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 without traverse of Group I (claims 23-34) in the reply filed on 3/16/2026 is acknowledged.
Claims 35-44 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, there being no allowable generic or linking claim.
Claims 23-34 are pending and are examined on the merits herein. It is noted that for the withdrawn claims, the (Withdrawn) status identifier is not present. Applicant is required to include the correct status of each claim in their response. See MPEP 714 II (C).
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 112(a) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 17/221,451, now US Patent 11,155,887, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. Specifically, neither this application nor the associated patent describe the use of poloxamers. This, claims 23-34 will be given the priority date of Application No. 17/406,959, now US Patent 11,345,970, August 19, 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 8/18/2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1), 1.835(a)(2), or 1.835(b)(2) is missing, defective or incomplete. Specifically, the file size is listed in kilobytes, not bytes.
Required response - Applicant must:
• Provide a substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities: it is noted that the “Cross-Reference” section of the specification that lists the priority applications is not complete, as it does not include all of the applications listed in the filing receipt. Additionally, the Sequence Incorporation by Reference paragraph is defective, as noted above.
Appropriate correction is required.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Specifically, these hyperlinks appear on page 22, para. 3, page 92, para. 6, page 110, para. 7, and page 127, para. 1.
Claim Objections
Claim 23 is objected to because of the following informality: in step (a), the comma in line 1 show be removed. Appropriate correction is required.
Claim Interpretation
Claim 23 recites heating a sample to 95°C in step (b). MPEP 2144.05 I states that, regarding overlapping, approaching, and/or similar ranges/amounts, “In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976)…Similarly, a prima facie case of obviousness exists where the claimed ranges or amounts do not overlap with the prior art but are merely close. Titanium Metals Corp. of America v. Banner, 778 F.2d 775, 783, 227 USPQ 773, 779 (Fed. Cir. 1985).” Section II (A) states, “Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).” Applicant does not describe their particular heating temperature as critical to their invention, and does not note that said temperature produces unexpected results, and so the above guidance with regard to overlapping, approaching, and/or similar ranges/amounts applies in the prior art rejections below.
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 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 23-24, 28-29, and 31 are rejected under 35 U.S.C. 103 as being unpatentable over Diaz et al. (WO 2020/014704 A1).
Diaz is drawn to sample preparation for downstream methods such as LAMP (Abstract). Page 4, para. 3 describes a method involving supplying a sample, performing DNA extraction, amplifying the released nucleic acids, and identifying pathogens using specific primers. The amplification assay can be LAMP, and the sample can be bodily fluids (page 4, para. 4). On page 18, para. 4, Diaz notes that bodily fluids can be saliva. Page 5, para. 1 states that the sample can be contacted with a surfactant such as Pluronic F-68 (PF68). Page 9, paras. 3-4 shows working examples that include PF68 and LAMP in combination. Page 51, para. 1 exemplifies methods associated with this combination, and states that E. coli bacteria were cultured, PF68 was added, and cell lysis occurred at 100°C for 5 minutes, followed by vortexing. Multiple sample fractions were analyzed, where the fractions were then used in LAMP assays. These assays used the same methods as the LAMP assays described on page 48, which involved the modified primer set EcolC 3109_1 and the original primer set EcolC 3109_0 (see also Table II and Table III).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Diaz to arrive at the inventions of claims 23-24, 28-29, and 31. Specifically, this would involve using the method described by the working examples of Diaz above on a bodily fluid sample, such as saliva, from a human subject. Though Diaz performed these working examples on bacterial cultures from an isolate (page 43, para. 2), the reference notes that detection of disease is generally important to their methods. Page 25, para. 3 states that their invention is, “…ideally suited to point of care (POC) or other on-site applications, including providing a rapid response system for detecting new outbreaks of emerging diseases in human[s]…” and page 19, para. 4 notes that the present invention may be used for diagnostics to determine the presence of absence of a pathogen. Given that the reference also teaches that food borne diseases, such as those caused by E. coli, “result in hundreds of thousands of cases of illness, thousands of hospitalizations, and hundreds of deaths in the United States annually,” (page 1, para. 3), the ordinary artisan would be motivated to use the methods of Diaz to non-invasively test patients for the presence of pathogenic E. coli, particularly to determine if the amount of the bacteria present is associated with infectious levels/disease. As page 31, para. 3 of the reference teaches that the use of PF68 with the E. coli samples increased detection rate, the ordinary artisan would be motivated to use this method shown by Diaz specifically. Thus, this combination of the teachings of Diaz would involve collecting a saliva sample, contacting the processed sample with PF68, heating the sample to 100°C, and then adding two sets of LAMP primers. As noted above in the “Claim Interpretation” section, Applicant’s use of 95°C in the instant claim is not noted to be critical or to produce unexpected results, and so the use of 100°C by Diaz is considered to render obvious this limitation in the claim. Additionally, it is noted that in the working example of Diaz described above, fractional portions of the sample are used and replicates were run with the LAMP reaction buffer (page 51, para. 1). This would amount to using aliquots of the sample as claimed. The ordinary artisan would note the general value of using fractions of a sample (e.g. preserving a portion of the sample in the event the initial analyses are flawed or contamination of fractions occurs), as well as the benefits of performing replicate assays (e.g. to ensure the accuracy and validity of results). Thus, the ordinary artisan would also be motivated to use this aliquot method in the combination of teachings described above. Generally, there would be a reasonable expectation of success in combining these teachings of Diaz as this would amount to performing a specific embodiment of the general teachings of Diaz stated on pages 4-5, as well as performing a slightly altered version of one of the working examples of the invention of Diaz, which has already been shown to successfully detect E. coli.
