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Patent Application 17761064 - MATERIALS AND METHODS FOR DETECTING HUMAN - Rejection

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Patent Application 17761064 - MATERIALS AND METHODS FOR DETECTING HUMAN

Title: MATERIALS AND METHODS FOR DETECTING HUMAN PAPILLOMA VIRUS

Application Information

  • Invention Title: MATERIALS AND METHODS FOR DETECTING HUMAN PAPILLOMA VIRUS
  • Application Number: 17761064
  • Submission Date: 2025-04-10T00:00:00.000Z
  • Effective Filing Date: 2022-03-16T00:00:00.000Z
  • Filing Date: 2022-03-16T00:00:00.000Z
  • National Class: 435
  • National Sub-Class: 005000
  • Examiner Employee Number: 88973
  • Art Unit: 1671
  • Tech Center: 1600

Rejection Summary

  • 102 Rejections: 0
  • 103 Rejections: 3

Cited Patents

No patents were cited in this rejection.

Office Action Text


    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
Acknowledgement is hereby made of receipt and entry of the communication filed on Oct. 17, 2022. Claims 1-4, 7-9, 11-21, 27, 35 and 36 are pending and currently examined. 

Claim Rejections - 35 USC § 112
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 1-4, 7-9 and 11-17 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.
Claim 1 recites “wherein (a) and (b) are capable of detecting each of the hrHPV polynucleotides, if present, in the sample by recombinase amplification (RPA).” It is not clear what (a) and (b) refer to. 
To facilitate examination, (a) and (b) are considered as referring to the aforementioned “a primer pair” and “a detection probe”. 

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 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.

Claims 1-4, 9, 11-16 and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Qu et al. (JOURNAL OF CLINICAL MICROBIOLOGY, 1997, 35(6): 1304–1310; submitted in IDS filed on Oct. 31, 2023).
These claims are directed to a kit for the detection of high-risk human papillomavirus (hrHPV) polynucleotides in a biological sample comprising a primer pair and a detection probe, wherein the primer pair and the detection probe are capable of detecting each of the hrHPV polynucleotides, if present, in the sample by recombinase polymerase amplification.
Qu teaches that the authors have compared the two most commonly used PCR primer sets, MY09/MY11 (MY-PCR) and GP5+/GP6+ (GP+-PCR), for the detection of HPV DNA in cervicovaginal lavage samples from 208 women. Oligonucleotide probes for 39 different HPV types were used. Both primer sets amplified a wide spectrum of HPV genotypes and detected similar overall prevalence of 45% (94 of 208) and 43% (89 of 208), respectively. The MY-PCR system detected 27 of 30 (90%) samples with multiple HPV types, whereas the GP+-PCR system detected 14 of 30 (47%) samples with multiple HPV types. Differences in the detection of HPV types 35, 53, and 61 were noted between the two primer systems. Serial dilution of plasmid templates indicated a 3-log decrease in the amplification of HPV type 35 by MY-PCR and HPV types 53 and 61 by GP+-PCR. See Abstract.
Table 4 of Qu shows the consensus primers MY09, MY11, GP5+ and GP6+. See below:

    PNG
    media_image1.png
    382
    780
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    Greyscale

Table 2 of Qu shows frequency of detection of HPV types in multiple HPV-positive samples. See below.

