DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election of claims 1-5, 7, 8, 10, 13, 15, 17-19, 22, 23, 25, and 27 and the following species in the reply filed on August 7, 2026 is acknowledged:
Method: RT-DAMP
Sample type: the combination of saliva and nasal mucus
Media: the combination of solution and cellulose fiber matrix
Pathogenic organisms: SARS-CoV-2
Applicant traversed the election of sample type, arguing that saliva and nasal mucus (alone and in combination) were used in the examples section of the application, are highly related, share common properties, and do not require differing reaction conditions and reagents for amplification reactions. While it is noted for the record that there does not appear to be an Example in the instant specification wherein biological samples comprising a combination of nasal mucus and saliva were lysed and then assayed, as recited in the claims, the prior art (as demonstrated by Bearinger – published Dec. 1, 2011; Patent Application Publication No. US 20110294199 A1) appears to indicate detection that the recited species may be considered interchangeable in point-of-care isothermal nucleic acid testing methods (Bearinger: par. 62, 70). Therefore, the election of species requirement for sample types, as set forth in the office action mailed June 16, 2026, has been reconsidered and is hereby withdrawn.
Claims 1-5, 7, 8, 10, 13, 15, 17-19, 22, 23, 25, 27, 28, and 36 are currently pending.
Claims 28 and 36 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected subject matter, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on Aug. 7, 2026.
Claims 1-5, 7, 8, 10, 13, 15, 17-19, 22, 23, 25, and 27 are herein examined to the extent they read on the elected species.
Priority
It is acknowledged that the instant application is a 371 of international PCT Application No. PCT/US2022/079923, filed November 16, 2022, and that it claims benefit of provisional 63/281,458, filed November 19, 2021. The effective filing date is considered to be November 19, 2021.
Drawings
The drawings are objected to because the resolution is insufficient to distinguish details and/or text (see particularly, Figures 1-3). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claim 27 is objected to because of the following informalities: “genome equivalent” should read “genome equivalents.” Appropriate correction is required.
Claim 1 is objected to because of the following informalities: The step “a.” and step “b.” should not include a period (“.”). Instead of recitation of “a.”, the limitation could be recited as “a)” or “(a)”. Appropriate correction is required.
MPEP 608.01(m) Form of Claims [R-10.2019]: Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations. See Fressola v. Manbeck, 36 USPQ2d 1211 (D.D.C. 1995).
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 1-5, 7, 8, 10, 13, 15, 17-19, 22, 23, 25, and 27 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.
Claims 1-5, 7, 8, 10, 13, 15, 17-19, 22, 23, 25, and 27 are rejected for the recitation of “nucleic acid sample bound in cellulose fibers” in claim 1, line 3; “to bind the nucleic acid sample to the cellulose fibers” in claim 2, lines 4 and 5; and “nucleic acid sample…binds to the pH sensitive element” in claim 4, because it is unclear what is meant by binding in this context. For example, it is unclear whether the claims are requiring that the nucleic acids are somehow chemically associated with the cellulose fibers (e.g. ionic/covalent bonds), or if they require that the nucleic acids and cellulose fibers are physically or spatially associated (e.g. co-located), or if they require something else. Clarification is requested. For the purposes of compact prosecution, and as supported by the instant specification, the claims are interpreted to mean that the two elements are spatially associated.
Claim 5 is rejected for the recitation of “filtering the biological sample” because it is unclear whether the filtered sample is intended to be the “processed biological sample” recited in claims 2 and 4 which is generated by lysis, or the (unprocessed) “biological sample” prior to lysis recited in claims 1 and 2. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter.
Claim 7 is rejected for the recitation of “wherein the lysing, contacting, or filtering…” because it lacks antecedent basis in the claims on which it depends. Claim 2 recites “lysing” and “contacting,” but does not recite a step of “filtering.” If the claim is intended to depend from claims 4 or 5, which do recite a step of “filtering,” the claim must be modified to reflect that dependency.
