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 .
Response to Amendment/Disposition of Claims
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 18 August 2025 has been entered.
Applicant’s Amendment filed on 18 August 2025 has been received and entered. Claims 12-13 and 26-28 were pending. Claims 12-13 and 26-28 have been amended. Claims 1-11 and 14-25 have been cancelled. No new claims have been added.
Accordingly, Claims 12-13 and 26-28 are currently pending and will be examined on their merits.
Examiner’s Note
All paragraph numbers (¶) throughout this office action, unless otherwise noted, are from the US PGPub of this application US 2022/0347284 A1, Published 03 November 2022. Applicant’s amended Specifications as presented on 18 August 2025, 21 June 2022, and 24 August 2021 are acknowledged and entered.
Applicant is encouraged to utilize the new web-based Automated Interview Request (AIR) tool for submitting interview requests; more information can be found at https://www.uspto.gov/patent/laws-and-regulations/interview-practice.
Response to Arguments
Applicant's arguments filed 18 August 2025 regarding the previous Office action dated 26 February 2025 have been fully considered. If they have been found to be persuasive, the objection/rejection has been withdrawn below. Likewise, if a rejection/objection has not been recited, said rejection/objection has been withdrawn. If the arguments have not been found to be persuasive, or if there are arguments presented over art that has been utilized in withdrawn rejections but utilized in new rejections, the arguments will be addressed fully with the objection/rejection below.
Drawings and Specification; Sequence Disclosure Requirements
(Objection withdrawn) – The objection to the Drawings and Specification for failing to comply with Sequence Disclosure Requirements is withdrawn in light of the amendments to the Drawings and the Specification.
(New Objection – necessitated by amendment) – The Specification is objected to for failing to comply with Sequence Disclosure Requirements. Specifically, the amended Sequence Listing, filed on 18 August 2025, was deemed defective by the Office on 18 August 2025. Correction is required.
Additionally, the incorporation by reference statement of the Sequence Listing in the Specification must be updated again once the Sequence Listing is amended.
Applicants must comply with sequence rules in order to be considered a complete response to this Office Action.
Specification
(Objection withdrawn) – The objection to the Abstract of the disclosure for containing legal phraseology is withdrawn in light of the amendments to the Abstract.
(Objection withdrawn) – The objection to the title of the invention for containing the word “novel” is withdrawn in light of the amendment to the title.
(Objection withdrawn) – The objection to the disclosure for containing an embedded hyperlink or other form of browser-executable code is withdrawn in light of the amendments to the Specification.
(New Objection – necessitated by amendment) - The abstract of disclosure is objected to because of the following informalities: it is suggested that it say “…The length and organization of the genome and encoded proteins, together with sequence analyses, are also provided.” There should be a comma after “analyses”.
Appropriate correction is required.
Claim Objections
(Objection withdrawn) – The objection to Claim 13 for containing minor informalities is withdrawn in light of the amendments to the claim.
(Objection withdrawn) – The objection to Claim 12 for containing minor informalities is withdrawn in light of the amendments to the claim.
(Objection withdrawn) – The objection to Claims 12 and 26-28 for containing minor informalities is withdrawn in light of the amendments to the claims.
(New Objection – necessitated by amendment) – Claims 12-13 and 27-28 are objected to because of the following informalities: In Claims 12 and 27-28, it is suggested that they say “…wherein said nucleic acid sequence of ORF-1, ORF-2, ORF-3, ORF-4, or ORF-5 contains the base uracil…”.
In Claim 13, it is suggested that it say “…a protein that is at least 95% identical to SEQ ID NOs:_7, 8, 9, 10, or 11…”. There should be a space after the colon in “NO:” and there should be an “s” to pluralize “NO”.
Appropriate correction is required.
(New Objection) – Claims 12 and 26 are objected to because of the following informalities: In Claim 12, it is suggested that it say “…thymine (T), and, (b) determining whether, upon subjecting the mixture of a) to amplification, an amplification product is present…” instead of “…thymine (t), and, (b) determining whether upon subjecting the mixture of a) to amplification an amplification product is present…”.
In Claim 26, it is suggested that it say “…a sequence which is at least 80% identical to a sequence , selected from the group…” instead of “…a sequence which is at least 80% identical to a sequence which is, or which is complementary to, a sequence selected from the group…”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b); Second Paragraph
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.
