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 .
Status of Claims
The amended claims filed 04/09/2026 are acknowledged and entered.
Claims 12, 14-16, 18, 20, 18, and 20 have been amended
Claims 21-23 are added.
Claims 12-23 are pending and examined on their merits.
Response to Amendment
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Examiner’s Note
Examiner acknowledges that applicant has properly invoked the 102(b)(1)(A) exception by stating in the Affidavit under 37 § CFR 1.130(a) that the subject matter of the ICMR Advisory reference (ICMR) (published November 26, 2020) is less than one year prior to the EFD of the present application (EFD of December 4, 2020) and was obtained directly from a joint inventor of the present application.
The MPEP discusses in 706.07(a): When applying any 35 U.S.C. 102(a)(2) or pre-AIA 35 U.S.C. 102(e) /103 references against the claims of an application, the examiner should anticipate that a statement averring common ownership may qualify the applicant for the exception under 35 U.S.C. 102(b)(2)(C) or a statement of common ownership at the time the invention was made may disqualify any patent or application applied in a rejection under 35 U.S.C. 103 based on 35 U.S.C. 102(e). If such a statement is filed in reply to the 35 U.S.C. 102(a)(2) or pre-AIA 35 U.S.C. 102(e) /103 rejection and the claims are not amended, the examiner may not make the next Office action final if a new rejection is made. See MPEP §§ 2146.03 and 2154.02(c). In this case, the ICMR is regarded as 102(a)(1) reference, the ICMR does not cite any named author (acknowledged by applicant in Remarks, Page 9, third paragraph) and new limitations have been introduced into the claims, including claim 12. There is nothing that could bar the examiner to make a Final Action and, thus, this Final Action would be deemed proper.
Claim Rejections - 35 USC § 112 withdrawn
The rejections for claim 12 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite is withdrawn in view of the amendment of claim 12.
The rejections for claims 1-17 and 19-23 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for lack of enablement is withdrawn in view of the amendment of claim 12 and 16.
Claim Rejections - 35 USC § 103 withdrawn
The rejections of claims 12-15 and 19-20 under 35 U.S.C. 103 as being unpatentable over ICMR (previously cited) in view of Srivatsan (previously cited) and Thermoscientific (previously cited) and Stanford (previously citer) are withdrawn in view of Applicant’s Affidavit regarding the 102(a)(1) ICMR reference.
The rejections of claims 16-18 under 35 U.S.C. 103 as being unpatentable over ICMR (previously cited) in view of Srivatsan (previously cited) and Thermoscientific (previously cited), Stanford (previously cited), Helix (previously cited), Compass (previously cited) and Chen (previously cited) are withdrawn in view of Applicant’s Affidavit regarding the 102(a)(1) ICMR reference.
Rejections Maintained
Claim Rejections - 35 USC § 112 - Maintained
1. Claim 14 remains rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite because of the term “single layer packing”. The claim was not amended in such a way to overcome this rejection. Please refer to the previous office action.
2. Claim 18 remains rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claim 18 recites the limitation: “… detecting SARS-CoV-2 and other viruses…”. The claim was not amended in such a way to overcome this rejection. Please read the previous Office Action for the complete discussion as to why it lacks enablement.
New Objections and Rejections Necessitated by Amendments
Specification Objections
The specification is objected as it does not provide antecedent support for the claim 12 limitation “a sealed collection tube enclosed within a single biohazard bag”
Claim Objections
3. Claims 14, 20 are objected to because of the following informalities: Claim 12 has been amended but those amendment are now inconsistent with some of the limitations of dependent claims 14 and 20, which still recite the previous limitations of claim 12. For example: RNA extraction instead of RNA isolation, new 12(a) limitation for single biohazard bag, the use of sample instead of dry swab in claim 20, etc. Please ensure that all claims depending on claim 12 reflect the amended limitations of claim 12. For the purposes of compact prosecution, it has been interpreted that limitations of instant claims 14(i) and 20 (i) have the same limitations as claim 12.
Appropriate correction is required.
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.
Claims 12-17 and 19-23 are rejected under 35 U.S.C. 112, 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(s), at the time the application was filed, had possession of the claimed invention.
This is a New Matter rejection.
