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 .
All of the amended claims, claims 1-5, 7-17, 19-21, and 23 submitted on 10/17/2025, are under examination on the merits.
Rejections Removed
The previous rejections under 35 U.S.C. §112(a) and 35 U.S.C. §112(b) are hereby withdrawn due to clarification presented by the Attorneys in an interview held 10/15/2025.
New Objections
Claim Objections
Claims 1-4 and 13-16 are objected to because of the following informalities: claims 1-4 and 13-16 recite the term “mass spectrums”, rather than “mass spectra”. Appropriate correction is required.
New Rejections
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.
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 1-5, 7-17, 19-21, and 23 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.
The claimed invention requires increasing at least one of a temperature and an incubation period (claim 1, line 4; claim 13, line 3). The claims are not sufficiently detailed to understand exactly what this means, and thus the metes and bounds of the claims are unclear. For example, the temperature could relate to that of the virus preparation in the cell culture and the ions could be virions with natural charges, the temperature could be that of ions from the virions after trypsin digestion, or the temperature of the ions within the mass spectrometer. Similarly, the incubation time could be that of ions in the virus preparation in cell culture, the virus preparation during trypsinization, or flow rates through the mass spectrometer. Where the elements of a claim have two or more plausible constructions such that the examiner cannot readily ascertain positional relationship of the elements, the claim may be rendered indefinite. See, e.g., Ex parte Miyazaki, 89 USPQ2d 1207 (Bd. Pat. App. & Inter. 2008). MPEP §2173.05(b). Here, any combination of temperature and incubation time are plausible and the presence of so many different interpretations renders the claims indefinite.
Claim 12 includes the limitation “wherein repeatedly increasing the at least one of the temperature and the incubation period comprises controlling a second thermal energy device”. However, neither claim 12 nor claim 1, from which claim 12 depends, recites a first thermal energy device. Thus, it is unclear whether the claims require a first thermal energy device that is distinct from the second thermal energy device.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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, 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention 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.
Claims 1-5, 7-17, 19-21, and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Fuerstenau, et al. (Angew Chem Int Ed Engl. 2001 Feb 2;40(3):541-544) in view of Kukreja, et al. (J Virol 2014 Dec;88(24):14105-15. Epub 2014 Sep 24), Horowitz, et al. (J Virol 2013 Mar;87(6):2994-3002), Tai, et al. (Mol Ther Methods Clin Dev 2018 Feb 13;9:130-141), Li et al. (Current Pharmaceutical Biotechnology, 2017, 18, 638-647), and Kirkpatrick et al. J Proteome Res. 2017 Sep 1;16(9):3255-3265).
The Prior Art
Fuerstenau discloses mass spectrometry of intact virus, wherein viruses can be observed with mass spectrometry, and withstand the rigors of vaporization, ionization, and the vacuum of a mass spectrometer (p. 542, para. 1). Additionally, Fuerstenau teaches that the mass measurement of viral subgroups within a population would allow virologists to better understand the diversity of viruses or to measure members of a population (p. 543, col. 2, para. 2). Fuerstenau further discloses that charge-detection mass spectrometry circumvents limitations associated with detecting large, highly charged ions by making a simultaneous measurement of charge (z) and mass-to-charge (m/z) ratio for individual ions (p. 542, col. 2, para. 2). The detection technique permits the mass analysis of electrospray ions with virtually unlimited mass and various mass analyzers, and the mass of each ion is obtained from a combination of both the charge and m/z value (Id.). Fuerstenau further discloses study of multiple, structurally distinct viruses were analyzed by their methods (p. 542, col. 2, para. 3), and mass spectrums of both rice yellow mottle virus (RYMV) and tobacco mosaic virus (TMV) were obtained (Fig. 2).
However, Fuerstenau does not teach repeatedly or sequentially reducing a heterogeneity of a virus preparation by increasing temperature or incubation period, determining a mass spectrum at each increase of temperature or incubation period, and determining based on mass spectrums optimum temperature and incubation period to minimize or reduce a heterogeneity of the virus preparation without aggregation of virus capsids in the virus preparation, nor does it teach varying a cooling profile.
