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 04/07//2026 are acknowledged and entered.
Claims 1, 2, 13, 19 and 20 have been amended.
Claims 48 and 49 have been added
Claims 6-7, 12, 18 and 21-47 are cancelled.
Claims 1-5, 8-11, 13-17, 19-20 and 48-49 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
1. As mentioned in the specification, the enzyme AacCas12b is obtained from Alicyclobacillus acidoterrestris, whereas AapCas12b is obtained from Alicyclobacillus acidophilus (Page 26 lines 12-14). AapCas12b is also known as AaCas12b.
Claim Rejections - 35 USC § 102 withdrawn
2. The rejections of claims 1, 2, 6-9 and 11-12, under 35 U.S.C. 102(a)(b) as anticipated by Broughton (previously cited) as evidenced by Chen (previously cited) and NEB (previously cited) are all withdrawn in view of Applicant’s amendments to claims 1 and 2.
Claim Rejections - 35 USC § 103 withdrawn
3. The rejections of claims 1-12 under 35 U.S.C. 103 as being unpatentable over Broughton in view of MN908947 (previously cited) are withdrawn in view of Applicant’s amendments to 1, 2.
4. The rejections of claims 1, 7, 13-17 and 19-20 under 35 U.S.C. 103 as being unpatentable over Broughton in view of Wang (previously cited) and Teng (previously cited) are withdrawn in view of Applicant’s amendments to 1, 13, 19 and 20
5. The rejections of claims 1, 20 and 44 under 35 U.S.C. 103 as being unpatentable over Broughton in view of Blake (previously cited) and Zhang ( previously cited) are withdrawn in view of Applicant’s amendments to 1 and 20
Double Patenting withdrawn
6. The provisional rejections of claim 44 on the ground of nonstatutory double patenting as being unpatentable over claims 1, 12, 13-15, 18 and 27 of co-pending Application No. 18/564,572 is withdrawn in view of Applicant’s cancellation of claim 44.
New Based on Amendments
Claim Objections
7. Claims 1, 2, 10, 20 and 49 are objected, as the term “about” is confusing. Applicants has provided a definition for the term “about”: “Use of the term "about" is intended to describe values either above or below the stated value in a range of approximately +/- 10%; in other forms the values may range in value either above or below the stated value in a range of approximately +/- 5%; in other forms the values may range in value either above or below the stated value in a range of approximately +/- 2%; in other forms the values may range in value either above or below the stated value in a range of approximately +/- 1%. The preceding ranges are intended to be made clear by context, and no further limitation is implied.” (Specification page 20, line 9). However, it is not clear from this definition which form corresponds to which percentage value in which range.
Recitation’s clarity is improved by the following changes: remove the word “about”.
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.
8 Claim 2 is 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. THIS IS A NEW MATTER REJECTION.
Claim 2 recites: “The method of claim 1, wherein the method is performed in about 60-80 minutes, inclusive, or about 60 minutes” Claim 1 recites a one-pod method and two enzymes: “….wherein the thermostable Cas12b comprises AacCas12b or AapCas12b….”, (amendment added to claim 1). Applicant argues that support for this amendment is provided in the specification as filed, at least on page 61, lines 19-28. Lines 19-28 discloses the one-pot iScan detection assays: ” …After the addition of all reagents, the reaction tubes were incubated horizontally in a water bath at 62°C for 30 minutes, then the tubes were spun down to mix the AapCas12b with the LAMP reaction, and incubated again at 62°C for 30 minutes for further AapCas12b based collateral activity. In case of AapCas12b direct addition to the total reaction mix, the tubes were incubated in heat block at 62°C for 1 hr….”. It appears that here is no support in the specification for the AacCas12b enzyme following the exact on-pot method procedure disclosed on page 61.
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.
9. Claim 13 is 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 13 recites: “…wherein the AacCasl2b or AapCasl2b comprises a droplet on the side of the container during step (a) and wherein the contacting in (b) comprises mixing the droplet with the product from (a).”. It is unclear how an enzyme can comprise a droplet.
Appropriate correction is required.