The terms “sealed collection tube” “single biohazard bag”, and “suitable for transport in a biohazard bag” as recited in claims 12 and 16, respectively, are not supported by the original disclosure or claim as filed.
Applicant’s amendment, filed 4/9/26, directs to support to paragraphs 43, 44, 89-91, and asserts that no new matter has been added. However, these paragraphs do not support these new limitations.
However, the specification as filed does not provide sufficient written description of the above-mentioned limitations. The specification does not provide sufficient support for a sealed collection tube, single biohazard bag, and suitable for transport in a biohazard bag. Therefore, the claims represent a departure from the specification and claims as originally filed.
Such limitations recited in the present claims, which did not appear in the specification, as filed, introduce new concepts and violate the description requirement of the first paragraph of 35 U.S.C. §112.
Applicant is required to cancel the new matter in the response to this Office Action. Alternatively, applicant is invited to provide sufficient written support for the “limitations” indicated above. See MPEP §714.02, §2163.05-06 and §2173.05(i).
4. The amended claims 14 and 20 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.
Claim 12 recites the limitation " ….(d) performing direct qRT-PCR on the heat-inactivated sample without RNA extraction to obtain qRT-PCR results ….”. This is interpreted as the RNA is still found in the extracted sample used to obtain results. That is, it has not been isolated
Claim 14 and 20 recite the limitation “The process of claim 12 (in the case of claim 14) or 19 (in the case of claim 20), further comprising …. (iv) isolating RNA from the heat inactivated TE-proteinase K buffer extract of (iii) to obtain isolated RNA; (v) performing qRT-PCR using the isolated RNA of (iv) as a template to obtain qRT-PCR results;…”. This is interpreted as the RNA was isolated from the extracted sample to obtained results.
These two interpretation are mutually exclusive. Either the RNA is extracted/isolated or not. The terms RNA extraction and RNA isolation are considered synonymous. For the purpose of compact prosecution, it has been interpreted that for claims 14 and 16, which depend directly or indirectly on claim 12, the RNA is not extracted (not isolated). Appropriate correction is required for claims 14 and 20 and any other claim that recites this limitation or implies such limitation.
5. Claim 17 recites the limitation "… wherein the primers, probes, dyes, enzymes, and RT-PCR buffer…”. There is insufficient antecedent basis for the term “dyes” in the claim.
Claim Rejections - 35 USC § 103
(New rejections necessitated by the Amendments and in view of the declaration identifying the 102(a)(1) ICMR reference as applicant’s own work)
6. Claims 12-15 and 19-23 are rejected under 35 U.S.C. 103 as being unpatentable over Srivatsan (bioRxiv preprint, April 23, 2020 pages 1-11), in view of Thermoscientific (Proteinase K (recombinant), PCR grade. Thermoscientific User guide. August 2, 2019), Miao (Breaking the Bad: An Introduction to Proteinase K a blog by Dennis Miao Mat 27, 2020, PDF provided) and Stanford (Stanford Health Care Clinical Virology Laboratory SARS-CoV-2 test EUA Summary, Updated November 20, 2020).
Srivatsan teaches a “dry swab, extraction free” protocol for SARS-CoV-2 testing via RT-qPCR (Title). The goal was to evaluate how eliminating the UTM (Universal Transport Medium) storage and RNA extraction steps would impact the results of molecular testing. A comparison of conventional (swab → UTM → RNA extraction → RT-qPCR) vs. simplified (direct elution from dry swab → RT-qPCR) protocols (Abstract). The dry swabs can be nasopharyngeal and these swabs were established to be COVID-19-positive via testing at the University of Washington’s Virology lab (testing center) (page 4, first paragraph) as required by limitations of instant claims 12(a), 14(i) and 20(i).