Claim 15 is rejected because it is unclear if the recited “a nucleic acid sample” is the same nucleic acid sample recited in claim 1, and because “the target nucleic acid” lacks antecedent basis. Claim 1 recites “a nucleic acid of interest” and “a nucleic acid sample” but not a target nucleic acid. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter.
Claim 15 is rejected because it is unclear whether it is intended to further limit the isothermal amplification options of claim 13 or if it is intended to require both (i) that the method utilize DAMP or RT-DAMP and (ii) that DAMP and RT-DAMP comprise the recited steps. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter.
Claim 17 is rejected for the recitation of “the biological sample” because it lacks antecedent basis in claim 1, on which it depends. If the claim is intended to depend from claim 2, which does recite “a biological sample,” the claim must be amended to reflect that meaning.
Claim 23 is rejected for the recitation of “the pathogenic organism” because it lacks antecedent basis in claim 1, on which it depends. If the claim is intended to depend from claim 22, which does recite “a pathogenic organism,” the claim must be amended to reflect that dependency.
Claim 27 is rejected for the recitation of “detect at least 1,000 genome equivalent(s) per microliter” because it is unclear whether the value of 1,000 genome equivalents per microliter represents an upper limit of detection, a lower limit of detection, or something else. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter. For the purposes of compact prosecution, the claim is interpreted to mean that the method is capable of detecting concentrations of target nucleic acids which are 1,000 genome equivalents per microliter or more.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim(s) 1-5, 7, 8, 10, 13, 15, 17-19, 22, 23, 25, and 27 is/are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims are drawn to a method of detecting a nucleic acid of interest requiring the use of a ‘pH sensitive element.’ Claim 1 recites the following steps: amplifying a nucleic acid of interest which is bound in cellulose fibers of a pH sensitive element by isothermal amplification; and identifying a pH detected by the pH sensitive element. Claim 2 recites the steps of: obtaining a sample, lysing cells in the sample to produce a processed biological sample, and contacting a processed biological sample with the pH sensitive element to bind the nucleic acid sample to the cellulose fibers of the pH sensitive element. Claim 3 recites that lysing comprises the step of treating the sample with a lysin or heat. Claim 4 recites that the contacting step comprises filtering the processed biological sample through the pH sensitive element, wherein the nucleic acid sample from the processed biological sample binds to the pH sensitive element. Claim 5 recites filtering the biological sample through the pH sensitive element by capillary force. Claim 7 requires one or more wash steps during lysing, contacting or filtering prior to amplification. Claim 15 recites the step of contacting nucleic acid with primers and cycling amplifying with particular primers.
The claimed ‘pH sensitive element’ is required to possess certain characteristics in order to
perform the functions as recited in the claimed method. It must:
Detect pH
Comprise or be capable of comprising cellulose fibers;
Be capable of containing isothermal amplification reagents;
Be capable of ‘binding’ to nucleic acids
Be capable of filtering processed biological samples, such as through capillary action
In the instant case, the claims do not set forth the ‘pH sensitive element’ in terms of sufficient relevant identifying characteristics. The claims encompass the use of any pH sensitive element. Claim 11 requires that the ‘pH sensitive element’ be non-bleeding pH paper and/or comprise colorimetric detection. Only non-bleeding pH paper is a particular species of pH sensitive element.
The specification does not provide a limiting definition of ‘pH sensitive element,’ but allows that :
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pH sensitive elements comprising cellulose fibers or suitable for combination with cellulose fibers include a large number of potential agents, such as pH test papers, a variety of optical or fluorescent pH indicator dyes (e.g. phenol red, cresol red, neutral red, etc.), a variety of electrochemical species, engineered proteins and/or enzymes, and pH meter devices.
Therefore, the size of the genus is very large, encompassing pH sensitive elements with a wide variety of chemical and physical structures and design mechanisms. Claim 11, which allows that the pH sensitive element comprise colorimetric detection, still encompasses a large genus; there are many types of colorimetric agents which are sensitive to pH.