Claim Rejections - 35 USC § 103
10. Claims 1-5, 8-11 and 13-17 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Broughton in view of MN908947 (previously cited), Wang (previously cited), Teng (previously cited) and Teng2 (Cell Discovery (2018) 4:63)
Broughton teaches the development and initial validation of a CRISPR–Cas12-based assay for detection of SARS-CoV-2 from extracted patient sample RNA (entire article), (instant claim 1). Figure 1d (below) teaches a schematic drawing depicting the entire method (named DETECTR): from swab to extracted viral RNA to RT-LAMP (with primers for the E and N genes) to Cas 12-based detection of E or N genes, which are visualized by fluorescent ssDNA probe cleavage (instant claim 1(a), 1(b) and 1(c)). Figure 1d also teaches the use of a fluorescent reader to visualize gene detection (instant claims 14-17).
Broughton’s Figure 1d:
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316
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The CRISPR-Cas 12a system works by the Cas12a-crRNA complex binding a dsDNA substrate and generates a nonspecific ssDNA cleavage (figure 1d). That is, the Cas12a effector protein would cleave an RNP containing the RT-LAMP product and a reporter moiety (figure 1d above), (as required in instant claims 1(b), 1(c)). The assay taught by Broughton (right column, second paragraph, page 870. Figure 1d) performs simultaneous reverse transcription and isothermal amplification using loop-mediated amplification (RT–LAMP) for RNA extracted (instant claim 1(a)) from nasopharyngeal or oropharyngeal swabs (as required in instant claim 8 and 9), followed by Cas12 detection of coronavirus sequences (N or E genes), after which cleavage of a reporter molecule (reads on an activatable ssDNA oligonucleotide comprising a reporter moiety (instant claim 1(b)(ii)) confirms detection of the virus (instant claim 1(c)). The designed primers in this assay target the E (envelope) and N (nucleoprotein) genes of SARS-CoV-2 (instant claim 1(a)), Broughton also teaches that the RT–LAMP was prepared as suggested by a protocol taught by NEB (instant claims 11 (The protocol taught by NEB used by Broughton includes their WarmStart® DNA polymerase and WarmStart® Reverse transcriptase)), and instant claim 13), (DETECTR assay, page 875), resulting in an amplification product.
In addition, Broughton teaches the use of PrimerExplorer v.5 software (https://primerexplorer.jp/e/) to design LAMP primers for SARS-CoV-2 against regions of the N gene and E gene using all SARS-CoV-2 sequences available from GISAID25 as of 27 January 2020 (since the first SARS-CoV-2 virus was made public on January 12, 2020 (MN908947.1), GISAID25 included MN908947.1), (Methods, Nucleic acid preparation section). The instant application discloses the use of PrimerExplorer v5 to design the claimed primers targeting several regions of the N gene and E gene of the SARS-CoV-2 genome (GenBank accession number MN908947) (page 59, Design and screening of LAMP primers section (line 20) (instant claims 3-5 and 10). Broughton also teaches that the LAMP primers were added to the RT-LAPM assay at a final concentration of 0.2 μM for F3 and B3, 1.6 μM for forward inner and backward inner primers and 0.8 μM for loop forward and loop backward primers. Reactions were performed independently for N gene, E gene and RNase P (control) using 2 μl of input RNA at 62 °C for 20–30 min (page 875, DETECTR assays section), (instant claim 10). In addition, Broughton teaches in Figure 2d the Limit Of Detection (LOD) for CDC qPCR and DETECTR assays and in both cases at least 10 viral copies/ μl can be easily detected (instant claim 19).
Broughton does not teach the use of Cas12b or that Cas12b comprises AacCas12b or AapCas12b (instant claims 1 and 13) or primer sequences and concentration (instant claims 3-5, 10), the use of a fluorophore-quencher pair (instant claims 14-17) or that the method is a one-pot method performed in the same container at a temperature between 60 and 62 Centigrade (instant claim 1 and 13).
