Detailed Office 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 the Claims
Acknowledgement is hereby made of receipt and entry of the communication filed 10 November, 2025. Claims 1-7 and 12-17 are pending in the instant application. Applicant’s election of Group I (claims 1-7 and 12-17) without traverse for examination on the merits is noted.
35 U.S.C. § 119
Acknowledgment is hereby made of Applicant’s claim for foreign priority based on AU 2020/902624, filed 27 July, 2020. A copy of the foreign priority document submitted under 35 U.S.C. § 119(a)-(d), has been received and placed of record in the file.
37 C.F.R. § 1.98
The information disclosure statements filed 27 January, 2023, and 16 August, 2024, have been placed in the application file and the information referred to therein has been considered.
37 C.F.R. § 1.84
The drawings filed 27 January, 2023, are objected to. Figures 1 and 2 fail to comply with the sequence requirements (see the next paragraph) and Figures 8 and 10 are illegible. Corrected drawing sheets in compliance with 37 C.F.R. § 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 C.F.R. § 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
37 C.F.R. § 1.821-1.825
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 C.F.R. § 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 C.F.R. § 1.831(b) must contain a "Sequence Listing XML", 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 C.F.R. § 1.831-1.835. This "Sequence Listing XML" part of the disclosure may be submitted:
1. In accordance with 37 C.F.R. § 1.831(a) using the symbols and format requirements of 37 C.F.R. § 1.832 through 1.834 via the USPTO’s patent electronic filing system (Patent Center) (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/patents-application-process/filing-online/legal-framework-efs-web), hereinafter "Legal Framework") in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 C.F.R. § 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 C.F.R. § 1.831(a) using the symbols and format requirements of 37 C.F.R. § 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 C.F.R. § 1.52(e)(1)(ii), labeled according to 37 C.F.R. § 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 C.F.R. § 1.52(e)(8) and 37 C.F.R. § 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 C.F.R. § 1.821(a)(1) and (a)(2) (see Figures 1 and 2, as well as, the specification at p. 30). However, this application fails to comply with the requirements of 37 C.F.R. § 1.821 through 1.825 for the reason(s) set forth below. Applicants are reminded that the sequence rules embrace all unbranched nucleotide sequences with ten or more bases and all unbranched, non-D amino acid sequences with four or more amino acids, provided that there are at least 4 “specifically defined” nucleotides or amino acids. The rules apply to all sequences in a given application, whether claimed or not. All such sequences are relevant for the purposes of building a comprehensive database and properly assessing prior art. It is therefore essential that all sequences, whether only disclosed or also claimed, be included in the database. See 37 C.F.R. § 1.821(a) and M.P.E.P. § 2421.02.
Specific deficiencies and the required response to this Office Action are as follows:
1) Sequences appearing in the drawings (e.g., see Figs. 1 and 2) are not identified by sequence identifiers in accordance with 37 C.F.R. § 1.821(d). Sequence identifiers for sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response–Applicant must provide:
- Replacement and annotated drawings in accordance with 37 C.F.R. § 1.121(d) inserting the required sequence identifiers;
AND/OR
- A substitute specification in compliance with 37 C.F.R. § 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, 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.
Claim Objections
Claim 14 is objected to because of the following informalities: “SEQ ID NOs:6” should read -SEQ ID NO.: 6-. Appropriate correction is required.
35 U.S.C. § 112(b)
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.
Claims 4 and 13 are rejected under 35 U.S.C. § 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention. Two separate requirements are set forth under this statute: (1) the claims must set forth the subject matter that applicants regard as their invention; and (2) the claims must particularly point out and distinctly define the metes and bounds of the subject matter that will be protected by the patent grant.
Regarding claim 4, 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 M.P.E.P. § 2173.05(d).
Concerning claim 13, the reference to a mRNA that comprises an E gene or gene product is confusing. The mRNA can comprise the E gene and encode the gene product. However, it doesn’t comprise the actual protein. Appropriate correction is required.
35 U.S.C. § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. § 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless --
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 3, 4, and 12-17 are rejected under 35 U.S.C. § 102(a)(1) as being clearly anticipated by Wölfel et al. (U, May 2020, Virological assessment of hospitalized patients with COVID-2019, Nature 581:465-476, published online 01 April, 2020) and Wölfel et al. (V, May 2020, Virological assessment of hospitalized patients with COVID-2019, Supplementary Information, Nature 581:S1-S5, published online 01 April, 2020). The claims are directed toward a method of detecting SARS-CoV-2 replication in a sample comprising amplifying a subgenomic target region and detecting the presence of said target.