The specification allows for any pH sensitive element but only explicitly mentions and thus only provides written description for commercially available pH papers and non-bleeding pH paper. The specification does not describe any other species within the claimed genus to show possession of those species.
Regarding the genus ‘pH sensitive element,’ the specification does not describe any structural features of the disclosed pH sensitive elements (i.e. pH papers) which would have been expected to be shared by all members of the claimed genus (i.e. optical dyes, fluorescent dyes, engineered proteins, pH meters). The specification does not describe physical and/or chemical characteristics of the disclosed pH sensitive elements that would be shared by members of the claimed genus. All members of the genus have the same function, i.e., they are elements which detect pH sensitive elements which are possess the characteristics set forth above. However, the level of knowledge and skill in the art does not allow those skilled in the art to structurally envisage or recognize additional members of the claimed genus. Because the species within the claimed genus are expected to vary unpredictably from the structure of the pH sensitive elements disclosed in the specification, the disclosed pH sensitive elements are not a “representative number” of species within the claimed genus.
Because the pH sensitive elements are not representative of the entire claimed genus, and the specification does not disclose structural features shared by members of the genus, the description of the pH sensitive elements of ‘commercially available pH paper’ and ‘non-bleeding pH paper’ would not have put the applicant in possession of common structural attributes or features shared by members of the genus that structurally distinguish the members of the genus from non-members of the genus at the time of filing. Thus, the description of pH sensitive elements is not sufficient to describe the claimed genus of pH sensitive elements. Accordingly, the specification does not provide a representative number of species or sufficient common structural features to show that the applicant would have been in possession at the claimed genus as a whole at the time of filing.
Regarding the genus of pH sensitive elements, the level of knowledge and skill in the art does not allow those skilled in the art to structurally envisage or recognize all pH sensitive elements, because the term ‘pH sensitive element’ encompasses agents which are not known to: be useful for the particular ranges of pH relevant to the invention (claims 1, 8, 19); and/or be suitable for use under the claimed conditions (in the presence of particular isothermal amplification reagents, or between the claimed temperatures for the claimed time periods, or in the presence of lysates from the claimed types of biological samples).
Therefore, those skilled in the art would have recognized that the specification’s disclosure of ‘commercially available pH paper’ and ‘non-bleeding pH paper’ would not have put the applicant in possession of any type of ‘pH sensitive element’ at the time of filing. Thus, the specification does not describe sufficiently detailed, relevant characteristics to show that the applicant was in possession of the claimed genus of ALL ‘pH sensitive elements.’
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-5, 7, 8, 10, 13, 15, 17-19, 22, 23, 25, and 27 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims have been evaluated using the 2019 Revised Patent Subject Matter Eligibility Guidance (see Federal Register Vol. 84, No. 4, Monday, January 7, 2019).
Step 1: The claims are directed to the statutory category of a process.
Step 2A, prong one: Evaluate Whether the Claim Recites a Judicial Exception
The instant claims recite abstract ideas. The claims recite a step of “identifying a pH” detected by a pH sensitive element” recited in step b) of claim 1. Neither the specification nor the claims set forth a limiting definition for “identifying” and the claims do not set forth how this step is accomplished other than a mental step and that the pH is detected “by the pH sensitive element.” The “identifying” step broadly encompasses mental processes. For example, one may “identify” a pH by looking at pH test strip and thinking about what the color indicates. Mental processes, which are concepts performed in the human mind (including observation, evaluation, judgement, and opinions) are considered to be abstract ideas.
Step 2A, prong two: Evaluate Whether the Judicial Exception Is Integrated Into a Practical Application
The claims do NOT recite additional steps or elements that integrate the recited judicial exception(s) into a practical application of the exception(s). For example, the claims do not practically apply the judicial exception by including one or more additional elements that the courts have stated integrate the exception into a practical application:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or a technological field;
An additional element that applies or used a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
An additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
An additional element effects a transformation or reduction of a particular article to a different state or thing;
An additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
In addition to the judicial exceptions, the claims recite steps of “amplifying” nucleic acids, “lysing” cells, “obtaining,” “contacting,” “treating,” “filtering” samples or “exposing” them to heat, and wash steps. These are not considered to integrate the judicial exceptions into a practical application because they merely add insignificant extra-solution activity (data gathering) to the judicial exceptions or are merely instruction to apply the exception in generic ways. Thus, the steps do not integrate the mental analysis step into a practical application.
