Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election of distinct set of primers: Set 4: SEQ ID NO: 7-12 and distinct set of detection reagents: Set4: SEQ ID NO: 16 and 17 in the reply filed on 3/23/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Upon further consideration, the election of species for a fluorescent DNA intercalating dye, a target organism, and a target human gene is WITHDRAWN.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," 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 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) 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") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) 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 of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application contains sequence disclosures in accordance with the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 - 1.825.
The sequence disclosures are located Table 1. The FIP primer identified for Gene M in primer sets 2, 3, and 4 IS NOT in the sequence listing. Although this sequence is identified as SEQ ID NO: 9 in Table 1, it is not identical to SEQ ID NO: 9 in the sequence listing.
Required response – Applicant must provide:
A "Sequence Listing" part of the disclosure, as described above in item 1); as well as
An amendment specifically directing entry of the "Sequence Listing" part of the disclosure into the application in accordance with 1.825(b)(2);
A statement that the "Sequence Listing" includes no new matter in accordance with 1.825(b)(5); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(b)(4).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also 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;
If the "Sequence Listing" part of the disclosure is submitted according to item 1) b), c), or d) above, Applicant must also provide:
A replacement CRF in accordance with 1.825(b)(6); and
Statement according to item 2) a) or b) above.
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 1-28, 36, and 37 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The limitations “without the need for a pre-treatment of the biological sample” and “wherein the biological sample or the lysed sample has not undergone a pre-treatment step” are new matter. In support of the amendment, the response points to paragraphs 48, 151, and 152, as well as Example 6 and Figures 7 and 8. These have been carefully reviewed.
Paragraph 48 does not mention “pre-treatment of the biological sample” generically. It discusses placing the tip of a collection apparatus into a buffer for elution and lysis, as well as a clarification step. It further teaches “the methods described herein can be practiced without the need for a standard nucleic acid purification step.” However, it does not contemplate excluding all “pre-treatment” of a biological sample, as currently claimed. Example 6, including paragraphs 151 and 152 teach eluting a swab by swirling in a buffer 30 times, which is within the metes and bounds of a “pretreatment.” Figures 7 and 8 do not speak to these limitations. The disclosure at ¶17 contemplates steps prior to the isothermal nucleic acid amplification reaction, including a clarification step, chemical lysis and or thermal treatment, but it does not contemplate excluding any or all possible “pre-treatment” of the biological sample. Therefore, the newly added exclusionary proviso is new matter.
Further, with regard to claims 36 and 37 no basis could be identified for excluding “timed incubation” as a pre-treatment or standard nucleic acid or purification step.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-28 and 36-37 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.
The claims are unclear when they recite “without the need for a pre-treatment of the biological sample and a standard nucleic acid extraction or purification step” and it is unclear if this is intended to require that the method must be without the need for one of pre-treatment or standard extraction or purification or if the method is intended to exclude both. In claim 1, the claim further recites “wherein the biological sample or the lysed sample has not undergone a pre-treatment step and a standard nucleic acid extraction or purification. Furthermore, it is not clear how “the need” modifies the claim. It is not clear if this is meant to imply that the encompassed method cannot have one or both of these steps, or if “the need” is theoretical.
Claim 1 and claim 23 both refer to “a standard nucleic acid extraction or purification step.” The specification does not provide a limiting definition for "standard nucleic acid purification." Paragraph 48 of the description teaches examples of standard nucleic acid purification but does not provide a clear definition of a purification that is "standard" relative to one which is not "standard." It is unclear what the metes and bounds of the phrase are, and as a consequence the scope of the claim is unclear.
Claim 1 recites “directly” subjecting the sample to lysis and then “directly” subjecting the lysed sample to an isothermal nucleic acid amplification reaction. The specification does not define “directly.” In para 137 a "direct assay" is described which does not use lysis or heat treatment of sample prior to RT-LAMP. The assay does include addition of RNAse inhibitor (which is reasonably considered as a "sample treatment"). However, it is clear that claim 1 does not mean "directly" to exclude lysis, and so it is not clear what the metes and bounds of "directly" are. Paragraph 139 teaches an assay in which "lysed sample was then added directly to RT-LAMP reaction," but those lysed samples had been lysed and heat treated, which maybe is excluded from the instant claims.
Further, claims 1 and 23 recite “pre-treatment.” The specification fails to define what is within the metes and bounds of "pre-treatment" and thus it is unclear what the boundaries of the excluded material is. As a consequence, the scope of the claims is unclear.