The dry swabs are eluted directly into TE buffer [10 mM Tris pH-7.4, 0.1 mM EDTA], (page 7, Dry swab elution) and can support molecular detection of SARS-CoV-2 via endpoint RT-qPCR (Abstract), (RT-qPCR reads on qRT-PCR) ((instant claims 12(b)(d)(e), 14(ii) (v)(vi) and 20(ii)(v)(vi)). The RNA was isolated using the MagnaPure 96 RNA extraction platform (page 2, second paragraph), ((limitation of instant claims 14 (iv), and 20(iv)). Regarding the RT-PCR kit manufacturer's recommendations limitation of 12(e), 14(vi) and 20 (vi), MPEP 2112.01(3) Where the only difference between a prior art product and a claimed product is printed matter that is not functionally related to the product, the content of the printed matter will not distinguish the claimed product from the prior art. In re Ngai, 367 F.3d 1336, 1339, 70 USPQ2d 1862, 1864 (Fed. Cir. 2004) (Claim at issue was a kit requiring instructions and a buffer agent. The Federal Circuit held that the claim was anticipated by a prior art reference that taught a kit that included instructions and a buffer agent, even though the content of the instructions differed, explaining "[i]f we were to adopt [applicant’s] position, anyone could continue patenting a product indefinitely provided that they add a new instruction sheet to the product."). See also In re Gulack, 703 F.2d 1381, 1385-86, 217 USPQ 401, 404 (Fed. Cir. 1983) ( "Where the printed matter is not functionally related to the substrate, the printed matter will not distinguish the invention from the prior art in terms of patentability….[T]he critical question is whether there exists any new and unobvious functional relationship between the printed matter and the substrate." ); In re Miller, 418 F.2d 1392, 1396 (CCPA 1969) (finding a new and nonobvious relationship between a measuring cup and writing showing how to "half" a recipe); In re Seid, 161 F.2d 229, 73 USPQ 431 (CCPA 1947) (matters relating to ornamentation only which have no mechanical function cannot be relied upon to patentably distinguish the claimed invention from the prior art); In re Xiao, 462 Fed. App'x 947, 950-51 (Fed. Cir. 2011) (non-precedential) (affirming an obviousness rejection of claims directed to a tumbler lock that used letters instead of numbers and had a wild-card label instead of one of the letters); In re Bryan, 323 Fed. App'x 898, 901 (Fed. Cir. 2009) (non-precedential) (printed matter on game cards bears no new and nonobvious functional relationship to game board). Srivatsan teaches in Figure 1(A) a comparison of RT-qPCR detection of inactivated virus from conventional (received in UTM) and from dry swabs for both the Orf1b and spike. Blue dots are the samples reconstituted in TE and green dots are UTM-extracted samples (the two middle dot lines). A head-to-head comparison of RT-qPCR Ct values showed that dry swabs collected and eluted directly into TE with no RNA extraction steps performed comparably to conventionally collected and processed swabs (page 4, third paragraph) as required by instant claim 23.
Srivatsan does not teach the use of serine protease (proteinase k) at the 0.5 mg/mL to 5.0 mg/ml dose range, to be added to the TE buffer to obtain an extracted sample In addition, It does not teach heat inactivation (limitations in 12(b) and (c), 14(ii) and (III) and 20 (ii) and (iii)) or how to pack a sample (limitations in (12(a), 14(i) and 20(i)).
Thermoscientific teaches that Proteinase K is an endolytic protease that cleaves peptide bonds at the carboxylic sides of aliphatic, aromatic or hydrophobic amino acids and is classified as a serine protease (product description). Some of its applications are the removal of DNases and RNases when isolating DNA and RNA from tissues or cell lines and improving cloning efficiency of PCR products (Applications). These applications would make the presence of Proteinase K in a TE buffer to obtain an extracted sample obvious due to the improvements seen on PCR protocols (limitations of claims 12-23). The recommended working concentration for Proteinase K is 0.05-1 mg/ml (note). Since this is a recommendation, the final concentration can be optimized, please see below.
Thermoscientific does not teach heat inactivation or how to pack a sample.
Miao teaches that Proteinase K is a highly activated serine protease often used in DNA and RNA extraction protocols for sample purification and removal/digestion of RNAses and DNases and these purified samples can then be used in a variety of downstream application such as PCR (Page 1, second paragraph). Proteinase K is highly resistant to denaturation by heat and will continue to function up to a 65 oC (Page 1, third [paragraph). Inactivation of Protein K is achieved at high temperatures by heating Proteinase K to 95 oC for 10 minutes (Page 2, How do we inactivate Proteinase K). In other words, If the Proteinase K is not inactivated prior to PCR, it can digest the Reverse Transcriptase and DNA polymerase enzymes needed for qRT-PCR (inactivation step limitation of instant claims (12(c), 14(iii), 20(iii) and 21).