Step 2B: Evaluate Whether the Claim Provides and Inventive Concept
In addition to the judicial exceptions, the claims recite steps of “amplifying” nucleic acids, “lysing” cells, “obtaining,” “contacting,” “treating,” “filtering” samples or “exposing” them to heat, and wash steps. These steps do not amount to significantly more because they simply append well-understood, routine, and conventional activities previously known in the art, specified at a high level of generality, to the judicial exceptions.
These steps are recited a high level of generality. “amplifying” nucleic acids, “lysing” cells, “obtaining,” “contacting,” “treating,” “filtering” samples or “exposing” them to heat, and ‘washing’ merely instruct a scientist to use any known technique for these purposes. The claims do not require the use of any particular non-conventional reagents or equipment or methodology. When recited at this high level of generality, there is no meaningful limitation that distinguishes these steps from well-understood, routine, and conventional activities engaged in by scientists prior to applicant’s invention and at the time the application was filed.
Additionally, the teachings in the specification demonstrate the well-understood, routine, and conventional nature of additional elements because it teaches that the additional elements are well-known or commercially available. For example, the specification teaches the following:
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Further, it is noted that the courts have recognized the following laboratory techniques as well-understood, routine, and conventional activity in the life science arts when they are claimed in a merely generic manner (e.g. at a high level of generality) or as insignificant extra-solution activity.
Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
Immunizing a patient against a disease, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119 USPQ2d at 1375;
Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014)
For the reasons set forth above the claims are not directed to patent eligible subject matter.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1, 8, 10, 11, 17-19, 22 and 25 are rejected under 35 U.S.C. 103 as unpatentable over Kaarj (published Aug. 20, 2018; Kaarj et al. Sci Rep. 2018 Aug 20;8(1):12438) in view of Jaroenram (published Jan 2019; Jaroenram et al. J Microbiol Methods. 2019 Jan;156:9-14).
Regarding claim 1, Kaarj teaches a method of detecting a nucleic acid of interest comprising amplifying by isothermal amplification a nucleic acid of interest present in a nucleic acid sample bound in cellulose fibers of a pH sensitive element to generate an amplification product (Figure 1) and identifying a pH of a pH-sensitive element (pg. 9, first full par.; Figure 7A).
For clarity, in this rejection of claim 1, the pH sensitive element in Kaarj is interpreted to be the detection area of the paper microfluidic chip (comprising cellulose fibers) to which RT-LAMP reaction mixture comprising a pH indicator phenol red (pg. 9: “Primers and RT-LAMP master mix” and “RT-LAMP on paper microfluidic chip”) is added. Subsequent to the addition, amplification is initiated. Samples were loaded onto the microfluidic chips and capillary action filtered these samples as the nucleic acids were forced to the detection area of the chip (or ‘bound’; pg. 9: “Sample loading…”).The pH indicator dye ‘detects’ the pH of the RT-LAMP reaction through an identifiable colorimetric change that results from amplification.
Although Kaarj does not explicitly recite that isothermal amplification of the nucleic acid of interest results in release of hydrogen ions, the RT-LAMP reaction does occur on the pH sensitive element and polymerase-based amplification methods such as LAMP produce hydrogen ions as a result of nascent nucleic acid synthesis (Jaroenram: Abstract). Therefore, Kaarj is considered to have met the limitation.
Kaarj teaches buffer intended for use in colorimetric LAMP and is silent regarding the presence of ‘pH buffers’ such as Tris in the reaction mixture (pg. 9, 1st full par.). However, Kaarj’s ‘WarmStart colorimetric LAMP master mix’ may contain some form of pH buffer. Therefore, Kaarj is not considered to have taught performing isothermal amplification in the absence of a pH buffer.
