL-6 and IL-1b were lower at 4 dpi after VSV-eGFP-SARS-CoV-2 vaccination. Similarly, levels of mRNAs encoding chemokines CXCL1, CXCL10, and CXCL11, which recruit immune cells to the lung, were decreased at 4 dpi in VSV-eGFP-SARS-CoV-2 in comparison with VSV-eGFP immunized mice. See [0168].
Accordingly, teachings of Whelan indicate that SARS-CoV-2 is virus of importance, and that studies on immune response against SARS-CoV-2 in a subject are desired.
Cai teaches that “[v]arious methods for DNA and RNA extraction from WHB have been developed. However, these methods are generally time-consuming and labor-intensive and increase cost. Furthermore, the multiple sample processing steps involved in these methods increase the risk of cross-contamination and lead to the loss of target. In addition, some PCR inhibitors still exist even after DNA and RNA extraction.” See page 1, para 2.
Cai teaches a study on direct DNA and RNA detection from large volumes of whole human blood using Thermus thermophilus (Tth). Thermus thermophilus (Tth) polymerase is resistant to several common PCR inhibitors and exhibits reverse transcriptase activity in the presence of manganese ions. In combination with optimized concentrations of magnesium ions and manganese ions, Tth polymerase enabled efficient detection of DNA and RNA from large volumes of WHB treated with various anticoagulants. The applicability of these methods was further demonstrated by examining WHB specimens collected from different healthy individuals and those stored under a variety of conditions. The detection limit of these methods was determined by detecting exogenous DNA, RNA, and bacteria spiked in WHB. The results of the developed methods can be obtained within 4 hours, making them possible for rapid and accurate detection of disease-causing agents from WHB. See Abstract.
Accordingly, teachings of Cai indicate that it was contemplated and practiced before the effective filing date of the current invention to develop PCR assays, including RT-PCR assays, that are directly performed on a tissue sample (here, whole blood) to same time and reduce potential contamination.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the current invention to expand the studies of Deml to include the SARS-CoV-2 virus, disclosed in Whelan, so that the immune response status related to SARS-CoV-2 infection and/or vaccination can be determined using the invention of Deml. One of skill in the art would also have found it obvious to introduce the practice of performing PCR reactions directly on tissue samples taught in Cai into the studies suggested by the teachings of Deml and Cai to reducing time and risk of contamination comparing to assays that include prior sample processing for nucleic acid extraction. There is a reasonable expectation of success that the method taught in Deml can be applied to a subject in need of a determination of immune response status against SARS-CoV-2, and qPCR assay efficiency directly on diluted tissue samples can be tested, based on teachings of Deml, Whelan and Cai.
As to the limitation of “diluting the stimulated tissue sample in a ratio from about 1:1 to 1:5 with a diluent that is protease free; performing at least one quantitative PCR (qPCR) assay on said diluted tissue sample”, Deml, Whelan and Cai are silent on how samples are to be diluted for qPCR. It would have been prima facie obvious for one of ordinary skill in the art to determine how to dilute a qPCR sample through routine experimental optimization. Processing, including dilution, of test samples for PCR analysis is routine in the art, especially when PCR inhibitors are expected in the original tissue samples. This is especially true for the claimed invention where the sample, dilution solution and qPCR process are highly generic. As to the exclusion of protease in dilution solution, one of skill in the art would have found it obvious to do so to avoid damage of PCR reaction enzymes by contaminating protease.
Regarding claims 28-29, the claims recite “comprising providing a SARS-CoV-2 vaccination to said subject” (claim 28) and “comprising administering to said subject a therapeutic selected from the group consisting of: antivirals, corticosteroids, monoclonal antibodies, NSAIDs, convalescent plasma, or antidepressants” (claim 29). Since the claims do not correlate the specified vaccination/treatments with the determination specified in claim 1, it would have been well within the purview of one of ordinary skill in the art to determine what treatment measure to perform based on the artisan’s judgement as well as situations of the subject.
Response to Applicant’s Arguments
Applicant’s arguments filed on Jul. 6, 2026 have been fully considered. Arguments regarding withdrawn rejections are moot. Applicant’s arguments relevant to the current rejections are addressed as follows.
Applicant’s arguments to the 112(b) rejection are addressed in the modified 112(b) rejection above.
To the 103 rejection, Applicant argues that Deml misses disclosure related to or suggesting the claimed method for detecting “the presence of T-cells specific for SARS-CoV-2” using quantitative RT-PCR on a tissue sample stimulated with “the SARS-CoV-2 spike protein” and diluted with a diluent that is “protease free” to detect the “relative concentration of CXCL10 mRNA in the sample.” Applicant argues that Whelan does not address to deficiencies in Deml. Applicant further argues that Al-Soud et al. (J Clin Microbiol. 2001 Feb; 39(2):485-493)) and Biskup et al. (Separations. 2022; 9(11):324)) teach away from the current invention as they teach that tissue samples contain PCR inhibitors and that proteases are the reagents used in RT-PCR to eliminate nucleases from the sample during the protocol.
Applicant’s arguments are not persuasive. As indicated in the art rejection above, Whelan teaches that assay for the immune status of a subject with SARS-CoV-2 infection is desired; and Cai teaches that it was contemplated and practiced to develop PCR assays directly on a tissue sample without the steps for nucleic acid extract. Therefore, Whelan and Cai remedy the deficiencies of Deml.
To applicant’s argument about teaching away, Al-Soud teaches a study on effects of potential inhibitors, hemoglobin and lactoferrin, on PCR reaction, showing varying inhibitory results on different polymerase enzymes. See e.g. Table 4. Biskup teaches importance of proteinase K in the extraction process of nucleic acids for RT-PCR. None of the references teach or suggest that RT-PCR cannot be performed directly on a diluted tissue sample, or that a protease needs to be included in such a PCR assay.
MPEP section 2145 X.D relates to assertions that the art teaches away from the claimed invention. Such teachings are not considered to be a teaching away merely by indicating that something is in some manner inferior to another. In essence, a teaching away must criticize, discredit, or otherwise discourage the solution.
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 extension fee 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 NIANXIANG (NICK) ZOU whose telephone number is (571)272-2850. The examiner can normally be reached on Monday - Friday, 8:30 am - 5:00 pm, EST. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MICHAEL ALLEN, on (571) 270-3497, can be reached. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/NIANXIANG ZOU/
Primary Examiner, Art Unit 1671
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