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 .
DETAILED ACTION
Priority
This application is a U.S. national stage of PCT/EP2021/087512 filed on December 23, 2021, which claims priority to and the benefit of Italian Patent Application No. 102020000032351 filed on December 23, 2020 that is hereby acknowledged by the Examiner.
Status of the Claims
The amendment dated 06/21/2023 is acknowledged. Claims 1-13 are pending and under examination.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 06/21/2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement(s) is/are being considered by the Examiner.
Specification
The disclosure is objected to because of the following informalities: The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see page 6 and 13). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Appropriate correction is required.
Claim Objections
Claim 13 are objected to for the following informalities:
Claim 13 does not contain a period at the end of the sentence.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
Claims 1-3, 6-8 and 10-11 are rejected under 35 U.S.C. 103(a) as being unpatentable over Perera et al. “Perera” (Emerging Infectious Diseases, 2020, 26(11):2701-2704, IDS of record dated 06/21/2023) in view of Roman et al. “Roman” (Nature, 2020, 581(7809):465-569, IDS of record dated 06/21/2023).
The claims are directed to an in vitro method for determining the presence of active SARS-CoV2 infection in a subject, wherein said infection is at an early stage and is characterized by a high viral load, said method comprising detecting viral subgenomic RNA encoding the nucleoprotein N (sgN) and viral subgenomic RNA encoding the envelope protein (sgE) in a biological cell or tissue sample from the subject.
Regarding claims 1-3, Perera discloses the characterization of SARS CoV-2 infection by detection of subgenomic RNA (sgRNA) in nasopharyngeal aspirates and throat swabs of patients (Table 2). SgRNA was detected by RT-PCR using sgN specific primers (Supplementary page 2) (instant claims 1-3). The sgRNA is detected at early stages of infection and in combination with high viral load measured by N gene copies/ml (Figure 2) (instant claim 7).
Perera does not teach detection of sgE in a biological sample.
Roman, however, discloses the detection of sgE RNA as an indicator of active replicating virus in throat swab and sputum samples (page 466 second column para. 4 and Fig. 1). The sgE RNA is more abundant in early days of infection (Fig. 1hr.) (instant claims 1-3).
Accordingly, it would have been obvious to one of ordinary skill in the art to generate an in vitro method for determining the presence of active SARS-CoV2 infection in a subject by detecting viral subgenomic RNA encoding the nucleoprotein N as disclosed by Perera whereby the detection is combined with detecting subgenomic RNA encoding the envelope protein as disclosed by Roman. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success given the fact that both Perera and Roman demonstrate the detection of sgN and sgE in patient samples at early stages of SARS-CoV2 infection by RT-PCR in order to increase the accuracy of an early-stage active SARS-CoV2 infection in a subject. Therefore, the claimed invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Regarding claim 6, Perera discloses Virus was isolated from 16 specimens for 16 patients. The median age of the culture-positive patients was 39 years and of the culture-negative patients was 38 years. SARS-CoV-2 N gene copy number in the specimens overall ranged from 9.5 log10 copies/ mL to undetectable (limit of detection 10 copies/mL) (Figure 1).
Regarding claim 8, with respect to the method predicting viral “negativization” by detecting expression levels at different times, it is not inventive and considered well-known, conventional and routine to one of ordinary skill in the art to detect the expression levels in a subject to determine benign SARS-CoV-2 “negativization” in said patient. One of ordinary skill in the art would be motivated to do so with a reasonable expectation of success given the knowledge that the method’s detection and expression levels are correlative to the viral load of said patient as an indicator of severity and/or clearance of infection in said patient. Additionally, according to MPEP 2111.04, it appears Applicant is claiming a feature that is only determined after the method is performed and the assay results are analyzed.
Regarding claim 10, Perera discloses patients analyzed for sgN expression at 3 to 7 day intervals (Table 2).
Regarding claim 11, Perera discloses the characterization of SARS CoV-2 infection by detection of subgenomic RNA (sgRNA) in nasopharyngeal aspirates and throat swabs of patients (Table 2).
Therefore, the claimed invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claims 4-5, 9 and 12 are rejected under 35 U.S.C. 103(a) as being unpatentable over Perera et al. “Perera” (Emerging Infectious Diseases, 2020, 26(11):2701-2704, IDS of record dated 06/21/2023) in view of Roman et al. “Roman” (Nature, 2020, 581(7809):465-569, IDS of record dated 06/21/2023) as applied to claims 1, 3 and 8, and further in view of Cao et al. “Cao” (CN113444835, filing date October 9, 2020), Wu et al. “Wu” (CN111257559, June 9, 2020), Gao et al. “Gao” (CN112760341, filing date November 3, 2020); Yang et al. (CN111187858, IDS of record dated 06/21/2023) and An et al. “An” (US PGPUB 2003/0050470). The teachings of Perera and Roman are outlined above and incorporated herein.