MN908947 teaches the SARS-CoV-2 isolate Wuhan-Hu-1, complete genome and the claimed primers are found in the viral genome ((instant claims 3-5, 10). See examples below:
F3-N3-1 (SEQ ID NO: 17): ccgaagagct accagacgaa
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103
927
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B3-N3-1 (SEQ ID NO: 18): tgtagcacgattgcagcatt
Complementary reverse sequence: aatgctgcaa tcgtgctaca
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102
934
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LF-N3-1 (SEQ ID NO: 21): agaaatacca tcttggactg ag
Complementary reverse sequence: ctcagtccaa gatggtattt ct
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113
966
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Greyscale
LB-N3-1 (SEQ ID NO: 22): actgagggag ccttgaatac ac
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120
942
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Greyscale
Wang teaches a one-pot toolbox (OCTOPUS) based on Cas12a/crRNA, that enables rapid foodborne pathogen detection at attomolar level (entire article). This one-pot detection means that the reagents, crRNA, and ssDNA-FQ reporter are all in one tube with the subsequent addition of the Cas12a enzyme, omitting the extra cap opening process to avoid practical inconvenience and possible cross-sample contamination (Abstract). This reads on same container as required by instant claim 1 and 13 and the Cas enzyme being added prior (and not after) completion of the RT-lamp reaction (there is no extra cap opening, all of the needed reagents are in one tube). This is confirmed by the figure found in the abstract and attached below: there is only one tube with everything inside.
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274
500
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Wand also teaches the design of a specific crRNA probe, cleaved by Cas12a upon binding to the target substrate and the dual-labeled reporter (fluorophore and quencher) will be cleaved and the separated fluorophore can emit fluorescence which can be measured under a microplate reader (page1427 last paragraph, figure 1, Cas12a/crRNA Nucleic Acid Detection Section page1429), (instant claims 14-17).
Wang does not teach the use of any Cas12b enzyme (instant claims 1 and 13).
Teng teaches a CRISPR-Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity (entire article). In addition, it teaches a previously reported AacCas12b protein with loop-mediated isothermal amplification (LAMP). Teng’s work on AaCAs12b (also known as AspCAs12b, see examiner’s note above), together with the AacCas12b-based work demonstrates that Cas12b-based nucleic acid detection method should be a feasible platform for molecular diagnostics (page 4 second column, second paragraph), (instant claims 1 and 13).
Teng2 teaches the identification of a Cas12b system from the Alicyclobacillus acidiphilus (AaCas12b, also known as AapCas12b, see examiner’s note above), which maintains optimal nuclease activity over a wide temperature range (31 °C–59 °C). AaCas12b can be repurposed to engineer mammalian genomes for versatile applications (abstract). AaCas12b could cleave target DNAs between 4 °C and 100 °C (that is, it is thermostable) in vitro, and maintained the maximal cleavage activity between 31°C and 59°C. (Page 2 Results second paragraph). In other words, the enzyme is functional and very close to maximum activity between 60°C and 62°C (Figure 1b - In vitro cleavage activity) as required by claim 1(b) and (1(c).
One of ordinary skill in the art would have been motivated to combine the teachings of Broughton and MN908947 to develop a RT-LAMP/CRISPR-Cas12 system and to find primers for the specific detection of SARS-CoV-2 N and E genes (as taught by Broughton). It would further be obvious to use the SARS-CoV-2 sequence as first published on MN908947 in combination with PrimerExplorer v5 to develop effective primers. using these tools as required by instant claims 3-5 and 10. One of ordinary skill would have been motivated to do so because software like PrimerExplorer v5 have been specifically developed for the purpose of primer optimization. There would be a reasonable expectation of success because PrimerExplorer v5 is known to make the process of designing highly specific primers very simple and effective.
It would further be obvious that the primer concentrations in a reaction, the reaction time (instant claim 2), reaction temperature, gene copy number or other reaction conditions 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 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.
One of ordinary skill in the art would have been motivated to combine the teachings of Broughton with Wang to develop an one-pot in one single container (as taught by Wang) RT-LAMP/CRISPR-Cas12 system for SARS-CoV-2 detection and incorporate a dual-labeled reporter (fluorophore and quencher) to be cleaved so fluorescence (also disclosed by Broughton) can be measured. It would further be obvious to combine the teachings of Broughton and Wang with Teng and Teng2 and test different enzymes including Cas12a and Cas12b (such as AapCas12b) and optimize the method accordingly. One of ordinary skill would have been motivated to do so because having a reliable detection system, and some flexibility regarding which enzyme to use, is needed for a consistent RT-LAMP/CRISPR-Cas system. There would be a reasonable expectation of success because the dual-labeled reporter (fluorophore and quencher) has been shown to be very effective in multiple types of assays at providing accurate results, and several Cas enzymes (including AapCas12b) are known to be both thermostable and functional in LAMP assays (Teng and Teng2)
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.