Thus, claims 23-24, 28-29, and 31 are prima facie obvious over Diaz.
Claims 25-26 are rejected under 35 U.S.C. 103 as being unpatentable over Diaz et al. (WO 2020/014704 A1) in view of Zhang et al. (medRxiv, 2020).
Diaz teaches the method of claims 23-24, 28-29, and 31, as described above. Diaz also teaches that their technology can be used to detect viruses, and specifically viral pathogens (page 19, para. 4), and notes that viruses can specifically be analyzed with LAMP methods (page 28, para. 3). RNA is also specifically noted to be compatible with these methods (page 19, para. 4), and page 28, para. 3 notes the use of RT-LAMP. However, the reference does not provide specific examples in which viruses are used.
Zhang teaches detecting SARS-CoV-2 using colorimetric LAMP, and notes that this method is simple, sensitive, and provides an opportunity to detect the virus in the field (Abstract). The reference notes that disease symptoms can be similar those of the flu or common cold, so accurate molecular diagnostics are important (page 2, para. 1). The reference shows the validation of 5 LAMP primer sets for detecting SARS-CoV-2 (page 5, para. 3), and page 6, para. 1 notes that these LAMP methods can still work even if cell lysate is used, rather than purified RNA. The reference closes with, “This combination of a quick sample preparation method with an easy detection process may allow the development of portable, field detection in addition to a rapid screening for point-of-need testing applications. This virus represents an emerging significant public health concern and expanding the scope of diagnostic utility to applications outside of traditional laboratories will enable greater prevention and surveillance approaches. The efforts made here will serve as a model for inevitable future outbreaks where the use of next generation portable diagnostics will dramatically expand the reach of our testing capabilities for better healthcare outcomes,” (page 7, para. 1).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Zhang in the method of Diaz, specifically to detect the coronavirus SARS-CoV-2. Zhang teaches that LAMP primers can be developed for this virus, and notes that samples were from patient swabs (page 4, para. 2), showing that patient samples can be used. Thus, the methods of Diaz and Zhang are very similar to one another. This combination of teachings would amount to detecting viral SARS-CoV-2 in the saliva samples of Diaz, utilizing the cell PF68/cell lysis heating methods of Diaz, and performing the general LAMP described by Diaz with the primer sets described by Zhang. As Diaz teaches that using P68 can improve pathogen concentration/detection via general means that are not specific to bacteria (see page 32, paras. 2-3), the ordinary artisan would recognize that the benefits of this surfactant are not limited to bacteria, and would therefore be motivated to use this reagent with viral samples. This is particularly true in light of the importance of SARS-CoV-2 detection described by Zhang, as accurate diagnostics are key to controlling outbreaks. The importance of detecting SARS-CoV-2 generally, as stressed by Zhang (see Abstract and page 2, para. 1, for example) would also generally motivate the ordinary artisan to detect this virus. There would be a reasonable expectation of success as Zhang teaches that SARS-CoV-2 can be detected in cell lysate and successfully teaches the use of LAMP in detecting this virus.
Thus, claims 25-26 are prima facie obvious over Diaz in view of Zhang.