Jaroenram teaches isothermal amplification reactions which are performed in the absence of pH buffers (pg. 10, col. 1, last par.).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Kaarj and Jaroenram. One would have been motivated to do so in order to provide optimal conditions for colorimetric LAMP (pg. 10, col. 1, last par.). One would have had reasonable expectation of success because Jaroenram demonstrates successful isothermal amplification under such conditions (Fig. 2A).
Regarding claims 1 and 8, Kaarj does not explicitly recite that a pH of 7.5 or less, or that a pH of between 6 and 7.5 indicates the presence of the nucleic acid of interest in the nucleic acid sample, and/or that a pH of more than 7.5 indicates the absence of the nucleic acid of interest in the nucleic acid sample. However, Applicants are reminded that claim scope is not limited by claim language such as wherein clauses which suggest or make optional but do not require steps to be performed. Please also note that Jaroenram does teach that isothermal amplification (with initial reaction conditions having a pH of 8.0 – 9.0) can be considered positive when the pH of a reaction is between 6.0 and 6.5 (pg. 13, col. 1, first full par.), which overlaps the claimed range. Implicitly, Jaroenram also teaches that pH of 8.0 – 9.0 would be considered negative for amplification. These ranges overlap with the claimed ranges with sufficient specificity that the limitations are considered to have been addressed. Thus, even a positive recitation of the ‘wherein’ limitations would be obviated by the combination of Kaarj and Jaroenram.
Regarding claim 10, Kaarj teaches the nucleic acid sample and/or the nucleic acid of interest is RNA or DNA (pg. 5: “Sample matrices” and pg. 9: “Sample preparation”). In this case, the nucleic acid of interest is ZIKV RNA, while the nucleic acid sample comprises human and ZIKV RNA and/or DNA (present in human plasma samples which are spiked with ZIKV RNA).
Regarding claim 11, Kaarj teaches a pH sensitive element which comprises colorimetric detection (pg. 9, 1st full par: “phenol red as a pH indicator dye”).
Regarding claim 17, Kaarj teaches biological samples which are plasma or urine (pg. 9: “Sample preparation”).
Regarding claim 18, Kaarj teaches a combination of performing isothermal amplification in solution and in a cellulose fiber matrix (pg. 9, last par.).
Regarding claim 19, Kaarj does not explicitly teach the pH of the solution prior to isothermal amplification.
Jaroenram teaches pHs of isothermal amplification reaction solutions which are more than 8.0 prior to isothermal amplification (pg. 11, col. 1, last par).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Kaarj and Jaroenram. One would have been motivated to do so because Jaroenram teaches that initial reaction pH is an optimizable variable (pg. 11, col. 1, last par). One would have had reasonable expectation of success because Jaroenram and Kaarj use related colorimetric isothermal assays and Jaroenram’s optimal pH was more than 8.0 (Jaroenram: pg. 11, col. 1, last par.; Fig. 2), as required by the claim.
Regarding claim 22, Kaarj teaches detection of a nucleic acid of interest which is specific for a pathogenic organism (Abstract). In this case, the pathogenic organisms is Zika Virus or ZIKV.
Regarding claim 25, Kaarj teaches that isothermal amplification is carried out between carried out at 65ºC, 68ºC, and 70ºC (pg. 9: “Temperature optimization”) and 68º C for 30min (pg. 9, last par.). The temperatures fall within the claimed range of 55º and 70ºC and the time falls within the claimed range of between 30 and 60 min. Therefore, the limitations are considered to have been met.
Claims 2-5 and 7 are rejected under 35 U.S.C. 103 as unpatentable over Kaarj (published Aug. 20, 2018; Kaarj et al. Sci Rep. 2018 Aug 20;8(1):12438) in view of Jaroenram (published Jan 2019; Jaroenram et al. J Microbiol Methods. 2019 Jan;156:9-14), as applied to claim 1 above, and further in view of Feng (published June 20, 2017; Feng et al. Anal Chem. 2017 Jun 20;89(12):6631-663) and Tanner (published April 6, 2021; US Patent No. 10,968,493).