11. Claims 20 and 48-49 are rejected under 35 U.S.C. 103 as being unpatentable over Broughton, Wang (previously cited) and Teng (previously cited) in view of Blake (US2023/0183783 A1; with provisional application No. 63/038,710, filed on June 12,2020) and
Broughton, Wang and Teng teachings have been described above and applied herein. As a reminder, Broughton teaches in Figure 2d the Limit Of Detection (LOD) for CDC qPCR and DETECTR assays and in both cases at least 10 viral copies/μl can be easily detected (instant claim 48 requires 20 copies/μl) so it would be obvious to detect 20 copies/μl (using any Cas enzyme) as it much higher than what the standard limit was at the time of the invention. In addition, Wang teaches that Cas12 and Cas13 are among the Cas enzyme family reported to generate collateral cleavage on DNA and RNA, respectively (page 1427 second column second paragraph) (as recited in instant claim 20 (c)(i) and 20(d)).
Blake teaches a detection method comprising steps of: contacting a CRISPR-Cas complex comprising: a Cas protein with collateral cleavage activity; and a guide RNA selected or engineered to be complementary to a target sequence; with a sample comprising the target sequence (instant claim 20). One of these Cas proteins includes a TccCAs13a Thermoclostridium caenicola (a Cas13 enzyme as required by instant claim 20) identified by SEQ ID NO: 1 [0086] which is 100% identical to the instant application SEQ ID NO: 67 recited in instant claim 20, see alignment below.
SEQUENCE ALIGNMENT FOR SEQ ID NO: 67
Title: US-18-000-055-67
Perfect score: 6359
Sequence: 1 MKITKRKWGEHHPPLYFYRD..........PSHGERFIDTLKALMVYPRG 1225
US-17-795-815-1
(NOTE: this sequence has 4 duplicates in the database searched)
Sequence 1, US/17795815
Publication No. US20230183783A1
GENERAL INFORMATION
APPLICANT: SHERLOCK BIOSCIENCES
TITLE OF INVENTION: IMPROVED DETECTION ASSAYS
FILE REFERENCE: 2013065-0427
CURRENT APPLICATION NUMBER: US/17/795,815
CURRENT FILING DATE: 2022-07-27
PRIOR APPLICATION NUMBER: PCT/US21/15306
PRIOR FILING DATE: 2021-01-27
PRIOR APPLICATION NUMBER: 63/139,267
PRIOR FILING DATE: 2021-01-19
PRIOR APPLICATION NUMBER: 63/038,710
PRIOR FILING DATE: 2020-06-12
PRIOR APPLICATION NUMBER: 62/970,159
PRIOR FILING DATE: 2020-02-04
PRIOR APPLICATION NUMBER: 62/967,536
PRIOR FILING DATE: 2020-01-29
PRIOR APPLICATION NUMBER: 62/966,527
PRIOR FILING DATE: 2020-01-27
NUMBER OF SEQ ID NOS: 294
SEQ ID NO 1
LENGTH: 1225
TYPE: PRT
ORGANISM: Thermoclostridium caenicola
Query Match 100.0%; Score 6359; Length 1225;
Best Local Similarity 100.0%;
Matches 1225; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKITKRKWGEHHPPLYFYRDEDSGRLLAQNDRKQDYTDTLFNDIAQDTFERSLRNRLLKT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKITKRKWGEHHPPLYFYRDEDSGRLLAQNDRKQDYTDTLFNDIAQDTFERSLRNRLLKT
Qy 61 PEKGDKRFYSNEIVKLVEKLCQGADVAEIMKSMERNEKLRPKNEKEIKNLKKQLDGTLSE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 PEKGDKRFYSNEIVKLVEKLCQGADVAEIMKSMERNEKLRPKNEKEIKNLKKQLDGTLSE
Qy 121 YGKRYTAPEGAMTLNDALFYLVEGNPLKQAMAKAELGKIREALIKEKENRINRVRYSIKN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 YGKRYTAPEGAMTLNDALFYLVEGNPLKQAMAKAELGKIREALIKEKENRINRVRYSIKN
