DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
2. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 January 7, 2026 has been entered.
Claims 34-38 and 60-70 are pending.
Claims 34-38, 61-64, and 66-68 are under examination. Claims 60, 65, 69, and 70 remain withdrawn as being drawn to a non-elected invention, but will be considered for rejoinder in accordance with MPEP 821.04 when the elected invention is allowable.
Response to Arguments
3. Applicant’s arguments filed on January 7, 2026 have been fully considered.
Objections to the Substitute Specification
Applicant argues that the objections to the substitute specification should be withdrawn in view of the substitute specification filed with the response (Remarks, pages 1-2).
This argument was persuasive. The objections have been withdrawn.
Objections to claims 34, 61, 62, 64, 67, and 68
Applicant argues that the objections should be withdrawn in view of the amendments to the claims, which adopt the suggestions made in the last Office action (Remarks, page 2).
This argument was persuasive. The objections have been withdrawn.
Rejection of claims 34-38, 61-64, and 66-68 under pre-AIA 35 U.S.C. 112, first paragraph (new matter)
Applicant argues that the rejection should be withdrawn in view of the amendments to claims 34-38, 61-64, and 66-68 (Remarks, pages 2-4). Here, Applicant also points to paras. 44, 47, 48, and 93 of the replacement specification as providing support for the amended claims (Remarks, page 3).
These arguments have been fully considered and are persuasive in part. More specifically, Applicant’s argument was not persuasive with respect to claims 34-37 because, as discussed in the modified rejection, these claims still encompass longer nucleic acids that are not supported by the original disclosure. Applicant’s argument was persuasive with respect to claims 38, 61-64, and 66-68, however. These claims remain rejected under 35 U.S.C. 112, first paragraph for containing new matter, but the issues set forth in the previously made new matter rejection have been addressed by the amendments to these claims.
Rejection of claim 38 under pre-AIA 35 U.S.C. 112, first paragraph (enablement)
Applicant argues that the rejection should be withdrawn in view of the amendments to claims 34 and 38 (Remarks, page 4).
This argument was persuasive. The rejection has been withdrawn.
Rejection of claims 38 and 63 under pre-AIA 35 U.S.C. 112, second paragraph
Applicant argues that the rejection should be withdrawn in view of the claim amendments (Remarks, page 4).
This argument was persuasive. The rejection has been withdrawn.
Rejection of claim 38 under pre-AIA 35 U.S.C. 112, fourth paragraph
Applicant argues that the rejection should be withdrawn in view of the claim amendments (Remarks, page 5).
This argument was persuasive. The rejection has been withdrawn.
Rejection of claims 34-36, 61-64, and 66 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Cockerill in view of Riffelmann and further in view of Whitcombe
Applicant argues that the rejection should be withdrawn in view of the amendments to claims 34 and 64 to incorporate subject matter indicated to be allowable in the last Office action (Remarks, pages 5-6).
This argument was persuasive. The rejection has been withdrawn.
Specification
4. The substitute specification filed on January 7, 2026 has been entered.
Claim Interpretation
5. Claim 64 uses the transitional phrase “having” or “has” to describe a particular nucleic acid. More specifically, the claim recites, “a first oligonucleotide that specifically hybridizes to a nucleic acid having the sequence of SEQ ID NO: 2, or a complement thereof” in lines 1-2.
As discussed in MPEP 2111.03 IV, the transitional phrase “having” (or has) must be interpreted in light of the specification to determine whether open (comprising) language or closed (consisting of) language is intended.
In this case, the transitional phrase “having” is treated as open (i.e., equivalent to “comprising”) because the disclosure is directed to nucleic acids capable of hybridizing to the IS481 sequence of Bordetella pertussis, of which SEQ ID NO: 2 is a part (see, e.g., paras. 9-11, 22, 34, 64, and 91 of the originally filed specification).
Claim Objections
6. Claim is objected to because of the following minor informalities. Inserting the word “also” or “further” before “comprises” in line 3 is suggested. As well, “oligonucleotide” in line 3 should be replaced with “first oligonucleotide” to maintain internal claim consistency.
Claim Rejections - 35 USC § 112(a) (New Matter)
7. 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 34-38, 61-64, and 66-68 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.