Please note that the limitation “contacting the processed biological sample with the pH sensitive element to bind the nucleic acid sample to the cellulose fibers of the pH sensitive element” recited in claim 2 is interpreted here as an intended consequence or result of the contacting step.
Kaarj and Jaroenram teach the limitations of claim 1, as discussed above.
Regarding claim 2, Kaarj teaches that prior to the amplifying, the method comprises obtaining the nucleic acid sample from a biological sample and contacting the processed biological sample with the pH sensitive element (pg. 9: “Sample preparation,” “Sample loading…,” and “RT-LAMP…”). Here, the nucleic acids of interest are spiked ZIKV nucleic acids which are added to any endogenous nucleic acids to form a nucleic acid sample in a human plasma or urine biological sample. These processed samples are contacted on cellulose fibers with an RT-LAMP reaction mixture comprising a pH sensitive element, and subsequently subjected to amplification.
Regarding claims 4 and 5, Kaarj teaches that contacting comprises filtering a processed biological sample through the pH sensitive element by capillary force (pg. 9, 2nd to last par.).
Regarding claim 2, Kaarj does not teach that the obtaining step comprises lysing cells present in the biological sample to generate a processed biological sample.
Feng teaches a method in which prior to the amplifying, the method comprises obtaining the nucleic acid sample from a biological sample, wherein the obtaining comprises lysing cells present in the biological sample to generate a processed biological sample (pg. 6632, col. 2, par 1).
Regarding claim 3, Kaarj does not teach that the lysing comprises treating the biological sample with a lysin or exposing the biological sample to heat.
Feng teaches sample lysis using TRIzol (pg. 6632, col. 2, par. 1). As the instant specification teaches that ‘lysin’ encompasses any substance which causes the lysis of a cell, Feng is considered to have met the limitations of claim 3.
Regarding claim 7, Kaarj does not explicitly teach a lysing, contacting, or filtering step which comprises one or more wash step(s) wherein the one or more wash steps occurs prior to the isothermal amplification.
Feng teaches that the lysis step comprises one or more wash step(s) and wherein the one or more wash steps occurs prior to the isothermal amplification (pg. 6632: col. 2, par. 1).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Kaarj and Feng. One would have been motivated to do so in order to use a method of lysing cells which is suitable for the release of nucleic acids from biological samples and subsequent isothermal amplification (Feng: pg. 6632, col. 2, par 1). One would have had reasonable expectation of success because Feng demonstrates that TRIzol-based lysis is capable of releasing nucleic acids for successful detection of isothermal amplification of nucleic acids (Feng: Figure 5).
Neither Kaarj nor Feng teach that the contacting step is done in order to bind the nucleic acid sample to the cellulose fibers of the pH sensitive element. However, this limitation represents an intended result or consequence of the actively recited step which does not limit the scope of the claim. As the combination of Kaarj and Feng teaches each positively recited step of the method, the combination is considered to have met the recited limitations.
Claims 13 and 15 are rejected under 35 U.S.C. 103 as unpatentable over Kaarj (published Aug. 20, 2018; Kaarj et al. Sci Rep. 2018 Aug 20;8(1):12438) in view of Jaroenram (published Jan 2019; Jaroenram et al. J Microbiol Methods. 2019 Jan;156:9-14), as applied to claim 1 above, and further in view of Ding (published September 26, 2019; Ding et al. Anal Chem. 2019 Oct 15;91(20):12852-12858).
Kaarj and Jaroenram teach the limitations of claim 1, as discussed above.
Regarding claim 13, the combined references do not teach that the isothermal amplification comprises RT-DAMP. Instead, they teach isothermal amplification comprising RT-LAMP (Kaarj: Abstract) or LAMP (Jaroenram: Abstract).