Qy 181 NKIPLRIQEDGGITPNNDRAAWLLGLMKPADPAKGITDCYPLLGELEEVFDFDKLSKTLH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 NKIPLRIQEDGGITPNNDRAAWLLGLMKPADPAKGITDCYPLLGELEEVFDFDKLSKTLH
Qy 241 EKISRCQGRPRSIAMAVDEALKQYLRELWEKSPSRQQDLKYYFQAVQEYFKDNFPIRTKR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 EKISRCQGRPRSIAMAVDEALKQYLRELWEKSPSRQQDLKYYFQAVQEYFKDNFPIRTKR
Qy 301 MGARLRQELLKDKTSLSRLLEPKHMANAVRRRLINQSTQMHILYGKLYAYCCGEDGRLLV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 MGARLRQELLKDKTSLSRLLEPKHMANAVRRRLINQSTQMHILYGKLYAYCCGEDGRLLV
Qy 361 NSETLQRIQVHEAVKKQAMTAVLWSISRLRYFYQFEDGDILSNKNPIKDFRDKFLRDTNK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 NSETLQRIQVHEAVKKQAMTAVLWSISRLRYFYQFEDGDILSNKNPIKDFRDKFLRDTNK
Qy 421 YTHEDVEACKEKLQDFFPLKELQEKIKEDAKGLQETDNKQADTTDFKAIGHIVRDDRKLC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 YTHEDVEACKEKLQDFFPLKELQEKIKEDAKGLQETDNKQADTTDFKAIGHIVRDDRKLC
Qy 481 NQLLAECVSCIGELRHHIFHYKNVTLIQALKRIADKVKPEDLSVLRAIYLLDRRNLKKAF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 NQLLAECVSCIGELRHHIFHYKNVTLIQALKRIADKVKPEDLSVLRAIYLLDRRNLKKAF
Qy 541 AKRISSMNLPLYYREDLLSRIFKKEGTAFFLYSAKIQMTPSFQRVYERGKNLRREFECER
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 AKRISSMNLPLYYREDLLSRIFKKEGTAFFLYSAKIQMTPSFQRVYERGKNLRREFECER
Qy 601 MKAEASNGQNGQDGDRLKWFRQLAAGDSADTHFNWAVEAYAESAADVENNVEFDTDVDAQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 MKAEASNGQNGQDGDRLKWFRQLAAGDSADTHFNWAVEAYAESAADVENNVEFDTDVDAQ
Qy 661 RALRNLLLLIYRHHFLPEVQKDETLVTGKIHKVLERNRQLSEGQGPNQGKAHGYSVIEEL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 RALRNLLLLIYRHHFLPEVQKDETLVTGKIHKVLERNRQLSEGQGPNQGKAHGYSVIEEL
Qy 721 YHEGMPLSDLMKQLQRRISETERESRELAQEKTDYAQRFILDIFAEAFNDFLEAHYGEEY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 YHEGMPLSDLMKQLQRRISETERESRELAQEKTDYAQRFILDIFAEAFNDFLEAHYGEEY
Qy 781 LEIMSPRKDAEAAKKWVKESKTVDLKTSIDEKEPEGHLLVLYPVLRLLDERELGELQQQM
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 LEIMSPRKDAEAAKKWVKESKTVDLKTSIDEKEPEGHLLVLYPVLRLLDERELGELQQQM
Qy 841 IRYRTSLASWQGESNFSEEIRIAGQIEELTELVKLTEPEPQFAEEVWGKRAKEAFEDFIE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 IRYRTSLASWQGESNFSEEIRIAGQIEELTELVKLTEPEPQFAEEVWGKRAKEAFEDFIE
Qy 901 GNMKNYEAFYLQSDNNTPVYRRNMSRLLRSGLMGVYQKVLASHKQALKRDYLLWSEKHWN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 GNMKNYEAFYLQSDNNTPVYRRNMSRLLRSGLMGVYQKVLASHKQALKRDYLLWSEKHWN
Qy 961 VKDENGADISSAEQAQCLLQRLHRKYAESPSRFTEEDCKLYEKVLRRLEDYNQAVKNLSF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 VKDENGADISSAEQAQCLLQRLHRKYAESPSRFTEEDCKLYEKVLRRLEDYNQAVKNLSF
Qy 1021 SSLYEICVLNLEILSRWVGFVQDWERDMYFLLLAWVRQGKLDGIKEEDVRDIFSEGNIIR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 SSLYEICVLNLEILSRWVGFVQDWERDMYFLLLAWVRQGKLDGIKEEDVRDIFSEGNIIR
Qy 1081 NLVDTLKGENMNAFESVYFPENKGSKYLGVRNDVAHLDLMRKNGWRLEAGKTCSVMEDYI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1081 NLVDTLKGENMNAFESVYFPENKGSKYLGVRNDVAHLDLMRKNGWRLEAGKTCSVMEDYI
Qy 1141 NRLRFLLSYDQKRMNAVTKTLQQIFDRHKVKIRFTVEKGGMLKIEDVTADKIVHLKGSRL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1141 NRLRFLLSYDQKRMNAVTKTLQQIFDRHKVKIRFTVEKGGMLKIEDVTADKIVHLKGSRL
Qy 1201 SGIEIPSHGERFIDTLKALMVYPRG 1225
|||||||||||||||||||||||||
Db 1201 SGIEIPSHGERFIDTLKALMVYPRG 1225