(Rejection maintained) – The rejection of Claim 12, and dependent claim 27 thereof, under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is maintained.
(Rejection withdrawn) – The rejection of Claims 12 and 27-28 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in light of the amendments to the claims.
(Rejection withdrawn) – The rejection of Claim 28 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in light of the amendments to the claim.
(New Rejection – necessitated by amendment) – Claim 13, and dependent claim 28 thereof, 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.
Regarding Claim 13, it recites the limitation “a reference sequence within a genome of said virus”. The use of the indefinite article “a” with “a genome” renders the claim indefinite because it appears to imply that the virus in question has more than one genome and that only one is required or being selected. It is suggested that the claim be amended by replacing “a” with “the”, but Applicant is free to amend the claim as they deem necessary.
Since a skilled artisan would not be reasonably apprised as to the metes and bounds of the claimed invention, instant Claim 13 is rejected on the grounds of being indefinite. Claim 28 is also rejected since it depends upon Claim 13, but does not remedy the deficiencies of Claim 13.
(New Rejection – necessitated by amendment) – Claim 13, and dependent claim 28 thereof, 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.
Regarding Claim 13, it recites the limitation “…wherein said nucleic acid sequence encodes a protein that is at least 95% identical to SEQ ID NO: 7, 8, 9, 10, or 11”. It is unclear which sequence is being referenced by the phrase “said nucleic acid sequence” because the claim references three different types of sequences. In step (b), it recites “comparing the resulting nucleic acid sequence with a nucleic acid sequence”. Step (b) also recites “a reference sequence” and “wherein said reference sequence is selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 6”. This lack of clarity renders the claim indefinite. It is suggested that the claim be amended by clarifying which sequence is being referenced, but Applicant is free to amend the claim as they deem necessary.
Since a skilled artisan would not be reasonably apprised as to the metes and bounds of the claimed invention, instant Claim 13 is rejected on the grounds of being indefinite. Claim 28 is also rejected since it depends upon Claim 13, but does not remedy the deficiencies of Claim 13.
Response to Arguments
Applicant's arguments with respect to the rejection of Claim 12, and dependent claim 27 thereof, under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, have been fully considered but they are not persuasive.
In their Response, Applicant argues that “it is respectfully submitted that the limitation should be read not in a vacuum but in view of the specification and in the surrounding context, which is amplification reaction” and that the surrounding context is amplification reaction that leads to the detection of the virus” (See Page 2 of Remarks, Last Paragraph). They also argue that “the primer should be sufficiently complementary to specifically recognize (i.e., hybridize to) the template and to be able to initiate elongation reaction” and that since “the rules for designing primers and amplification conditions are well known, with computer-assisted tools and with knowledge of the sequences provided in the specification, it is respectfully submitted that one would be able to at once envisage all suitable primers with sufficient clarity” (see Page 2, Last Paragraph; Page 3, First Paragraph). Examiner respectfully disagrees. As stated in the Advisory Action, primers do not necessarily have to be 100% identical to a template sequence in order to hybridize to said template sequence. As also noted in the Advisory Action, and the previous Office Action, there is no a threshold for complementarity or sequence identity provided in the claim. All that is provided is a minimum sequence length. As such, the claim reads on and encompasses sequences which are sufficiently long enough to enable hybridization without necessarily having a high degree of complementarity. This is particularly important since the instant Specification states that the percent identity, if it was recited in this instance, can be over a continuous sequence or a non-continuous sequence (see Paragraph 0064). As such, the rejection of Claim 12, and dependent claim 27 thereof, under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is maintained.