Ding teaches isothermal amplification comprising RT-DAMP (pg. 4: “DAMP and RT-DAMP assays”).
Regarding claim 15, the combined references do not teach RT-DAMP comprising: a. contacting a nucleic acid sample suspected of containing the target nucleic acid with primers; and b. cyclically amplifying the target nucleic acid to provide amplified target nucleic acid, wherein the primers comprise a forward outer primer (FO), a reverse outer primer (RO), a forward inner primer (FI), a reverse inner primer (RI), a forward reverse pairing-competition primer (FC), a reverse pairing-competition primer (RC) or a combination thereof.
Ding teaches RT-DAMP comprising: a. contacting a nucleic acid sample suspected of containing the target nucleic acid with primers; and b. cyclically amplifying the target nucleic acid to provide amplified target nucleic acid, wherein the primers comprise a forward outer primer (FO), a reverse outer primer (RO), a forward inner primer (FI), a reverse inner primer (RI), a forward reverse pairing-competition primer (FC), a reverse pairing-competition primer (RC) or a combination thereof (pg. 5: “Principle of the DAMP assay” & Figure 1).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Kaarj and Jaroenram with the teachings of Ding. One would have been motivated to do so in order to achieve higher amplification yield and faster reaction speed than conventional methods (pg. 8, par. 1) or to avoid nonspecific amplification (pg. 3, par. 1 & Fig. 5C). One would have had reasonable expectation of success because Ding demonstrates successful RT-DAMP (Fig. 5C).
Claim 23 is rejected under 35 U.S.C. 103 as unpatentable over Kaarj (published Aug. 20, 2018; Kaarj et al. Sci Rep. 2018 Aug 20;8(1):12438) in view of Jaroenram (published Jan 2019; Jaroenram et al. J Microbiol Methods. 2019 Jan;156:9-14), as applied to claim 1 above, and further in view of González-González (published online Dec. 18, 2020; González-González et al. Anal Methods. 2021 Jan 21;13(2):169-178).
Kaarj and Jaroenram teach the limitations of claim 1, as discussed above.
Regarding claim 23, the combined references do not teach that the nucleic acid of interest is a nucleic acid specific for SARS-CoV-2.
González-González teaches colorimetric LAMP where the nucleic acid of interest is a nucleic acid specific for SARS-CoV-2 (Abstract).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Kaarj and Jaroenram with the teachings of González-González. One would have been motivated to do so because point-of-care diagnostics are urgently needed for SARS-CoV-2 (pg. 170, col. 1, par 1-3). One would have had reasonable expectation of success because isothermal methods have successfully been applied to SARS-CoV-2 (Fig. 1).
Claim 27 is rejected under 35 U.S.C. 103 as unpatentable over Kaarj (published Aug. 20, 2018; Kaarj et al. Sci Rep. 2018 Aug 20;8(1):12438) in view of Jaroenram (published Jan 2019; Jaroenram et al. J Microbiol Methods. 2019 Jan;156:9-14), as applied to claim 1 above, and further in view of Ye (published Sept. 2016; Ye et al. Infect Genet Evol. 2016 Sep;43:43-9).
Kaarj and Jaroenram teach the limitations of claim 1, as discussed above.
Regarding claim 27, Kaarj teaches that the method is capable of detecting as little as 1 copy of ZIKV RNA per microliter (Abstract).
Regarding claim 27, Kaarj does not explicitly teach the detection of at least 1,000 genome equivalents per microliter. However, Kaarj does teach RT-LAMP primers which are specific to the NS5 gene of ZIKV.
Ye teaches that NS5 is present as a single copy in the ZIKV genome (Ye: Fig. 1A, pg. 45, col. 1, par. 1).
Given that NS5 is present as a single copy in the ZIKV genome, the amount detected by Kaarj (i.e. 1 copy of ZIKV RNA per microliter) is interpreted to be 1 genome equivalent per microliter, which meets the limitation of claim 27.
Conclusion
No claims are allowed.
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/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