The response cites to "Example 6" as providing basis for the claim amendment that adds this limitation. This example teaches "sample elution" and it is unclear if this is a "pre-treatment step." The specification does not define what constitutes a "treatment" of the sample. As another example, paragraph 151 teaches "swirling the swab in buffer" and it is not clear if this is a "treatment" such that such swirling would be excluded from the claim or if this is permissible within the claim. Furthermore, claim 82 refers to "additional steps prior to the isothermal amplification" and it is not clear if these steps such as concentration and thermal treatment are considered "pre-treatment" steps. Further still, the claim states that the sample must not have undergone "a pre-treatment step" AND "extraction or purification" step. It is unclear if this means a sample that has been pretreated, but not extracted could be within the claim since it has not undergone BOTH pretreatment and extraction or purification. Furthermore, it is relevant that the RT-LAMP in paragraph 153 occurs at 67C, which is higher than room temperature and would require heating of the sample. It is unclear how this required heating is distinguished from other "pre-treatment" that is being excluded from the claims.
Claim 23 recites “directly” subjecting a sample to a RT-LAMP reaction, and the metes and bounds of this limitation are unclear. It is unclear, for example, if the sample is on a swab, if “directly” is meant to exclude eluting the sample. The specification uses this phrase, but does not provide any guidance as to what qualifies as “directly” detecting an organism in a biological sample. For example, ¶151 and 153, cited as basis for the amendment that included the “directly” limitation describe eluting a sample by swirling and then subjecting the elution solution to RT-LAMP. It is unclear if this is within the metes and bounds of “directly” subjecting a sample to RT-LAMP.
Claim 2 recites “RT” without defining the acronym and it is unclear if “RT” refers to reverse transcription or real time or something else.
Claim 4 recites “a polynucleotide…that is constitutively expressed” and then recites “beta-actin DNA” as an option, which is unclear because DNA is no typically considered as an “expressed” molecule.
Claim 5 contains the trademark/trade multiple trademarks, including all recited reagents with the exception of “ethidium bromide” and “oxazole yellow-based cyanine dyes.” Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe the required dye and, accordingly, the identification/description is indefinite.
Regarding claim 5, the phrase "e.g." and the limitations in parentheticals render the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Regarding claim 6, the phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claims 21 and 23-28 are indefinite when they refer to SEQ ID NO: 9 as this sequence is different in Table 1 relative to the sequence listing and it is unclear which sequence is meant to be required by the claim. For the purposes of initiating a search and examination the sequence recited in the sequence listing has been considered, as this is the sequence available for search in the USPTO systems. Furthermore, these claims are indefinite when they refer to SEQ ID NO: 16 and 17 because in Table 1 the oligos identified with these SEQ ID NO: have attached modifications, but these are not included in the sequence listing. It is unclear if the modifications are intended to be required elements of the elected invention.
Claim Rejections - 35 USC § 112
Claims 21 and 23-28 and 37 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of all of the different primer sets is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the alternatives do not share a common structure as each set is a unique combination of sequences.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
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. 119(e) 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. 63199515, 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.
The instant claims do not have basis in the provisional application, at least for the same reasons the claims are new matter as discussed herein. Further, with regard to claim 1, the provisional application does not disclose a reaction mixture that comprises more than one set of 4-6 oligonucleotide primers, each to a different target, and two different reagents “for independent detection” of amplified target nucleic acid. Further, and in addition, with regard to instant claim 21 and 23, the provisional does not teach primer set 4 which includes instant SEQ ID NO: 16 and SEQ ID NO: 17. Nor does the provisional teach a primer that comprises instant SEQ ID NO: 9 as represented in the sequence listing.
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.
Claim(s) 1-7, 9, 10, 17-20, 22, and 36 is/are rejected under 35 U.S.C. 103 as being unpatentable over KR102109196B1, published 5/11/2020, herein referred to as KR, in view of Holger (WO 2023/057422 A1) and Zhang et al. (medRxiv preprint doi: https://doi.org/10.1101/2020.10.26.20219972; version posted October 29, 2020, 22 pages).
Paragraph numbering for the KR reference is according to the partial translation provided with the document enclosed with the Office action.
KR teaches a method where a nasal swab sample was directly mixed with lysis buffer containing a buffering agent and a non-ionic surfactant. See translation ¶0060.
The lysed sample was directly subjected to isothermal amplification in a reaction mix comprising 6 primers directed to a first target nucleic acid, dNTP, a source of magnesium ions (MgSO4), a DNA polymerase (Bst polymerase I) (¶0060).
The amplified target was detected every 15 seconds, and the results show that the target was confirmed only in samples infected with the 2019 novel coronavirus. See ¶0061.
Regarding the final wherein clause, the reference teaches that the lysed sample has not undergone any pretreatment step, referring to the reaction as Direct RT-LAMP and teaching that the reaction does not include a separate nucleic acid extraction and purification step. See ¶0061.
Regarding claim 5, KR teaches including SYBR Green I in the reaction mixture. ¶60.
Regarding claims 9 and 10, KR teaches that the isothermal reaction was performed at 65C for 50 minutes (¶60), but teaches that infected samples were confirmed after 42 minutes of reaction time ¶61.
Regarding claims 17-20, KR teaches that the target is a virus, namely SARS-Cov-2, Example 3.