Kukreja teaches a method of applying charge detection mass spectrometry to study viruses and incubating viruses at a range of temperatures to study virus particle characteristics such as initial assembly (Abstract; p. 14107, col. 2; p. 14113, col. 2, para. 1; p. 14113, col. 1, para. 1). Kukreja discloses that human hepatitis B virus capsid assembly is linear with temperature dependence, but woodchuck hepatitis virus, a close relative of human hepatitis B virus, displays nonlinear temperature dependence (Fig. 5; Abstract). Additionally, Kukreja discloses cooling samples and incubating at lower temperatures after previous heating, wherein HBV or WHV core proteins were disassembled from capsids at 4°C or capsids were plunged into liquid nitrogen-cooled ethane bath for cry-electron microscopy analysis(p. 14107, col. 1, paras. 1-3).
Horowitz discloses biophysical and ultrastructural characterization of virus genome release, and observed the trend that thermally induced DNA release is dependent on genome length—AAV capsid stability appears to increase as genome size is reduced (Fig. 3A, p. 2996;, col. 1, last para.; col. 2, paras 1-2) Horowitz also discloses incremental heating of AAV capsids to study the proportion of uncoated AAV capsids (Abstract; Fig. 5). A linear correlation is observed, where the melting temperature (Tm) is inversely proportional to genome length of ssAAV, such that 50% of genomes are released at ~50 °C, 56°C, and 65°C, for 3.4kb, 4.1kb, and 4.7kb genome lengths, respectively (Fig. 5A). Horowitz’s assay involves viral vectors heated in 2°C increments and held for 5 min at each temperature prior to acquiring fluorescent signal to assess capsid uncoating (Fig. 5, legend).
Tai discloses that truncated genomes, reverse-packaged genomes, genomes containing sequences from packaging and helper plasmids, and even host-cell genomic sequences that are chimeric with inverted terminal repeat (ITR)-containing vector sequences can be observed in recombinant AAV vectors (Abstract; Figs. 3-5). Additionally, Tai discovered that some AAV package sequences ranging beyond the ITR regions of the vector genomes, which could be larger-than-unit-length molecules that package sequences beyond the ITR (p. 133).
Li discloses the effects of temperature on the stability of HSV-2 particles, as analyzed by RALS and tryptophan intrinsic fluorescence (Fig. 2a; p. 643, col. 2, para. 3). Li observed two thermal transitions with maxima at approximately 62 °C and 67°C, wherein the 62 °C transition is most likely associated with the capsid protein unfolding, and the 67 °C transition is likely associated with DNA melting and aggregation (p. 645, col. 1, para. 1). The sharp drop-off in RALS intensity observed at temperatures higher than 68 °C was likely due to the formation of larger aggregates which are contributed from both viral proteins and residual proteins (p. 645, col. 1, para. 1). The accompanied decrease in intrinsic fluorescence intensity is consistent with protein self-association or aggregation that would be expected to accompany aggregation of virions and/or host cell proteins—aggregation begins slowly at ~45 °C and dramatically increases at temperatures higher than 59 °C (p. 645, col. 1, para. 1). Along those lines, particle size distribution increased at elevated temperatures (Fig. 2c). Li further discloses a proposed mathematical model that can be used to predict the temperature induced aggregation, to benefit challenges posed for product storage and handling (p. 646, col. 1, para. 2).
Kirkpatrick discloses that intact protein analysis by liquid chromatography-mass spectrometry (LC-MS) is now possible due to the improved capabilities of mass spectrometers yielding greater resolution, mass accuracy, and extended mass ranges (Abstract). Kirkpatrick specifically examined the effect of various instrument parameters, including temperatures at source, capillary, and HESI, and found that the quality of spectra are affected (p. 4, para. 3; Abstract; p. 6, para. 4; p. 7, paras. 1-3; Fig. 1). Kirkpatrick discloses that a key finding was that use of a lower capillary temperature than recommended by the manufacturer (300 °C instead of 350 °C) improved S/N for all proteins, which aided proteoform stability and retention of labile post-translational modifications (p. 12, para. 3). Kirkpatrick also teaches that the automatic gain control (AGC), which limits the total number of ions trapped, reduces space-charge effects on the ions and can lead to improved resolution and mass accuracy; together with the maximum ion injection time, the AGC limits the total length of each MS scan; thus, in studying the effect of AGC, Kirkpatrick held the ion injection time constant to ensure that only AGC values were influencing results (p. 6, para. 2).