The exemplary reaction taught by Blake was incubated at 58°C (instant claim 20(c)). for 120 minutes [0099], (instant claim 49). However, It would further be obvious with that the temperatures and incubation time in a reaction 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 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.
One of ordinary skill in the art would have been motivated to combine the teachings of Broughton, Wang and Teng with Blake to develop a RT-LAMP/CRISPR-Cas system for SARS-CoV-2 detection and test the Cas13 enzymes claimed by Blake to optimize the method. One of ordinary skill would have been motivated to do so because these CAS13 enzymes have been successfully characterized. There would be a reasonable expectation of success because these Cas 13 enzymes have been shown to effectively work in the CRISPR-Cas system..
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 new claims
Applicant’s arguments have been fully considered and are not persuasive. Therefore, the rejections are maintained.
Applicant’s Arguments:
The starting point for an obviousness determination must be the Supreme Court's
decision in KSR v. Teleflex, 550 U.S. 398 (2007). There, the Court had held that the obviousness determination should address four factors, all of which must be considered, though not in any prescribed order: (1) the scope and content of the prior art; (2) the level of ordinary skill in the art; (3) the differences between the claimed invention and the prior art; and (4) any secondary considerations suggesting nonobviousness, such as commercial success, failure of others, and long felt but unmet need. Id. The Court cautioned that the fact finder should be careful about reading the teachings of the invention at issue into the prior art, to avoid applying inappropriate hindsight, ex post reasoning. Id. at 36.
Examiner’s Response:
Applicant’s arguments have been carefully considered but are not found persuasive.
Please see 103 rejection above for points (1)-(4) factors that need to be considered. In response to Appellants’ argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). As discussed below, there is ample motivation to combine the references independent of the inherent feature.
Applicant’s Arguments:
Applicant was first to investigate and characterize the application of thermostable AacCas12b/AapCas12b, and TccCas13a/HheCas13 enzymes, which retain activity, even when exposed to temperatures up to 62 °C, or 70 °C, respectively, for prolonged periods of time, for use in the claimed single-solution "one-pot" isothermal RT-LAMP methods for detection of SARS-CoV-2, and thereby provide a significant advance over the prior art.
Examiner’s Response: Applicant’s arguments have been carefully considered but are not found persuasive.
Improvements to existing methods can be patented, as long as they are new, useful, and non-obvious. Being the first to investigate is not a reason for patentability if the invention is found obvious based on the existing prior art at the time of filing (priority date). Please see discussion above for the obviousness rejection issued under 35 U.S.C. Section 103 of U.S. patent law (103 rejection).