During SARS-CoV-2 viral replication, a full-length genomic RNA is produced along with nine major subgenomic RNAs (sgRNAs), including the envelope (E). During transcription a leader sequence is attached to the 5’ end of each sgRNA. The utilization of an sgRNA leader-specific primer enable detection of the sgRNA. Wölfel et al. (2020U/V) disclose an RT-PCR method for the amplification and detection of subgenomic SARS-CoV-2 mRNA from the E gene (see RT-PCR, replication sites, and infectivity, rt. col., p. 466; Extended Data Fig.1; and Supplementary description of RNA extraction and RT-PCR methods, b. RT-PCR for subgenomic RNA for SARS-CoV-2, S3). This teaching utilized the same primers set forth in SEQ ID NOS.: 4 and 5, which produce the amplicon set forth in SEQ ID NO.: 6 (see Extended Data Fig.1). These primers were directed toward a subgenomic mRNA with a leader sequence (see Supplementary description of RNA extraction and RT-PCR methods, b. RT-PCR for subgenomic RNA for SARS-CoV-2, S3). This teaching clearly meets all of the claimed limitations.
Claims 5-7 are rejected under 35 U.S.C. § 102(a)(1) as being clearly anticipated by Wölfel et al. (May 2020, Virological assessment of hospitalized patients with COVID-2019, Nature 581:465-476, published online 01 April, 2020) and Wölfel et al. (May 2020, Virological assessment of hospitalized patients with COVID-2019, Supplementary Information, Nature 581:S1-S5, published online 01 April, 2020). Claims 5-7 are directed toward a method of determining the prognosis for a SARS-CoV-2 infection in a subject comprising amplifying a subgenomic SARS-CoV-2 mRNA from a sample and detecting the presence or absence of the target nucleic acid. Target nucleic acid levels are correlated with the clinical outcome.
Wölfel et al. (2020U/V) disclose an RT-PCR method for the amplification and detection of subgenomic SARS-CoV-2 mRNA from the E gene (see RT-PCR, replication sites, and infectivity, rt. col., p. 466; Extended Data Fig.1; and Supplementary description of RNA extraction and RT-PCR methods, b. RT-PCR for subgenomic RNA for SARS-CoV-2, S3). In particular, see Fig. 1 wherein the level of detectable subgenomic mRNA declined as neutralizing antibody responses developed. The detection of sgRNA is indicative of active viral replication. As sgRNA levels drop, they are associated with a positive outcome (e.g., elimination of symptoms). This teaching clearly meets all of the claimed limitations.
Joint Inventors, Common Ownership Presumed
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were effectively filed absent any evidence to the contrary. Applicant is advised of the obligation under 37 C.F.R. § 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned at the time a later invention was effectively filed in order for the examiner to consider the applicability of 35 U.S.C. § 102(b)(2)(C) for any potential 35 U.S.C. § 102(a)(2) prior art against the later invention.
35 U.S.C. § 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 of this title, 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 2 is rejected under 35 U.S.C. § 103 as being unpatentable over Wölfel et al. (U, May 2020, Virological assessment of hospitalized patients with COVID-2019, Nature 581:465-476, published online 01 April, 2020) and Wölfel et al. (V, May 2020, Virological assessment of hospitalized patients with COVID-2019, Supplementary Information, Nature 581:S1-S5, published online 01 April, 2020) in view of Hewson et al. (October 2010, Application of high-resolution melt curve analysis for classification of infectious bronchitis viruses in field specimens, Australian Vet. J. 88(10):408-413). Claim 2 is directed toward a method for detecting SARS-CoV-2 in a sample comprising amplifying a subgenomic SARS-CoV-2 mRNA target and subjecting/detecting said target using high resolution melt analysis.
Wölfel et al. (2020U/V) disclose an RT-PCR method for the amplification and detection of subgenomic SARS-CoV-2 mRNA from the E gene (see RT-PCR, replication sites, and infectivity, rt. col., p. 466; Extended Data Fig.1; and Supplementary description of RNA extraction and RT-PCR methods, b. RT-PCR for subgenomic RNA for SARS-CoV-2, S3). This teaching does not disclose the utilization of high resolution melt (HRM) analysis to detect nucleic acids.
Hewson et al. (2010) discloses a real-time PCR/high-resolution melt (HRM) curve analysis to detect different coronavirus strains (e.g., infectious bronchitis virus). Detailed methodologies were provided (see Materials and methods, pp. 2-3). This procedure was highly effective at detecting different IB viral strains.
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to utilize HRM curve analysis, as provided by Hewson et al. (2010), to detect different variants in the procedure of Wölfel et al. (2020U/V). One of ordinary skill in the art would have been motivated to perform this additional analysis to detect SARS-CoV-2 variants with different genotypes and phenotypes.
Correspondence
Any inquiry concerning this communication should be directed to Jeffrey S. Parkin, Ph.D., whose telephone number is (571) 272-0908. The Examiner can normally be reached Monday through Friday from 10:00 AM to 6:00 PM. A message may be left on the Examiner's voice mail service. 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 are unsuccessful, the Examiner's supervisor, Michael Allen, Ph.D., can be reached at (571) 270-3497. Direct general status inquiries to the Technology Center 1600 receptionist at (571) 272-1600.
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Respectfully,
/JEFFREY S PARKIN/Primary Examiner, Art Unit 1671 21 February, 2026