Claim 27 is rejected under 35 U.S.C. 103 as being unpatentable over Diaz et al. (WO 2020/014704 A1), in view of Zhang et al. (medRxiv, 2020), and further in view of Mahony et al. (Journal of Clinical Virology, 2013).
Diaz in view of Zhang teaches the methods of claims 25-26, as noted above. As also noted above, Diaz generally teaches the detection of viruses in their methods, and Zhang notes the symptomatic similarities between SARS-CoV-2 and influenza.
Mahony teaches the use of a multiplex LAMP assay to detect various influenza types (Abstract). Clinical specimens from patients were used (page 128, “Clinical specimens”), and the LAMP assay was performed with the same mastermix that was used in Diaz (the OptiGene ISO001 mastermix, see page 48, para. 1 of Diaz). Multiple LAMP primers were used (see Table 1). Mahony notes that their methods can work with both extraction methods and rapid specimen processing, the latter consisting of rapid vortexing followed by heating (page 130, “Rapid specimen processing”). The reference states that their LAMP methods are faster than traditional PCR methods, and notes that their methods can be used for inexpensive, rapid testing in clinical settings (pages 130-131, “Discussion”). Mahony also generally describes the importance of evaluating influenza (page 127, column 1, para. 1).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to combine the teachings of Diaz in view of Zhang with those of Mahony to include primer sets for both SARS-CoV-2 and influenza in their LAMP assays. Mahony teaches that LAMP assays, with similar sample preparation to that of Diaz, can be used to successfully detect influenza, and Zhang teaches that SARS-CoV-2 and influenza share a similar symptom profile. As SARS-CoV-2 and influenza can both cause epidemics and can be a source of mortality, accurate diagnosis of the particular disease a patient has is of paramount importance to both patients and clinicians. Thus, by including primer sets for both diseases in a single assay, the presence of either virus can be identified, which would allow for appropriate treatment and contagion mitigation measures. There would be a reasonable expectation of success in incorporating these primers as Mahony teaches that they can be used with cell lysate, and the LAMP mastermix reagents of Mahony are the same as those used in Diaz.
Thus, claim 27 is prima facie obvious over Diaz, in view of Zhang, and in view of Mahony.
Claims 30 and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Diaz et al. (WO 2020/014704 A1) in view of Tanner et al. (Current Protocols in Molecular Biology, 2014).
Diaz teaches the method of claims 23-24, 28-29, and 31, as described above. Though the reference does teach the use of fluorescence measurements (page 48, para. 1), this is due to the use of a mastermix that contains dye, and not a fluorophore/quencher system on LAMP primers.
Tanner teaches general LAMP protocols, as well as alternate protocols, and particularly those with labeled primers (page 15.14.1, para. 2). Such an alternative protocol is shown in Figure 15.14.1 with DARQ LAMP. This version of LAMP includes an Fd primer that binds to the typical FIP primer, and includes a fluorophore and quencher on the Fd and F1c portions, respectively. When stand displacement occurs during elongation (i.e. in the presence of the sample), the fluorophore and quencher are separated, producing a fluorescent signal. As the LAMP reaction proceeds, exponential amplification produces additional fluorescence (see figure caption). Tanner teaches that DARQ LAMP contains identical primers to typical LAMP reactions outside of the changes to the F1c and Fd portions, and the primer duplex formed from the FIP:Fd hybridization functions as a standard LAMP primer. Tanner goes on to state, “DARQ LAMP primers are designed using standard recommendations and software. DARQ requires no alterations to the primer design described for the standard LAMP process, other than modification of FIP (or BIP) and addition of the modified Fd sequence,” (page 15.14.7, paras. 1-2). Page 15.14.8 specifically shows an example protocol that is noted to work on E. coli (see “Set 1”). Tanner teaches that these reactions allow for real-time detection of multiple, distinct targets, which can lessen post-reaction processing time (page 15.14.7, para. 1). Table 15.14.1 of the reference also notes different fluorophores and quenchers that may be used with the DARQ LAMP method, including the detection wavelengths for each.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Tanner to make the LAMP assay of Diaz a DARQ LAMP assay. Tanner teaches that DARQ LAMP has primers that are functionally the same as in standard LAMP, and that these primers can be designed using commercially available means. Thus, the ordinary artisan would have a reasonable expectation of incorporating DARQ LAMP methods into the existing LAMP methods of Diaz described above in the rejection of claim 23, particularly in light of the fact that Tanner specifically notes the use of E. coli. Tanner also teaches that DARQ LAMP provides processing benefits over traditional LAMP, which would be motivating for the ordinary artisan. Table 15.14.1 of Tanner also provides many examples of fluorophores and quenchers that can be used, showing the multiplex capabilities of the DARQ method, and specifically noting detection wavelengths so that multiplex fluorescent signals have little to no overlap. This would be further motivating to the ordinary artisan, as it would allow for many different gene targets, or potential pathogenic strains, to be measured simultaneously in the method of Diaz.
Thus, claims 30 and 34 are prima facie obvious over Diaz in view of Tanner.
Claim 32 is rejected under 35 U.S.C. 103 as being unpatentable over Diaz et al. (WO 2020/014704 A1) in view of OptiGene (“GspSSD Isothermal Mastermix (ISO-001)”, 20171).
Diaz teaches the method of claims 23-24, 28-29, and 31, as described above. The reference also teaches that for the working example LAMP assays, the LAMP primers were used with Isothermal Mastermix ISO001 obtained from OptiGene (page 48, para. 1).
OptiGene teaches that this mastermix contains their original DNA polymerase that has “superior strand-displacement activity and speed.”
Thus, the LAMP assays of the working examples of Diaz utilize a strand-displacement polymerase. It would therefore be prima facie obvious to use this strand-displacement polymerase in the teachings of Diaz described above in the rejection of claim 23, as this polymerase, and the mastermix generally, have already been shown to successfully detect E. coli in methods described by Diaz (also providing a reasonable expectation of success). Different components may result in less effective or accurate methods. OptiGene also teaches benefits of using this particular mastermix (namely speed) that would motivate the ordinary artisan.
Thus, claim 32 is prima facie obvious over Diaz in view of OptiGene.
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Diaz et al. (WO 2020/014704 A1), in view of Zhang et al. (medRxiv, 2020), and in view of OptiGene (“GspSSD Isothermal Mastermix (ISO-001)”, 2017).
Diaz teaches the method of claims 23-24, 28-29, and 31, as described above. Diaz in view of OptiGene teach the use of a strand displacing polymerase, as described in the rejection of claim 32 above. However, as noted in the rejection of claim 23, Diaz teaches using aliquots of samples, and does not teach adding LAMP primers directly to a sample.
Zhang, as noted above in the rejection of claims 25-26, teaches the detection of SARS-CoV-2. For the data generated for Figure 3, total cell lysate was used, where samples were collected, stored, (page 4, para. 2), and then sample cells were lysed and combined with primers, in order to avoid an RNA purification step (page 6, para. 1). Zhang indicates that this method does not interfere with target detection, and is an efficient method that is less expensive and involved than PCR workflows (page 6, para. 1).
As noted above in the rejection of claims 25-26, it would be prima facie obvious to combine Diaz in view of Zhang to examine SARS-CoV-2. Additionally, Zhang provides motivation to add primers directly to samples, without using fractions of said samples. The reference teaches that this provides a rapid, inexpensive method for virus detection, and eliminates the need for a purification step, thus requiring less equipment and reagents. This would allow the method to be performed in more clinical spaces rather than requiring specimen transport to specialized laboratories. This would be particularly motivating for an incredibly infectious disease such as SARS-CoV-2, where rapid and accurate diagnosis can prevent epidemic expansion. Though not using sample fractions would mean that fractional replicates could not be used, as the samples are obtained non-invasively from bodily fluids, obtaining multiple samples from a patient would be possible, thereby still providing the benefits associated with replicates. Additionally, not using sample fractions eliminates concerns regarding pathogen nucleic acids being unequal between fractions. As the LAMP method of Diaz would be unchanged in the combination of Diaz in view of Zhang (with the exception of the target and the use of SARS-CoV-2 primers), it would still be prima facie obvious to use the OptiGene mastermix in these methods, with its strand displacing polymerase, as these have been shown to work with the larger LAMP methods of Diaz. There would be a reasonable expectation of success as Zhang shows that successful SARS-CoV-2 can be performed with LAMP methods on cell lysate.
Thus, claim 33 is prima facie obvious over Diaz, in view of Zhang, and in view of OptiGene.
Conclusion
No claims are currently allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
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/FRANCESCA FILIPPA GIAMMONA/Examiner, Art Unit 1681
1 This webpage is not catalogued on archive.org. However, the exact product cited by OptiGene is used in Diaz, which is dated before the effective filing date of the claimed invention. Additionally, Google notes the initial date of this webpage is 2/9/2017 (see Google Search results attached to the PDF of the reference).
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