Applicant’s Arguments:
Since none of the cited art describes RT-LAMP methods employing a thermostable
AacCas12b, or AapCas12b, or TccCas13a or HheCas13 enzyme to detect SARS CoV-2 RNA, the cited art does not teach or suggest assays that impart the same efficiency (i.e., lack of cross- contamination, rapidity or high sensitivity) of the claimed methods, that can be readily transferred into a test kit incorporating a single droplet and/or single reaction vessel. Rather, the cited art methods rely on transferring an RT-LAMP product to a second tube, and/or addition of a Cas enzyme after completion of the RT-LAMP reaction(s), RNAs which complicates handling and, more importantly, leads to aerosol formation that is detrimental to the accuracy of subsequent reactions, and/or do not consider the LOD necessary for detection of SARS CoV-2 in clinical samples.
Accordingly, the claimed methods address the shortcomings of the cited art by including the claimed thermostable Cas enzymes as part of a single reaction mixture that is incubated at a temperature optimal for RT-LAMP, without compromising the activity of the Cas enzyme. None of Broughton, MN908947, Wang, Teng, Blake, Zhang, or Chen teach or suggest how to achieve this goal, since none of the cited art provide methods to exploit the thermostable Cas reagents that can tolerate the temperatures required for detection of SARS CoV-2 in clinical samples via RT-LAMP reactions.
For at least the foregoing reasons the claims as amended are novel and non-obvious over Broughton, MN908947, Wang, Teng, Blake, Zhang and Chen.
Examiner’s Response: Applicant’s arguments have been carefully considered but are not found persuasive.
The teachings of Broughton, MN908947, Wang, Teng, Teng2, Blake are discussed in detail in the 103 rejection section above but in particular, Wang teaches a one-pot method in a single tube and Teng2 teaches a thermostable AapCas12b, which maintains optimal nuclease activity over a wide temperature range. In addition, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986) (see 103 rejection above regarding the teachings of the cited art and the motivation to combine these references).
In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (lack of cross-contamination, rapidity, lack of aerosol formation etc.) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). That being said, Wang discloses that their one-pot method avoids cross-contamination because it only uses one tube.
Regarding applicant’s claims of an improved method over the prior art teachings, a showing of unexpected results must be based on evidence, not argument or speculation. In re Mayne, 104 F.3d 1339, 1343-44, 41 USPQ2d 1451, 1455-56 (Fed. Cir. 1997) (conclusory statements that claimed compound possesses unusually low immune response or unexpected biological activity that is unsupported by comparative data held insufficient to overcome prima facie case of obviousness). MPEP § 2145. A greater than expected result is an evidentiary factor pertinent to the legal conclusion of obviousness ... of the claims at issue.” In re Corkill, 711 F.2d 1496, 226 USPQ 1005 (Fed. Cir. 1985). MPEP 716.02 (a). The evidence relied * > upon < should establish “that the differences in results are in fact unexpected and unobvious and of both statistical and practical significance.” Ex parte Gelles, 22 USPQ2d 1318, 1319 (Bd. Pat. App. & Inter. 1992). MPEP 716.02 (b). Applicant must further show that the results were greater than those which would have been expected from the prior art to an unobvious extent, and that the results are of a significant, practical advantage. Ex parte The NutraSweet Co., 19 USPQ2d 1586 (Bd. Pat. App. & Inter. 1991). MPEP 716.02 (b). See also In re Nolan, 553 F.2d 1261, 1267, 193 USPQ 641, 645 (CCPA 1977) and In re Eli Lilly, 902 F.2d 943, 14 USPQ2d 1741 (Fed. Cir. 1990) as discussed in MPEP § 716.02(c). Applicant has failed to provide evidence of unexpected results as the data is only showing some improvements that can be easily obtained by optimization. The prior art discusses thermostable enzymes, and the use of the one-pot method. Applicant has failed to provide evidence of such breakthrough in the claimed method.
Applicant has not sufficiently described why there is no prima facie case for obviousness.
Applicant argues as set forth above. Thus, for the reasons set forth above and the reasons of record, the rejection is maintained.
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
/Michael Allen/ Supervisory Patent Examiner, Art Unit 1671
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