    PNG
    media_image2.png
    130
    780
    media_image2.png
    Greyscale

Table 2 shows that the MY-PCR and GP+-PCR can both detect most of the HPV types tested. However, Qu is silent on if the primer pair MY09/MY11 or GP5+/GP6+ are capable of detecting EACH of the hrHPV polynucleotides, if present, in a sample by RPA. 
Here, primer GP5+ (TTTGTTACTGTGGTAGATACTAC) is identical to the instant SEQ ID NO: 9 (TTATTTGTTACTGTGGTAGATACTAC) except for the lack of the three bases “TTA” at the 5’ end, while primer GP6+ (GAAAAATAAACTGTAAATCATATTC) is identical to the instant SEQ ID NO: 11 (AATTGAAAAATAAACTGTAAATCATATTC) except for the lack of the four bases “AATT” at the 5’ end. Based on this high sequence similarity, especially with the 3’ majority of the GP5+/GP6+ primer pair identical to the primer pair 9/11 of the instant invention (see claim 4), the GP5+/GP6+ primer pair is expected to amplify all nucleotide sequences amplifiable by the claimed primer pair comprising sequences set forth in SEQ ID NOs: 9 and 11.
The Office does not have the facilities and resources to provide the factual evidence needed in order to establish that the GP5+/GP6+ primer pair is not capable of detecting each of the hrHPV polynucleotides in a sample by RPA. In the absence of evidence to the contrary, the burden is on the applicant to prove that primer pairs tight in Qu, especially the primer pair GP5+/GP6+, do not have the function as claimed and to establish patentable differences. See In re Best 562F.2d 1252, 195 USPQ 430 (CCPA 1977) and Ex parte Gray 10 USPQ 2d 1922 (PTO Bd. Pat. App. & Int. 1989). 
Accordingly, Qu teaches a primer pair GP5+/GP6+ and a probe that are capable of detecting each of the hrHPV polynucleotides by RPA. No universal probe is needed for the detection of EACH of hrHPV polynucleotides as long as a universal primer pair is used. Therefore, the type-specific probes are considered in the current rejection to read on the probe as claimed.  
One may argue that the claimed probe must be a universal probe (i.e., a probe hybridizing to EACH of all hrHPV polynucleotides which is less useful than type-specific probes), one of skill in the art would have found it obvious to develop one, if there is a need, by identifying a consensus sequence among all hrHPV types in the region amplified by the GP5+/GP6+ primer pair by sequence alignment and routine test procedures known in the art.
Qu is silent on making a kit including the primer pairs and probes. One of skill in the art would have found it obvious to do so to facilitate storage and/or shipping and handling of the reagents.
Regarding claim 3 and 16, Qu teaches dot blot hybridization for detection of PCR products, including dotting PCR products onto Biodyne B membrane filters. See page 1305, left column, para 2. These membrane filters, when made in shape of strips, can be considered as test strips.
Regarding claim 4, as indicated in the discussion above, GP5+/GP6+ primer pair comprise the most important 3’ portions of the primer pairs comprising the SEQ ID NOs: 9 and 11, respective, with differences in only the less important 5’ termini of three and four base differences. One of skill in the art would have found it obvious to arrive at the claimed SEQ NOs: 9 and 11 from the GP5+/GP6+ sequences through routine experimental optimization unless there is evidence that the 5’ additional bases in the claimed sequences are critical.
Regarding claim 9, which specifies that the detection probe comprises a sequence set forth in SEQ ID NO: 14 or SEQ ID NO: 23, one of skill in the art would have found it obvious to arrive at them by identifying a consensus sequence by aligning all hrHPV types in the region amplified by the GP5+/GP6+ primer pair by sequence alignment and routine test procedures known in the art, unless there is evidence that these two probes are critical.
Regarding claim 11, Qu teaches that probes may be biotinylated. See page 1305, left column, para 2.
Regarding claims 14-15, the claims do not specify what the “running buffer” is used in. One of skill in the art would have found it obvious to include a buffer (a solution or a stock solution) in a “kit” comprising MgCl2 and NaCl as claimed, both chemicals are commonly included in buffer solutions, for potential use.
Accordingly, claims 1-4, 9, 11-16 and 36 are unpatentable over the teachings of Qu. 