Miao does not teach how to pack a sample
Stanford teaches that after the nasopharyngeal, oropharyngeal, nasal, or+ mid-turbinate nasal
swab specimen is collected, the swab is inserted, tip first, into the collection tube and the cap securely fastened. The tube is placed in the biohazard bag, and the bag is closed with the adhesive seal, which reads on a single-layer packing (packing limitation of instant claims 12(a), 14(i) and 20(i))
It would have been obvious to one of ordinary skill in the art to combine the teachings of Srivatsan, Thermoscientific and Miao to develop an in-vitro (since the reactions are carried out in test tubes, instant claim 19 and 20) method for SARS-CoV-2 detection. The steps of this method being the collection and transportation of a dry form sample (nasopharyngeal swab from a subject (human) without any other liquid media), sample extraction with a TE-Proteinase K buffer, heat inactivation step of Proteinase K without RNA extraction and qRT-PCR. It would further have been obvious with that the concentration of proteinase K, Tris and EDTA (adjusting the pH as needed), and the volume of TE buffer, times and temperatures needed for heat inactivation of proteinase K, are clearly a result effective parameter that a person of ordinary skill in the art would routinely optimize. Optimization of parameters is a routine practice that would be obvious for a person of ordinary skill in the art to employ. It would have been customary for an artisan of ordinary skill to determine the optimal amount and volume of each ingredient needed to achieve the desired results. The principle of law states from MPEP 2144.05: "The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages." (Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382); 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 2. It would also have been obvious to follow the manufacturer’s instruction manual when using a commercial RT-PCR kit and interpret the results according to those instructions as required by instant claims 12(d)(e), 14(vi) and 20(vi)).
One of ordinary skill would have been motivated to do so because a method that can save time and reduce cost with a quick turn-around can help clinical or surveillance testing for SARS-CoV-2 as explained above by Srivatsan. There would be a reasonable expectation of success because the different steps of the method are known to work in different settings and labs.
From the combined teachings of the references, it is apparent that one of ordinary skill in the art would have had a reasonable expectation of success in producing the claimed invention. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made, as evidenced by the references, especially in the absence of evidence to the contrary.
7. Claims 16-18 are rejected under 35 U.S.C. 103 as being unpatentable over Srivatsan (supra), in view of Thermoscientific (supra), Miao (supra), Stanford (supra), Helix (Accelerated Emergency Use Authorization (EUA) Summary, Helix COVID-19 Test (Helix OpCo, LLC), October 22,2020), Compass (Accelerated Emergency Use Authorization (EUA) Summary, Compass Laboratory Services SARS-COV2 ASSAY (Compass Laboratory Services, LLC) Priority date 07/13/2020 as found on website https://www.fda.gov/medical-devices/covid-19-emergency-use-authorizations-medical-devices/in-vitro-diagnostics-euas-molecular-diagnostic-tests-sars-cov-2#individual-molecular) and Chen (US 12,297,425 B2. Priority date Apr. 28, 2020).
The teachings of Srivatsan, Thermoscientific, Miao and Stanford have been discussed above and incorporated herein. In addition, Stanford teaches a FDA-approved (instant claim 17) SARS-CoV-2 RT PCR assay kit (title). This Assay kit enables the self-collection of nasal swab sample that is transported in dry conditions in a collection tube (page 3, 2nd paragraph), which reads on the limitation “first part comprising a collection tube and swabs” of instant claims 16 and 18. The assay is carried out on TE buffer for primers/probes (page 5), (second part of instant claims 16 and 18) and includes positive (ssDNA for SARS-CoV-2 E gene and negative controls. The E gene is the target gene for amplification (which reads on the assay utilizing primers and probes for the E gene), (page 7, section 2), (third part of instant claim 16 and fourth part of instant claim 18).