Claim Interpretation
In light of the issues raised above, the claims are being interpreted as reading upon the following:
Claim 12 is drawn to a method for detecting a virus that infects and is capable of killing fish, comprising the steps of: (a) contacting a nucleic acid extracted from a biological sample of a fish with at least one oligonucleotide primer to form a mixture, wherein the at least one oligonucleotide primer is at least 15 nucleotides long and is complementary to a nucleic acid sequence which is comprised within the genome of the virus wherein said genome comprises a sequence selected from the group consisting of ORF-1, ORF-2, ORF-3, ORF-4 and ORF-5; wherein ORF-1 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 1 and encodes a protein that is at least 95% identical to SEQ ID NO: 7, ORF-2 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 2 and encodes a protein that is at least 95% identical to SEQ ID NO: 8, ORF-3 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 3 and encodes a protein that is at least 95% identical to SEQ ID NO: 9, ORF-4 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 4 and encodes a protein that is at least 95% identical to SEQ ID NO: 10, and ORF-5 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 5 and encodes a protein that is at least 95% identical to SEQ ID NO: 11, wherein said nucleic acid sequence of ORF-1, ORF-2, ORF-3,ORF-4, or ORF-5 contains the base uracil (U) instead of the base thymine (T), and, (b) determining whether upon subjecting the mixture of a) to amplification an amplification product is present, wherein the presence of the amplification product indicates the presence of RNA associated with the virus, and hence the presence of the virus in the biological sample.
Claim 13 is drawn to a method for detecting a virus that infects and is capable of killing fish, comprising the steps of: (a) sequencing a nucleic acid extracted from a biological sample of a fish, and (b) comparing the resulting nucleic acid sequence with a nucleic acid sequence which is, or which is complementary to, a reference sequence within a genome of said virus, wherein said reference sequence is selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5 and SEQ ID NO: 6, and wherein said nucleic acid sequence encodes a protein that is at least 95% identical to SEQ ID NOs: 7, 8, 9, 10, or 11, and wherein an at least 80% sequence identity between the two sequences indicates the presence of the virus in the biological sample.
Further limitations on the method according to Claim 12 are:
33. The method of claim 12, wherein said at least one oligonucleotide primer comprises at least 15 consecutive nucleotides of a sequence which is at least 80% identical to a sequence, or which is complementary to a sequence, selected from the group consisting of SEQ ID NO: 12 to SEQ ID NO: 80, with the proviso that said oligonucleotide primer does not comprise a sequence selected from the group consisting of SEQ ID NO: 21 to SEQ ID NO: 23.
Further limitations on the method according to Claim 13 are:
27. The method of claim 12, wherein said genome comprises a sequence selected from the group consisting of ORF-1, ORF-2, ORF-3, ORF-4 and ORF-5; wherein ORF-1 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 1, ORF-2 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 2, ORF-3 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 3, ORF-4 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 4, and ORF-5 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 5, wherein said nucleic acid sequence of ORF-1, ORF-2, ORF-3, ORF-4, or ORF-5 contains the base uracil (U) instead of the base thymine (T).
28. The method of claim 13, wherein said genome comprises a sequence selected from the group consisting of ORF-1, ORF-2, ORF-3, ORF-4 and ORF-5; wherein ORF-1 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 1, ORF-2 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 2, ORF-3 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 3, ORF-4 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 4, and ORF-5 is at least 90% identical to the nucleic acid sequence of SEQ ID NO: 5, wherein said nucleic acid sequence of ORF-1, ORF-2, ORF-3, ORF-4, or ORF-5 contains the base uracil (U) instead of the base thymine (T).
Claim Rejections - 35 USC § 112(a); First Paragraph
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.
(Rejection maintained) – The rejection of Claims 12-13 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 is maintained.
(Rejection maintained) – The rejection of Claims 26-28 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 is maintained.
(New Rejection – necessitated by amendment) – Claims 12-13 and 26-28 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 instant application attempts to tie structure to function as it relates to sequence identity in the context of a method for detecting a virus that infects and is capable of killing fish, comprising the steps of: (a) contacting a nucleic acid extracted from a biological sample of a fish with at least one oligonucleotide primer to form a mixture, wherein the at least one oligonucleotide primer is at least 15 nucleotides long and is complementary to a nucleic acid sequence which is comprised within the genome of the virus wherein said genome comprises a sequence selected from the group consisting of ORF-1, ORF-2, ORF-3, ORF-4 and ORF-5; wherein ORF-1 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 1 and encodes a protein that is at least 95% identical to SEQ ID NO: 7, ORF-2 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 2 and encodes a protein that is at least 95% identical to SEQ ID NO: 8, ORF-3 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 3 and encodes a protein that is at least 95% identical to SEQ ID NO: 9, ORF-4 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 4 and encodes a protein that is at least 95% identical to SEQ ID NO: 10, and ORF-5 is at least 80% identical to the nucleic acid sequence of SEQ ID NO: 5 and encodes a protein that is at least 95% identical to SEQ ID NO: 11, wherein said nucleic acid sequence of ORF-1, ORF-2, ORF-3,ORF-4, or ORF-5 contains the base uracil (U) instead of the base thymine (T), and, (b) determining whether upon subjecting the mixture of a) to amplification an amplification product is present, wherein the presence of the amplification product indicates the presence of RNA associated with the virus, and hence the presence of the virus in the biological sample and a method for detecting a virus that infects and is capable of killing fish, comprising the steps of: (a) sequencing a nucleic acid extracted from a biological sample of a fish, and (b) comparing the resulting nucleic acid sequence with a nucleic acid sequence which is, or which is complementary to, a reference sequence within a genome of said virus, wherein said reference sequence is selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5 and SEQ ID NO: 6, and wherein said nucleic acid sequence encodes a protein that is at least 95% identical to SEQ ID NOs: 7, 8, 9, 10, or 11, and wherein an at least 80% sequence identity between the two sequences indicates the presence of the virus in the biological sample.