It would have been obvious to one of ordinary skill in the art to modify Fuerstenau’s methods of CDMS of whole virions to incorporate optimization of heating and time steps. As disclosed by Kukreja, varying heating and cooling steps is known in the art of virology and CDMS. Furthermore, Horowitz discloses that thermally induced DNA release is dependent on genome length, that AAV capsid stability is lower as the size of the packaged DNA increases, and assessing viral capsid uncoating by 2°C increments held for 5 min at each temperature. Tai discloses that viruses, recombinant AAV specifically, may package genomes containing sequences from packaging and helper plasmids, and host-cell genomic sequences that are chimeric with ITR-containing vector sequences, which could be larger-than-unit-length molecules that package sequences beyond the ITR. Li discloses thermally-induced aggregation of HSV-2 virus particles as temperature increases. This would clearly cause a mass spectrum with particles of mass greater than the highest capsid mass in the virus studied as multiple particles clump together and so aggregation would have been discernable via mass spectra with these features. Kirkpatrick discloses that the quality of mass spectra re influenced by temperatures at source, capillary, and HESI, and further suggests ion injection time could influence mass spectra. One of ordinary skill in the art would be motivated to heat an AAV preparation to remove the larger-than-unit-length molecule from an AAV population, so that the preparation would not contain host-cell genomic sequences that are chimeric with ITR-containing vector sequences or otherwise aberrantly long, to prevent AAV bearing such sequences from being administered to a subject or cell.
Each change of parameter will change the mass of the virions and so instead of a mass spectrum that has a few strong peaks, it will shrink them as some virions will be different masses and multiple smaller peaks will appear to represent then undesired virions.
It has long been settled to be no more than routine experimentation for one of ordinary skill in the art to discover an optimum value of a result effective variable. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum of workable ranges by routine experimentation." Application of Aller, 220 F.2d 454, 456, 105 USPQ 233, 235-236 (C.C.P.A. 1955). "No invention is involved in discovering optimum ranges of a process by routine experimentation." Id. at 458, 105 USPQ at 236-237. The "discovery of an optimum value of a result effective variable in a known process is ordinarily within the skill of the art." Application of Boesch, 617 F.2d 272, 276, 205 USPQ 215, 218-219 (C.C.P.A. 1980). Since Applicant has not disclosed that the specific limitations recited in instant claims are for any particular purpose or solve any stated problem, and the prior art teaches that parameter magnitudes that are encompassed by instant claims, often vary according to the sample being analyzed and various matrices, solutions and parameters appear to work equally as well, absent unexpected results, it would have been obvious for one of ordinary skill to discover the optimum workable ranges of the methods disclosed by the prior art by normal optimization procedures known in the art. In the instant case, optimizing the result effective variables of temperature, incubation period, cooling profile, and heating profile is no more than routine optimization to discover an optimum value of a result effective variable. The optimization of these result effective variables will ensure high quality MS spectra. Thus, temperature and time are result effective variables, and it would be obvious to optimize them as claimed via repeatedly adjusting them to find the optima. Once optima are identified, it would have been equally obvious to reuse these identified parameters with other samples.
With respect to claims 11-12, it is obvious to use thermal energy devices to control temperatures as evidenced by the art above both in the mass spectrometer and out. Therefore at least two thermal energy devices would transfer thermal energy to the virus preparation and the virus ions, one device per target.
There would be a reasonable expectation of success because Fuerstenau demonstrates the applicability of ESI and CDMS for studying whole viruses, Kukreja discloses heating and cooling profiles for CDMS applications, Horowitz shows applicability of incremental heating for AAV capsids to cause uncoating of viral DNA.
Therefore, claims 1-5, 7-17, 19-21, and 23 were prima facie obvious before the priority date of the instant invention.
Conclusion
No claim is allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEFFREY MARK SIFFORD whose telephone number is (571)272-7289. The examiner can normally be reached 8:30 a.m. - 5:30 p.m. ET with alternating Fridays off.
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/JEFFREY MARK SIFFORD/Examiner, Art Unit 1671 /Michael Allen/Supervisory Patent Examiner, Art Unit 1671