Claims 7-8, 18-21, 27 and 35 are rejected under 35 U.S.C. 103 as being unpatentable over Qu et al. (JOURNAL OF CLINICAL MICROBIOLOGY, 1997, 35(6): 1304–1310; submitted in IDS filed on Oct. 31, 2023), as applied above, in view of Ma et al. (Clin. Lab. 2017; 63:27-38; submitted in IDS filed on Oct. 31, 2023) and Hice et al. (Anal. Chem. 2019, 91: 1113-1120; published Nov. 30, 2018), and further in view of CN110205394A (published on Sep. 6, 2019).
Claims 7-8 further specify that one primer in the pair is phosphorylated and the other primer in the pair is labeled with 6-carboxyfluorescein (FAM).	
Claims 18-21, 27 and 35 are directed to a method for detecting high risk human papilloma virus (hrHPV) polynucleotides in a biological sample comprising: 
an amplifying step comprising adding the biological sample to a vessel containing a primer pair that is capable of amplifying each of the hrHPV polynucleotides, if present, in the biological sample, 
digesting amplified hrHPV polynucleotides in the vessel into a single-stranded amplified product; 
combining the single-stranded amplified product with a running buffer comprising a detection probe that is capable of detecting the single-stranded amplified product to form a mixture, and incubating the mixture for a period of time in the vessel; and, 
a detecting step comprising wicking the mixture into a test strip and visually detecting the detection probe on the test strip.
Relevance of Qu is set forth above. Briefly, it teaches the detection of a broad spectrum of HPV types of the consensus primer pair GP5+/GP6+ and probes. However, for claims 7-8, Qu is silent on the claimed labeling of the primers, especially the FAM labeling, even though it teaches other labeling approaches; for claims 18-21, 27 and 35, Qu is silent on the on the processes involving digesting amplified hrHPV polynucleotides into single-stranded amplified product, combining the single-stranded amplified product with a detection probe, and a detecting step comprising wicking the mixture into a test strip for visual detection, as claimed. 
Ma teaches a novel, rapid, sensitive and specific isothermal method of recombinase polymerase amplification (RPA), which is established to detect the two most common high-risk human papillomavirus type 16 and type 18 DNA. In this study, the authors evaluate the efficacy of the RPA assay, incubating clinical specimens of HPV16 and HPV18 using plasmids standard. The products can be detected via agarose gel electrophoresis assay, reverse dot blot assay, and quantitative real-time assay with SYBR Green I. Compared with TaqMan qPCR, the RPA technique achieves exponential amplification with no need for pretreatment of sample DNA at 37°C for 20 minutes, which reveals more satisfactory performance. Ma concludes that the RPA assay was demonstrated to be a useful and powerful method for detection of HPV virus, which therefore may serve as a valuable tool for rapid diagnosis of HPV infection in both commercial and clinical applications. See Abstract. Ma teaches using HPV16 or HPV18 specific primer pairs and probes targeting the region within the consensus GP5+/GP6+ target region. See Tables 1 and 2, and page 32, right column, para 2.  
Hice teaches a study on isothermal amplification and detection of Salmonella-specific DNA using recombinase polymerase amplification (RPA). See Abstract. Hice teaches that a 340 bp region of the putative dienelactone hydrolase gene (DLH) was amplified using the following primers: (Forward primer) 5′-GCC GGG CAG CRA TTA TTC TGC ATG AA-3′and (Reverse primer) 5′-TGG CGT ATA CGG GAA CCG TAA TAG CA-3′. See page 1115, right column, para 1. Hice teaches that for detection by lateral flow assay, single-tube amplification products generated using the TwistFlow Salmonella kit were added directly to a nucleic acid lateral flow immunoassay (NALFIA) disposable cartridge (Ustar Biotechnologies (Hangzhou) Ltd., Hangzhou, CN). The NALFIA relies on visual detection of a test band facilitated by the extension of biotin and 6-carboxyfluorescein (6-FAM) labeled primers during RPA. The amplification product is visible by eye as a result of aggregation of streptavidin-conjugated gold nanoparticles, which bind to the biotin-labeled 5′ end of the double-stranded amplicon. The terminal 6-FAM group of the amplicon is also selectively captured by the anti-FAM antibody, which is embedded in the test line on the lateral flow strip. See the para spanning pages 1115 and 1116.
Accordingly, Ma and Hice both teach the RPA technique in the detection of nucleic acids with advantages over the regular PCR amplification. Ma teaches the detection of HPV types with RPA. Hice teaches that visualization of RPA products with nucleic acid lateral flow assay (NALFA) in which one of the amplification primers is labeled with FAM.
CN110205394A teaches an invention about detection of Salmonella DNA using RPA. See Abstract.  CN110205394A teaches that the invention provides a method for detecting Salmonella, which combines the combination of recombinase, polymerase and lambda exonuclease (RPL principle) and hybridization chain reaction (HCR), and constructs a G-quadruplex trigger based on a universal linker. Dual-signal-amplified label-free visualization biosensor of chimeric HCR for detection of Salmonella. The double-stranded nucleic acid of Salmonella was amplified by a multi-enzyme system to obtain a large amount of dsDNA phosphorylated at the 5' end. In order to obtain a large number of phosphorylated amplification products, a general sequence with phosphorylated 5' end was added to the RPA reaction system, and the complementary chain of this general sequence was named as a universal linker. Lambda exonuclease selectively digests 5'-phosphorylated strands in dsDNA, and the RPA product becomes single-stranded after the undesired strands are digested. The universal linker is exposed, the HCR response is initiated, and the G-quadruplex in the H1 hairpin is released. G-quadruplex can combine with Hemin to form G4 DNAzyme with peroxidase activity. This mimetic enzyme can catalyze H2O2 to oxidize colorless TMB to blue oxTMB visible to the naked eye, and then detect Salmonella through color changes and changes in light absorption. See Google translate for paragraph [0010]. 
Accordingly, CN110205394A teaches an RPA method for detection of double stranded DNA molecules. The method includes addition of lambda exonuclease to selectively digest 5'-phosphorylated strands in dsDNA RPA product so that the RPA product becomes single-stranded after the undesired strands are digested. This teaching implies that one of the primers in the primer pair used in RPA is phosphorylated to the 5’ end while the other primer is not phosphorylated. The single-stranded DNA resulted from the exonuclease digestion of the RPA product is ideal for probe detection.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the current invention to combine the teachings of Qu, Ma, Hice and CN110205394A to arrive at the invention as claimed. One would have been motivated to do so to develop an RPA assay for detection of each of hrHPV types using the consensus primer pair GP5+/GP6+ disclosed in Qu based on the teachings of Ma, Hice, and CN110205394A, which teach the techniques and advantages of RPA in the detection of nucleic acids. In NCFLA visualization method of Hice, one of the primers is labeled with FAM, while teachings of CN110205394A implies that undesired strand in the dsDNA product of RPA is generated by a 5’-phophorylated primer. 

Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Qu et al. (JOURNAL OF CLINICAL MICROBIOLOGY, 1997, 35(6): 1304–1310; submitted in IDS filed on Oct. 31, 2023) in view of Ma et al. (Clin. Lab. 2017; 63:27-38; submitted in IDS filed on Oct. 31, 2023) and Hice et al. (Anal. Chem. 2019, 91: 1113-1120; published Nov. 30, 2018), as applied above, and further in view of Ereku et al. (Analytical Biochemistry 547 (2018) 84-88; submitted in IDS filed on Oct. 31, 2023).
Claim 17 further specify that the test strip of claim 3 comprises chitosan.
Relevance of Qu, Ma and Hice is set forth in the rejections above. However, they are silent on if test strips used in the detection of nucleic acid amplification products can contain chitosan.
Ereku teaches the application of chitosan membrane in a point-of-care device designed for detection of nucleic acids by RPA. It teaches that chitosan membrane is used to facilitate nucleic acid extraction and purification in the device. See Abstract and Figure 1. Accordingly, Ereku teaches that a test strip containing chitosan can be used in a device designed for RPA detection of nucleic acids.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the current invention to introduce the RPA device of Ereku into the studies of Qu, Ma and Hice to arrive at the invention as claimed. One would have been motivated to do so, e.g., to evaluate the effect of the device of Ereku in the detection of HPV nucleic acids.   

Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIANXIANG (NICK) ZOU whose telephone number is (571)272-2850.  The examiner can normally be reached on Monday - Friday, 8:30 am - 5:00 pm, EST. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, JANET ANDRES, on (571) 272-0867, can be reached.  The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system.  Status information for published applications may be obtained from either Private PAIR or Public PAIR.  Status information for unpublished applications is available through Private PAIR only.  For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.

/NIANXIANG ZOU/
Primary Examiner, Art Unit 1671









	
	
	



    
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
    


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