While Applicant defines and provides examples of what constitutes 80% sequence identity, for example, in the Specification (see Paragraphs 0063-0069), it is unclear which residues are essential and therefore are required to be present and unchanged. Even in the context of a protein sequence that is 95% identical to one of SEQ ID NOs: 7, 8, 9, 10, or 11, for example, the 5% variability could encompass critical residues which constitute the essential characteristics of the genus Applicant is claiming. Additionally, Applicant states that the percent identity can be over either a continuous sequence or a non-continuous sequence (see Paragraphs 0064 and 0067-0069), meaning that any sequence which meets the percent identity threshold is encompassed by the claimed invention, regardless of which or how many critical residues or bases are missing, which is particularly important in the context of any and all non-continuous sequences encompassed by the claimed invention. Thus, it would be unclear to a person having ordinary skill in the art to know what to change and what not to change. Furthermore, no variants having as little as 95-99% sequence identity are disclosed, especially variants with non-continuous sequences which meet the percent identity threshold.
As such, Applicant does not appear to be in possession of the full scope of the claimed invention and Claims 12-13 and 26-28 do not meet the written description requirement.
Response to Arguments
Applicant's arguments with respect to the rejection of Claims 12-13 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, have been fully considered but they are not persuasive.
In their Response, Applicant maintained their previous argument and further argued that the “structure-function (i.e., the structure of the DNA and its function) correlation is reflected in the claims” and that the “high similarity (95%) to the references SEQ ID NOs 7-11 implies high functional similarity” (see Page 3 of Remarks, Last Paragraph). Applicant then argues that “a virus that comprises proteins that are 95% identical to SEQ ID NOs 7-11 is likely to have properties to those of the reference virus” (see Page 3, Last Paragraph). While Examiner agrees with the arguments presented regarding the 95% cutoff, Examiner still holds that Applicant has again failed to disclose which residues or bases are essential and are therefore required to be present and unchanged, as noted previously. As also noted in previous Office Actions, Applicant has stated in the instant Specification that the claimed percent identities can be over either a continuous sequence or a non-continuous sequence. Additionally, Applicant has also still failed to demonstrate that any variants possessing any sequence identity less than 100% relative to the claimed sequences were disclosed. As such, a person having ordinary skill in the art would still not know which nucleotides or residues can be changed and which ones cannot be changed and it would still be unclear what the essential characteristics of the claimed sequences are. As such, the rejection of Claims 12-13 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 is maintained.
Applicant's arguments with respect to the rejection of Claims 26-28 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, have been fully considered but they are not persuasive.
In their Response, Applicant presents the same arguments above with regard to Claims 26-28, which depend upon independent Claims 12-13 (see Page 3, Last Paragraph). Examiner counters with the same arguments presented above as well. As such, the rejection of Claims 26-28 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is maintained.
Conclusion
No claims are allowed.
The prior art made of record, but not relied upon, and considered pertinent to applicant's disclosure is listed below:
Nylund et al. (US 2025/0270661 A1) (copending Application # 17/433,416)
Nylund et al. disclose a Totivirus, which causes mortality in fish, and methods of detecting said virus in fish.
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/CAREY ALEXANDER STUART/Examiner, Art Unit 1671
/JANET L ANDRES/Supervisory Patent Examiner, Art Unit 1671