Helix teaches a FDA-approved (instant claim 17) SARS-CoV-2 real time RT-PCR (page 1, Intended use, 1st paragraph). The kit consists of a swab and collection tube (page 2, Helix self-collection kit, 2nd paragraph), (first part of instant claims 16 and 18) and the assay includes primer and probe set(s) designed to detect simultaneously four targets: three SARS-CoV-2 viral targets, the N gene, the ORF1ab gene and the S gene, and one primer/probe set detecting MS2 phage RNA spiked into the reaction as an extraction and process control (page 3, Helix Covid19 test, 1st paragraph), ((third part of instant claim 16 and fourth part of instant claim 18). RNA extraction (RNA for all specimen types is performed using the MagMax Viral/Pathogen II(MVP II) Nucleic Acid Isolation kit ((page 3, Helix Covid19 test, 4th paragraph) (third part of instant claim 18).
Compass teaches a FDA-approved (emergency use authorization (EUA) by the FDA) (instant claim 17) SARS-CoV-2 real time RT-PCR (page 1, Intended use, 1st paragraph). The primers and probe were selected from the ORF 1ab genome region. labelled with the FAM fluorophore. RNA extraction is performed using the MagMax Viral Pathogen Kit (page 2, Device description and test principle, 1sty paragraph), (third part of instant claims 16 and third and fourth part of instant claim 18)
Chen teaches a nucleic acid extraction composition, reagents and kits containing the same which can be used for biological reactions such as PCR (abstract). This kit includes: lysis buffer, wash buffer, an enhancer (proteinase K at 20 mg/ml), an elution buffer (1xTE buffer with pH of 10.0) and spin columns (example 1) (second part of instant claim 16 and second and third part of instant claim 18). The reagents can be used for obtaining nucleic acids of DNA and RNA viruses from various complex samples such as blood, throat swab, saliva and the like, and is very suitable for clinical and scientific research application (column 3 lines 28-35).
It would have been obvious to one of ordinary skill in the art to combine the teachings of Srivatsan, Thermoscientific, Mao and Stanford for the development of an in-vitro method for SARS-CoV-2 detection and for designing a kit capable of performing the steps of such a method. The kit would require the material and reagents for each step to detect SARS-CoV-2. The first part being the collection and transportation of a dry swab in a collection tube (as taught by Stanford and Helix). The second part being the extraction of the viral particles from the swab using a TE-Proteinase K buffer with an optional part being the RNA extraction (as taught by Chen) or an optimized version of the reagents, see below). And the last part comprising running a FDA approved RT-PCR assay containing primers, probes, dyes, enzymes (DNA polymerase and Reverse Transcriptase are obviously necessary components of any RT-PCR kit), and RT-PCR buffer as taught by Stanford, Helix and Compass. All the Stanford, Helix and Compass assays include positive and negative controls such as ssDNA for the E gene and it would be obvious to use similar type of controls that would give the same kind of results like in vitro transcribed RNA for several SARS-CoV-2 genes. It would also be obvious to design primers and probes for any of the SARS-CoV-2 gene to detect the presence of the virus as they are part of the viral genome and even detect more than one gene simultaneously as taught by Helix. It would also be obvious to use fluorescence dyes such as FAM (as taught by Compass) or any other type of dye.
One of ordinary skill would have been motivated to do so because the availability of a kit containing all the steps necessary for the easy and accurate detection of SARS-CoV-2 can help diagnosing the disease. There would be a reasonable expectation of success because other tests such as those describe above have been shown to be useful for diagnosis and have been authorized by the FDA for emergency use.
From the combined teachings of the references, it is apparent that one of ordinary skill in the art would have had a reasonable expectation of success in producing the claimed invention. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made, as evidenced by the references, especially in the absence of evidence to the contrary.
Relevant arguments that apply to claims
Applicant’s Arguments:
The subject matter disclosed in the ICMR Advisory was obtained directly from a joint inventor of the Application, and the ICMR Advisory published less than one year prior to the earliest effective date of the present Application. Accordingly, the ICMR Advisory is not available as prior art against the present Application, under 35 U.S.C. § 102(a)(1).
Examiner’s Response to Arguments: Examiner acknowledges that applicant has properly invoked the 102(b)(1)(A) exception. Please see Examiner’s Note above.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/IMMA BARRERA/
Examiner, Art Unit 1671
/BENJAMIN P BLUMEL/Primary Examiner, Art Unit 1671
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