Regarding claims 4, 9 and 12, Perera teaches primer SEQ ID NO: 1 (supplemental 1 page 2)’ Cao discloses primer SEQ ID NO: 2 (SEQ ID NO: 9 of Liu; Example 1); Wu discloses probe SEQ ID NO: 3 (page 7 Example 1); Gao discloses primers SEQ ID NOs: 6 and 7 (SEQ ID NOs: 17 and 18, respectively; Example 9); and Yang discloses probe SEQ ID NO: 8 (SEQ ID NO: 11, claim 1). Moreover, An teaches "Various probes and primers can be designed around the disclosed nucleotide sequences. Primers may be of any length but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the second residue is 2, etc., an algorithm defining all primers can be proposed: n to n+y where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus one (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 . . . and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 . . . and so on. For a 20-mer, the probes correspond to bases 1 to 20, 2 to 21, 3 to 22 . . . and so on." (paragraphs [0065] – [0067]). Therefore, An not only taught designing primers of any length based on a known sequence, but also taught an algorithm for defining all possible primers of a given length based on a known sequence. In this respect, An taught that all possible subsequences of a known sequence could be considered as a primer for that sequence. While An was discussing in particular sequences having to do with prostate, bladder and breast cancer (see Abstract), one of ordinary skill in the art would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
It would have been obvious to one of ordinary skill in the art to generate primer pairs to the known subgenomic RNA of SARS CoV-2 as the primers were known in the prior art as taught by Perera, Liu and Gao; and the probes disclosed by Wu and Yang for rapid qualitative and quantitative determination of microorganisms by RT-PCR amplification. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success for the advantage of optimizing the RT-PCR for having rapid identification as well as accurate, reliable determination of the presence of active SARS-CoV2 infection in a subject given the fact that Liu disclose known primer sequences, SEQ ID NOs: 1 and 2 for the coronavirus N gene, Gao discloses SEQ ID NOs: 6 and 7, while Wu discloses the probe of SEQ ID NO: 3 and Yang discloses probe SEQ ID NO: 8; and An demonstrates the plain consideration of any subsequence of a known sequence as a primer for that sequence. With respect to claim 12 and a kit for performing the method comprising the primers and probes, the concept of packaging components into a kit is considered conventional, obvious and routine in the art. One would be motivated to do this for commercial exploitation of the invention and to provide convenience for the end user.
Regarding claim 5, with respect to the RT-PCR thermocycler conditions, it is not inventive and considered routine and obvious to one of ordinary skill in the art as merely routine experimentation.
In particular, contacting nucleic acids with a primer set specific to hybridize to SARS-CoV-2 nucleic acids and performing RT-PCR amplification is purely convention or routine in the relevant field.
Therefore, the claimed invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claim 13 is rejected under 35 U.S.C. 103(a) as being unpatentable over Perera et al. “Perera” (Emerging Infectious Diseases, 2020, 26(11):2701-2704, IDS of record dated 06/21/2023) in view of Roman et al. “Roman” (Nature, 2020, 581(7809):465-569, IDS of record dated 06/21/2023) as applied to claims 1 and 12, and further in view of Dong et al. “Dong” (CN111139315), Wu et al. “Wu” (CN111257559, June 9, 2020) and An et al. “An” (US PGPUB 2003/0050470). The teachings of Perera and Roman are outlined above and incorporated herein.
Regarding claim 13, Perera and Roman do not explicitly teach N gene primers comprising SEQ ID NOs: 11, 12 and probe SEQ ID NO: 13.
Dong, however, discloses N gene primers SEQ ID NOs: 11 and 12 (Example 1 page 9) and Wu discloses probe SEQ ID NO: 13 (Example 1 page 7). Moreover, An teaches "Various probes and primers can be designed around the disclosed nucleotide sequences. Primers may be of any length but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the second residue is 2, etc., an algorithm defining all primers can be proposed: n to n+y where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus one (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 . . . and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 . . . and so on. For a 20-mer, the probes correspond to bases 1 to 20, 2 to 21, 3 to 22 . . . and so on." (paragraphs [0065] – [0067]). Therefore, An not only taught designing primers of any length based on a known sequence, but also taught an algorithm for defining all possible primers of a given length based on a known sequence. In this respect, An taught that all possible subsequences of a known sequence could be considered as a primer for that sequence. While An was discussing in particular sequences having to do with prostate, bladder and breast cancer (see Abstract), one of ordinary skill in the art would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
It would have been obvious to one of ordinary skill in the art to generate primer pairs to the known subgenomic RNA of SARS CoV-2 as the primers were known in the prior art as disclosed by Dong; and the probe disclosed by Wu for rapid qualitative and quantitative determination of microorganisms by RT-PCR amplification. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success for the advantage of optimizing the RT-PCR for having rapid identification as well as accurate, reliable determination of the presence of active SARS-CoV2 infection in a subject given the fact that Dong disclose known primer sequences, SEQ ID NOs: 11 and 12 for the coronavirus N gene, while Wu discloses the probe of SEQ ID NO: 13. An demonstrates the plain consideration of any subsequence of a known sequence as a primer for that sequence. With respect to claim 13 and a kit for performing the method comprising the primers and probes, the concept of packaging components into a kit is considered conventional, obvious and routine in the art. One would be motivated to do this for commercial exploitation of the invention and to provide convenience for the end user. Therefore, the claimed invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Barry Chestnut whose telephone number is (571)270-3546. The examiner can normally be reached on M-Th 8:00 to 4:00.
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/BARRY A CHESTNUT/Primary Examiner, Art Unit 1672