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 .
Claim Status
The amended claim set filed 11 Nov 2025 is acknowledged. