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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 06/26/2026 has been entered.
Response to Amendment
The amendment received on 05/27/2026 is acknowledged. Claim 1 has been amended. Claims 1, 3, 5-7, 10-35 are currently pending and claims 22-35 remain withdrawn. Claims 1, 3, 5-7 and 10-21 have been treated on the merits.
Response to Arguments
Applicant argues that the rejection of record does not address newly added limitations. These limitations are addressed below.
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.
Claims 1, 3, 6, 7, 9-15, and 17-21 are rejected under 35 U.S.C. 103 as being unpatentable over Lalli et al. (medRxiv preprint, Cold Spring Harbor Preprints, 2020/ IDS submitted 5/28/2023) in view of Hardringe (“Reduced False Positives and Improved Reporting of Loop-Mediated Isothermal Amplification using Quenched Fluorescent Primers”, Scientific Reports, Nature, 9, 7400 (2019), 1-13 ) as evidenced by Promega (“TE Buffer”, available at https://www.promega.com/products/biochemicals-and-labware/biochemical-buffers-and-reagents/te-buffer_-1x_-molecular-biology-grade/?catNum=V6231, accessed on 11/26/2024).
Regarding claim 1 and the limitation “A method of preparing a saliva sample for loop-mediated isothermal amplification (LAMP) detection of a pathogen target, comprising:
providing an amount of saliva from a test subject; and diluting the saliva to 25% in water; diluting the saliva to a final concentration of 5% upon addition to a LAMP reaction, incorporating…guanidine hydrochloride” Lalli teaches “rapid colorimetric assay using reverse-transcription loop-mediated isothermal amplification (RT-LAMP) optimized on human saliva samples without an RNA purification step” (abstract) wherein “LAMP reactions proceed with saliva diluted 1:1 in [water]” (supplementary Figure 4A) and “found that dilution of saliva into water enabled sensitive detection of SARS-CoV-2 particles using LAMP” (page 5, lines 3-5). Lalli teaches RT-LAMP failed to detect pathogens in undiluted saliva even at high levels of particles (104) per reaction (Figure 2B). However, 1:1 dilution of the saliva in water increased the sensitivity of the assay to detection of 103 particles per reaction (Figure 2A). The act of dilution will result in a reduction in the buffering capacity of the saliva as solutes have been diluted including those which act as a buffer. Lalli further teaches that the addition of guanidine hydrochloride improved results by improving both speed and sensistivity (Page 11-12, Supplemental Figures 5 and 6).
Regarding claim 1 and the limitation “diluting the saliva in water to a saliva to water ratio of about 1:1 to about 1:20”, Lalli teaches 1:1 dilution. One of ordinary skill in the art would be able to determine workable or optimal ranges for dilution from the teaching of Lalli and arrive at ratios of about 1:1 to about 1:20.
It has long been settled to be no more than routine experimentation for one of ordinary skill in the art to discover an optimum value of a result effective variable. "[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." Application of Aller, 220 F.2d 454, 456, 105 USPQ 233, 235-236 (C.C.P.A. 1955). "No invention is involved in discovering optimum ranges of a process by routine experimentation." Id. at 458, 105 USPQ at 236-237. The "discovery of an optimum value of a result effective variable in a known process is ordinarily within the skill of the art." Application of Boesch, 617 F.2d 272, 276, 205 USPQ 215, 218-219 (C.C.P.A. 1980).
Regarding claim 1 and the limitation “diluting the saliva to a final concentration of 5% upon addition to a LAMP reaction” Lalli teaches using a 4:25 dilution for LAMP reaction resulting in a final concentration of 8% using the samples with a 1:1 dilution as disclosed by Lalli (High-Throughput Colorimetric Assay).
One of ordinary skill in the art would be able to determine workable or optimal ranges for final dilution in the reaction mixture from the teaching of Lalli and arrive at diluting the saliva to a final concentration of 5% in the reaction mixture.
It has long been settled to be no more than routine experimentation for one of ordinary skill in the art to discover an optimum value of a result effective variable. "[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." Application of Aller, 220 F.2d 454, 456, 105 USPQ 233, 235-236 (C.C.P.A. 1955). "No invention is involved in discovering optimum ranges of a process by routine experimentation." Id. at 458, 105 USPQ at 236-237. The "discovery of an optimum value of a result effective variable in a known process is ordinarily within the skill of the art." Application of Boesch, 617 F.2d 272, 276, 205 USPQ 215, 218-219 (C.C.P.A. 1980).
Regarding claim 1 and the limitation “incorporating carrier DNA or carrier RNA,” Lalli does not teach the incorporation of carrier DNA or RNA into the LAMP reaction. This difference however would have been obvious to one of ordinary skill in the art as it is taught in the same field of endeavor as optimizing LAMP reactions.
In the same field of endeavor Hardringe teaches that carrier DNA is frequently added to LAMP reactions to improve results, enhance sensitivity, reduce variation, increase reaction times and amplification frequencty (Page 7, Figure 8, Page 10).
One of ordinary skill in the art would find it obvious the carrier DNA could be added to the LAMP reaction method of Lalli, as Hardringe teaches the addition of carrier DNA into LAMP reactions is known to improve results. One of ordinary skill in the art would be motivate to do so to get improved results including enhance sensitivity, reduce variation, increase reaction times and amplification frequency as taught by Hardringe. One of ordinary skill in the art would further have a reasonable expectation of success in doing so as Hardringe teaches that this is known technique generally for LAMP and has been used in multiple references, and further Hardringe explores the general mechanism of why it leads to improved results.
Regarding claims 3 and the limitation “wherein the viscosity is reduced by dilution”, Lalli teaches “[s]aliva is a challenging clinical matrix due to variability across individuals in pH and viscosity…Here we have overcome these challenges and demonstrate a variety of saliva pretreatment protocols that enable sensitive detection of SARS-CoV-2… A 1:1 dilution of saliva followed by treatment with RNAsecure and 65 ˚C incubation potently reduces reaction inhibitors, and can be implemented with a single heat source isothermal with the LAMP reaction in a point-of-care setting.” (page 15, paragraph 3), and “LAMP reactions proceed with saliva diluted 1:1 in [water]” (supplementary Figure 4A) and “found that dilution of saliva into water enabled sensitive detection of SARS-CoV-2 particles using LAMP” (page 5, lines 3-5). The dilution of saliva with water results in a reduction in viscosity as components are diluted.
Regarding claim 6 and the limitation “wherein the viscosity is reduced compared to an original viscosity such that the reduced viscosity of the saliva sample facilitates more rapid, uniform and reliable uptake and distribution of the saliva in a solid phase medium”, The sample of Lalli has undergone dilution resulting in reduction in viscosity, the property claimed is a result of a lower viscosity sample. The steps made obvious by Lalli will result in the same method steps being performed and thus will result in the claimed property of the prepared sample.
Regarding claim 7 and the limitation “wherein the viscosity is reduced to a range of from about 1.0 cP to about 50 cP” The steps made obvious by Lalli will result in the same method steps being performed and thus will result in the claimed property as the saliva sample is diluted 1:1 in water (1.0 cP), as taught by Lalli, would necessarily reduce the viscosity to from about 1.0 cP to about 50 cP.
Regarding claim 9 and the limitation “further comprising adjusting the saliva sample to a pH of from about 7.2 to about 8.6.” Lalli further teaches embodiments in which TE buffer is added to the samples “To optimize assay compatibility with clinical samples that had already been diluted in PBS, we substituted TE instead of water in the LAMP master mix (Sup. Fig. 7C-D). This modification offers buffering against basal pH differences in saliva without affecting assay sensitivity (Page 12)”. As evidenced by Promega, TE buffer has a pH of 8.0. One of ordinary skill in the art would find it obvious that this buffer and mix could be used in the method of Lalli. The addition of this buffer to samples will result in the adjustment of the pH to from about 7.2 to about 8.6.
Regarding claim 10 and the limitation “wherein the saliva is diluted in the water to a saliva to water ratio of about 1:3.”, Lalli teaches 1:1 dilution and further makes obvious the dilution covering the ranges claimed as noted above which included 1:3. Regarding claim 11 and the limitation “wherein the saliva is diluted in the water to a degree that provides the sample with an optical density at 600 nm (OD600) of less than 0.2.” A reduction in OD600 is an inherent result of dilution. In the workable ranges made obvious by Lalli will result in samples having and OD600 of less than 0.2.
Regarding claim 12 and the limitation “wherein the water has a pH greater than 6.0 and is substantially free of contaminants”, although Lalli does not explicitly state the pH nor the sterility of the water used in the dilutions, working with biological materials in a lab setting involves sterile and pure water, the inherent properties of which would necessarily include an at or near neutral pH of 7.0.
Regarding claim 13 and the limitation “wherein the saliva sample consists essentially of saliva and water” The sample of Lalli consists of water and saliva (Page 5, Figures 1 and 2).
Regarding claims 14-15 and the limitations “wherein the saliva has a volume of from about 50 μL to about 100 μL”and “wherein the saliva sample has a volume of from about 100 μL to about 1 ml”, Lalli teaches the use of “50 μL saliva” working samples in early experiments which was later diluted 1:1 (page 17, paragraph 5). Therefore Lalli teaches 50 μL volume of saliva and the corresponding 100 μL volume of diluted saliva samples.
Regarding claims 17-21 and the limitations “wherein the pathogen target comprises a viral pathogen, a bacterial pathogen, a fungal pathogen, or a protozoa pathogen”, “wherein the pathogen target is a viral target”, “wherein the viral target comprises a dsDNA virus, an ssDNA virus, a dsRNA virus, a positive-strand ssRNA virus, a negative-strand ssRNA virus, an ssRNA-RT virus, or a ds-DNA-RT virus”, wherein the viral target comprises HIN1, H2N2, H3N2, HlNlpdm09, or SARS-CoV-2””, and “wherein the LAMP detection comprises reverse transcription LAMP (RT-LAMP) detection”, Lalli teaches “[t]he robustness of the LAMP […] makes it especially well-suited and widely used for pathogen detection in unpurified samples” (Page 2, paragraph 2). Additionally, the prior art “establish[es] and optimize[s] a simple [RT-]LAMP-based assay for the qualitative detection of SARS-CoV-2 directly from saliva” (Page 2, paragraph 4). Lalli teaches that SARS-CoV-2, a positive-strand ssRNA viral pathogen, can be targeted and detected from saliva by RT-LAMP.
Claims 1, 3, 6, 7, 9-15, and 17-21 are further rejected under 35 U.S.C. 103 as being unpatentable over Lalli and Hardringe as applied to claims 1, 3, 6, 7, 9-15, and 17-21above, and further in view of Oasis (“Pure·SALTM: Oral Specimen Collection System” Oasis diagnostics, 2016, Vancouver WA) as evidenced by Promega (“TE Buffer”, available at https://www.promega.com/products/biochemicals-and-labware/biochemical-buffers-and-reagents/te-buffer_-1x_-molecular-biology-grade/?catNum=V6231, accessed on 11/26/2024).
For a discussion of what Lalli and Hardringe teach, see the above section.
Regarding claim 1 and the limitation “optionally reducing a viscosity of the saliva is reduced as compared to an original viscosity by filtering with a 2 micron to 50 micron filter.” Lalli does not teach the act of filtering the saliva or a method of collecting and preparing a saliva sample in which the sample is filtered. This difference however would have been obvious to one of ordinary skill in the art as devices for collecting saliva for biological analysis using filters are taught in the same field of endeavor by Oasis.
In the same field of endeavor of obtaining and analyzing samples of saliva, Oasis teaches a device with a collection pad which absorbs saliva (Step 3), and when an adequate amount of saliva has been obtained as noted by an indicator (Step 4), the sample is prepared via compression against the filter (Step 5) to remove interferants or contaminants (Principles of the Device, Introduction, Intended Use).
The PureSAL device of Oasis is disclosed for use in the method by applicant in the specification ([0190]-[0191], Example 3). Further the device illustrated in the instant drawings (Figure 5), is the same as that shown by Oasis (Page 1). The device of Oasis will thus have the filter and effect claimed by applicant. Alternatively, the act of removing interferants or contaminants will inherently result in a reduction in viscosity.
One of ordinary skill in the art would find it obvious that a saliva collection device specifically designed for obtaining RNA and DNA samples from saliva could be used in the method of Lalli and Hardringe as it is taught in the same field of endeavor as analysis of polynucleotides present in saliva. One of ordinary skill in the art would be motivated to do so to use a device for easy collection of saliva and a device that had an indicator for showing when adequate sample had been obtained. One of ordinary skill in the art would further have a reasonable expectation of success in doing so as the device of Oasis is specifically designed for this purpose.
Regarding claims 3 and the limitation “wherein the viscosity is reduced by dilution”, Lalli teaches “[s]aliva is a challenging clinical matrix due to variability across individuals in pH and viscosity…Here we have overcome these challenges and demonstrate a variety of saliva pretreatment protocols that enable sensitive detection of SARS-CoV-2… A 1:1 dilution of saliva followed by treatment with RNAsecure and 65 ˚C incubation potently reduces reaction inhibitors, and can be implemented with a single heat source isothermal with the LAMP reaction in a point-of-care setting.” (page 15, paragraph 3), and “LAMP reactions proceed with saliva diluted 1:1 in [water]” (supplementary Figure 4A) and “found that dilution of saliva into water enabled sensitive detection of SARS-CoV-2 particles using LAMP” (page 5, lines 3-5). The dilution of saliva with water results in a reduction in viscosity as components are diluted.
Regarding claim 6 and the limitation “wherein the viscosity is reduced compared to an original viscosity such that the reduced viscosity of the saliva sample facilitates more rapid, uniform and reliable uptake and distribution of the saliva in a solid phase medium”, The sample of Lalli and Oasis has undergone dilution and filtration resulting in reduction in viscosity, the property claimed is a result of a lower viscosity sample. The steps made obvious by Lalli and Oasis will result in the same method steps being performed and thus will result in the claimed property of the prepared sample.
Regarding claim 7 and the limitation “wherein the viscosity is reduced to a range of from about 1.0 cP to about 50 cP” The steps made obvious by Lalli and Oasis will result in the same method steps being performed and thus will result in the claimed property as the saliva sample is diluted 1:1 in water (1.0 cP), as taught by Lalli, would necessarily reduce the viscosity to from about 1.0 cP to about 50 cP.
Regarding claim 9 and the limitation “further comprising adjusting the saliva sample to a pH of from about 7.2 to about 8.6.” Lalli further teaches embodiments in which TE buffer is added to the samples “To optimize assay compatibility with clinical samples that had already been diluted in PBS, we substituted TE instead of water in the LAMP master mix (Sup. Fig. 7C-D). This modification offers buffering against basal pH differences in saliva without affecting assay sensitivity (Page 12)”. As evidenced by Promega, TE buffer has a pH of 8.0. One of ordinary skill in the art would find it obvious that this buffer and mix could be used in the method of Lalli and Oasis. The addition of this buffer to samples will result in the adjustment of the pH to from about 7.2 to about 8.6.
Regarding claim 10 and the limitation “wherein the saliva is diluted in the water to a saliva to water ratio of about 1:3.”, Lalli teaches 1:1 dilution and further makes obvious the dilution covering the ranges claimed as noted above which included 1:3.
Regarding claim 11 and the limitation “wherein the saliva is diluted in the water to a degree that provides the sample with an optical density at 600 nm (OD600) of less than 0.2.” A reduction in OD600 is an inherent result of filtration and dilution. In the workable ranges made obvious by Lalli, Hardringe and Oasis will result in samples having and OD600 of less than 0.2.
Regarding claim 12 and the limitation “wherein the water has a pH greater than 6.0 and is substantially free of contaminants”, although Lalli does not explicitly state the pH nor the sterility of the water used in the dilutions, working with biological materials in a lab setting involves sterile and pure water, the inherent properties of which would necessarily include an at or near neutral pH of 7.0.
Regarding claim 13 and the limitation “wherein the saliva sample consists essentially of saliva and water” The sample of Lalli consists of water and saliva (Page 5, Figures 1 and 2).
Regarding claims 14-15 and the limitations “wherein the saliva has a volume of from about 50 μL to about 100 μL”and “wherein the saliva sample has a volume of from about 100 μL to about 1 ml”, Lalli teaches the use of “50 μL saliva” working samples in early experiments which was later diluted 1:1 (page 17, paragraph 5). Therefore Lalli teaches 50 μL volume of saliva and the corresponding 100 μL volume of diluted saliva samples.
Regarding claims 17-21 and the limitations “wherein the pathogen target comprises a viral pathogen, a bacterial pathogen, a fungal pathogen, or a protozoa pathogen”, “wherein the pathogen target is a viral target”, “wherein the viral target comprises a dsDNA virus, an ssDNA virus, a dsRNA virus, a positive-strand ssRNA virus, a negative-strand ssRNA virus, an ssRNA-RT virus, or a ds-DNA-RT virus”, wherein the viral target comprises HIN1, H2N2, H3N2, HlNlpdm09, or SARS-CoV-2””, and “wherein the LAMP detection comprises reverse transcription LAMP (RT-LAMP) detection”, Lalli teaches “[t]he robustness of the LAMP […] makes it especially well-suited and widely used for pathogen detection in unpurified samples” (Page 2, paragraph 2). Additionally, the prior art “establish[es] and optimize[s] a simple [RT-]LAMP-based assay for the qualitative detection of SARS-CoV-2 directly from saliva” (Page 2, paragraph 4). Lalli teaches that SARS-CoV-2, a positive-strand ssRNA viral pathogen, can be targeted and detected from saliva by RT-LAMP.
Claim 5 is rejected and claims 1, 3, 6, 7, 9-15, and 17-21 are further rejected under 35 U.S.C. 103 as being unpatentable over Lalli, Hardringe, and Oasis as applied to claims 1, 3, 6, 7, 9-15, and 17-21 above, and further in view of Libby (USPGPub 20100331725/previously cited).
For a discussion of what Lalli, Hardringe, and Oasis teach see the above sections.
Oasis further teaches that the PureSAL device is patented (Principles of the Device). And teaches that the product produces virtually cell free RNA, DNA and proteins (Introduction).
Regarding claim 5 and the limitation “wherein the viscosity is reduced using a 10 micron filter” and further regarding claim 1 and the limitation “by filtering with a 2 micron to 50 micron filter”, Lalli, Hardringe, and Oasis do not disclose the filter size; however, sizing of the filter would be viewed as a result effective variable by one of ordinary skill in the art as it is taught in the patent to the Oasis device by Libby.
In the same field of endeavor as saliva collection devices utilizing a collection pad and preparation of fluids through a filter Libby teaches the filters of the device may be selected as desired ([0114]), such as to remove food particles, clumps of cells or differentiated between human and bacterial cells.
One of ordinary skill in the art would thus view filter size as a result effect variable and would find it obvious to optimize to obtain viral and or nucleotides from the saliva for detection of the virus.
It has long been settled to be no more than routine experimentation for one of ordinary skill in the art to discover an optimum value of a result effective variable. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum of workable ranges by routine experimentation." Application of Aller, 220 F.2d 454, 456, 105 USPQ 233, 235-236 (C.C.P.A. 1955). "No invention is involved in discovering optimum ranges of a process by routine experimentation." Id. at 458, 105 USPQ at 236-237. The "discovery of an optimum value of a result effective variable in a known process is ordinarily within the skill of the art." Application of Boesch, 617 F.2d 272, 276, 205 USPQ 215, 218-219 (C.C.P.A. 1980).
One of ordinary skill in the art would thus find it obvious that the size of the filter could be adjusted to select for RNA, DNA and proteins while retaining cells present in saliva such as epithelial cells and arrive at filter sizes of from 2 to 50 and 10 microns.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Lalli, Hardringe and Oasis as applied to claims 1, 3, 6-7, 9-15, and 17-21 above, or in the alternative Lalli, Hardringe, Oasis and Libby as applied to claims 1, 3, 5-7, 9-15, and 17-21, and further in view of Robinson et al. (Clin. Infect. Diseases 2008:46 e61-64; Doi: 10.1086/529386/previously cited).
For a discussion of what Lalli, Hardringe, and Oasis, or in the alternative Lalli, Hardringe, Oasis and Libby teach, see the above sections.
Lalli, Hardringe, and Oasis, or in the alternative Lalli, Hardringe, Oasis and Libby do not teach an embodiment in which a sponge is used as the saliva collection pad. This difference however would have been obvious to one of ordinary skill in the art as the use of a sponge for this purpose is taught in the same field of endeavor as collecting saliva samples by Robinson.
Robinson teaches “throat swab and saliva specimens […] might be acceptable for [detection of respiratory viruses] in a setting where it is impractical to obtain [a nasopharyngeal] specimen” (page e61, abstract) wherein “[t]he saliva specimen was obtained by rubbing a sponge on a stick […] on the inside of the child’s mouth until the sponge was saturated” (page e62, paragraph 2).
One of ordinary skill in the art would thus have found it obvious that a sponge material could be used as the absorbent pad as the use of sponges for collecting saliva is taught in the same filed of endeavor. One of ordinary skill would be motivated to do so to use whatever material was readily available or cheapest at the time. One of ordinary skill in the art would further have a reasonable expectation of success in doing so as Robinson teaches that sponge collection is a viable means for collecting saliva for viral analysis.
Conclusion
No claim is allowed.
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/CHARLES Z CONSTANTINE/Examiner, Art Unit 1657
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