Regarding claim 22, the sample is a nasal swab (¶60).
KR does not teach a method wherein the lysis buffer comprises an RNase inhibitor, nor does the reference teach including a second set of primers directed to a second target. KR does not teach lyophilized reaction mixture and reconstituting the reaction mixture. KR does not teach wherein the method is performed wih6tin a time period from 10 to 45 minutes.
Like KR, Holger teaches LAMP-based methods for detecting coronavirus. The reference teaches LAMP based methods wherein a nose/throat swab specimens were lysed in a buffer comprising buffering agent, non-ionic surfactant (p. 41, Buffer B) and RNase inhibitor (p. 55, 57). The reference teaches that lysis with Buffer B leads to improved sensitivity and shorter detection times compared to a commercial LAMP kit which did not employ buffer B, an in particular showed that using the buffer with RNase inhibitor allowed the standard extraction step suggested by a commercial kit to be excluded (p. 57-58).
With regard to claim 6, as Holger teaches addition of the lyophilized reagents directly to the sample combined with the lysis buffer, the reaction mixture taught by Holger comprises Rnase inhibitor.
With regard to claim 7, Holger teaches lyophilized LAMP reagents and reconstituting the LAMP reagents (p. 54-58).
Zhang teaches multiplex fluorescent DARQ LAMP detection wherein three primary respiratory viral targets and an internal control are amplified in a single reaction. The reference teaches that the DARQ approach is rapid and is compatible with standard instruments (p. 8). The reference further teaches that positive signals can be reliably detected by endpoint scanning so reactions could by quick scanning (p. 8).
The reaction mix for DARQ LAMP includes six LAMP primers for each target and a reagent (duplex oligo) for each target wherein each reagent is suitable for independent detection of target nucleic acids (p. 9-10; Table 1 on p. 14). The reference teaches detecting a signal from each of at least two different reagents wherein the detection of at least two different signals indicates presence of the organism in the sample. See Figure 1. The DARQ detection reagents consist of a 5’ modified version of the FIP primer annealed to a 3’ modified oligo complementary to the FIP in the 5’ section, and the primers are modified with a quencher and a fluorophore, meeting the requirements of claim 3 (see p. 3 and Table 1).
With regard to claim 4, Zhang teaches detection of internal control beta-actin (Table 1).
It would have been obvious to have modified the method taught by KR so as to have included RNase inhibitor in the lysis buffer, because Holger teaches that the addition of lysis buffer increased sensitivity and speed of detection in LAMP reactions. Furthermore, it would have been obvious to have included additional primers to one or more additional targets and detection reagents to differentiate them as taught by Zhang because Zhang teaches that the multiplex technique increases the functionality of RT-LAMP and can aid in the global fight against the continuing public health threat (p. 1). Regarding claim 5, combining the intercalating detection taught by KR and the DARQ probe detection taught by Zhang would have been obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded predictable results before the effective filing date, namely a way to detect amplification products.
Regarding claim 5, KR teaches that the reaction products were detected after 42 minutes. Zhang teaches carrying out LAMP for 40 minutes for single channel or 49 minutes for 4-channel acquisition. Reaction length is well known to be an optimizable condition. Therefore, it would have been obvious to have modified KR to have a slightly shorter reaction time of 45 minutes as a routine optimization of the length of reaction variable.
Therefore, in view of the prior art, the claimed invention is prima facie obvious.
Claim(s) 7-8 is/are rejected under 35 U.S.C. 103 as being unpatentable over KR102109196B1, published 5/11/2020, herein referred to as KR, in view of Holger (WO 2023/057422 A1) and Zhang et al. (medRxiv preprint doi: https://doi.org/10.1101/2020.10.26.20219972; version posted October 29, 2020, 22 pages) as applied to claims 1-7, 9, 10, 17-20, 22, and 36 above, and further in view of Carter et al. (Journal of Virological Methods 244 (2017) 32–38).
The teachings of KR, Holger and Zhang are given previously in this Office action and are fully incorporated here. These do not teach a method wherein the lyophilized reaction mixture comprises trehalose.
Carter teaches that lyophilizing reagents is a way to promote long term storage (introduction) and teach a LAMP lyophilization mixture that includes trehalose, see p. 34.
It would have been obvious to have modified the methods taught by KR in view of Holger and Zhang so as to have provided a lyophilized reaction mixture for RT-LAMP containing trehalose as taught by Carter in order to provide a reagent mixture that is stable at room temperature.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. GenBank MT911467 teaches the SARS-CoV-2 membrane glycoprotein (M). Instant SEQ ID NO: 7, 8, 11, 12, 16 and 17 are fragments of this sequence, while SEQ ID NO: 10 is composed of fragments of this sequence. Instant SEQ ID NO: 9 in the sequence listing is not within this sequence. Upon amendment of the sequence listing or claims, further consideration will be made.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached at (571)-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
Prosecution Insights