Claim 34
Claim 34 has been amended such that it is drawn to “An isolated nucleic acid comprising a nucleotide sequence that is at least 95% identical to between about 10 and about 100 contiguous nucleotides of SEQ ID NO: 2, or a complement thereof.” The isolated nucleic acid must also contain a 5’ extended probe tail comprising a hairpin structure that includes a fluorophore/quencher pair and also comprises SEQ ID NO: 13 or its complement or SEQ ID NO: 28 or its complement.
Applicant’s response states that support for the claimed nucleic acid may be found at, for example, paras. 47 and 93 of the replacement specification filed with the response (Remarks, page 1).
The original disclosure, including the portions cited by Applicant, has been reviewed, but support was not found for the full scope of isolated nucleic acids encompassed by amended claim 34 for two reasons. First, the use of “comprising” in the preamble of the claim causes the claim to still encompass nucleic acids that are much longer than the lengths disclosed in the original disclosure for primers, probes and Scorpion™ primers. Second, the claim encompasses 5’ extended probe tails that comprise one of the recited sequences.
The original disclosure, though, is much more limited compared to the claim scope. More specifically, it discloses specific examples within the claimed genus in para. 117 of the replacement specification filed with the response, but these nucleic acids are only 48 or 50 nucleotides in length, and there is nothing to suggest that the much longer nucleic acids encompassed by claim 34 or nucleic acids with a 5’ extended probe tail comprising one of the recited sequences were contemplated. Para. 47 of the replacement specification filed with the response states that primers may be about 10-100 nucleotides in length, and para. 93 of the replacement specification filed with the response discloses particular primers and probes useful for amplifying SEQ ID NO: 2. Neither of these paragraphs provides support for the full scope of claim 34, though, which as noted above, encompasses much longer nucleic acids and also nucleic acids in which the 5’ extended probe tail comprises one of the recited sequences. Para. 30 of the replacement specification filed with the response only provides support for 5’ extended probe tails that have the sequence of SEQ ID NO: 13 or its complement, or SEQ ID NO: 28 or its complement. Thus, amended claim 34 still contains new matter.
Claims 35-38
These claims depend directly or indirectly from claim 34 and further limit the length of the nucleotide sequence in the isolated nucleic acid of claim 34. As with claim 34, these dependent claims still use open language to describe the isolated nucleic acid, and thus encompass nucleic acids with a total length much longer than the original disclosure supports. These dependent claims also do not address the new matter issue noted above concerning the sequence of the 5’ extended probe tail. Accordingly, amended claims 35-38 still contain new matter.
Claims 61 and 62
Claims 61 and 62 each depend from claim 34 and further limit the sequence of the 5’ extended probe tail. As with claim 34, these dependent claims still use open language to describe the isolated nucleic acid, and thus encompass nucleic acids with a total length much longer than the original disclosure supports. These dependent claims also do not address the new matter issue noted above concerning the sequence of the 5’ extended probe tail. Accordingly, amended claims 61 and 62 still contain new matter.
Claim 63
Claim 63 depends from claim 34 and recites “wherein the 5’ extended probe tail comprises a sequence that is complementary to and hybridizes to a portion of the nucleotide sequence.”
Applicant’s response states that support for this language may be found at, e.g., 48 of the replacement specification filed with the response (Remarks, page 3).
Claim 63 contains new matter for three reasons. First, as with claim 34, claim 63 still uses open language to describe the isolated nucleic acid, and thus encompasses nucleic acids with a total length much longer than the original disclosure supports. Claim 63 also does not address the new matter issue noted above concerning the particular nucleotide sequence of the 5’ extended probe tail. Third, the original disclosure does not provide clear support for the new “and hybridizes to a portion of the nucleotide sequence” language. This language indicates that part of the 5’ extended probe tail hybridizes to the nucleotide sequence also contained in the nucleic acid containing the 5’ extended probe tail (see amended claim 34). The original disclosure, though, only discloses 5’ extended probe tails that hybridize to a portion of the nucleic acid that results from extension of the nucleotide sequence contained in claim 34 (see, e.g., paras. 69 and 87 of the replacement specification filed with the response). Para. 48 of the replacement specification, cited in Applicant’s response as providing the required support, does not support the new language in claim 63 because it does not address the issue of a 5’ extended probe tail hybridizing to a nucleotide sequence attached thereto. Thus, amended claim 63 still contains new matter.
Claim 64
Claim 64 is a new independent claim drawn to a composition comprising a first oligonucleotide. The first oligonucleotide “specifically hybridizes to a nucleic acid having the sequence of SEQ ID NO: 2 or a complement thereof” and also contains a “first 5’ extended probe tail and a stem-loop structure comprising a fluorophore/quencher pair.” The first 5’ extended probe tail also “comprises the sequence of SEQ ID NO: 13 or the complement thereof, or the sequence of SEQ ID NO: 28 or the complement thereof.”
Similar to claim 34, claim 64 encompasses oligonucleotides in which the 5’ extended probe tail comprises SEQ ID NO: 13, the complement of SEQ ID NO: 13, SEQ ID NO: 28, or the complement of SEQ ID NO: 28. The original disclosure, though, only provides support for a first 5’ extended probe tail that has one of these sequences (see, e.g., para. 30 of the replacement specification filed with the response). Para. 48 of the replacement specification, which is cited in the Remarks on page 4 as providing support for amended claim 64 does not address the aforementioned issue concerning the specific nucleotide sequence of the first 5’ extended probe tail. Accordingly, amended claim 64 is still rejected for containing new matter.
Claims 66-68
Claims 66-68 also contain new matter because they depend from claim 64 and do not correct its new matter issue.
Claim Rejections - 35 USC § 112(b)
8. 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 63 and 66 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 63 depends from claim 34 and has been amended to recite “wherein the 5’ extended probe tail comprises a sequence that is complementary to and hybridizes to a portion of the nucleotide sequence.” As discussed above, this claim contains new matter because the original disclosure provides support for a 5’ extended probe tail that hybridizes to a portion of the nucleic acid that results from extension of the nucleotide sequence contained in claim 34 (see, e.g., paras. 69 and 87 of the replacement specification filed with the response), whereas claim 63, as written, requires part of the 5’ extended probe tail to hybridize to the nucleotide sequence also contained in the nucleic acid containing the 5’ extended probe tail (see amended claim 34). As a result of the new matter issue, it is not clear whether “the nucleotide sequence” in the last line of claim 34 was intended to refer to a nucleotide sequence other than that recited in lines 1-3 of claim 34. Thus, the intended scope of claim 63 is not entirely clear, and the claim is indefinite for this reason.
Claim 66 depends from claim 64 and recites “wherein the first oligonucleotide comprises the sequence of SEQ ID NO: 4.” Claim 66 is indefinite because it is not clear whether the claim intends to require (a) the first oligonucleotide to contain SEQ ID NO: 4 in addition to one of the sequences recited in claim 64 for the first 5’ extended probe tail or (b) the first oligonucleotide may contain just SEQ ID NO: 4 (i.e., not SEQ ID NO: 13 or its complement or SEQ ID NO: 28 or its complement). One way for Applicant to address the issue would be to amend the claim to require, for example, the oligonucleotide to “further comprise” SEQ ID NO: 4, provided that doing so would not introduce new matter.
Claim Rejections - 35 USC § 112(d)
9. The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 66 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 66 depends from claim 64 and recites “wherein the first oligonucleotide comprises the sequence of SEQ ID NO: 4.” As discussed above, claim 66 is indefinite because it is not clear whether the claim intends to require (a) the first oligonucleotide to contain SEQ ID NO: 4 in addition to one of the sequences recited in claim 64 for the first 5’ extended probe tail or (b) the first oligonucleotide may contain just SEQ ID NO: 4 (i.e., not SEQ ID NO: 13 or its complement or SEQ ID NO: 28 or its complement). If (b) is correct, claim 66 is not further limiting because it no longer requires all of the elements of the claim from which it depends.
Applicant may cancel the claim, amend the claim to place it in proper dependent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Conclusion
10. No claims are currently allowable.
The claims are free of the prior art because independent 34 and 64 have been amended to require subject matter identified in the last Office action as allowable (i.e., SEQ ID NO: 13 or SEQ ID NO: 28). The claims are rejected for other reasons, however.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Angela Bertagna whose telephone number is (571)272-8291. The examiner can normally be reached 8-5, M-F.
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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681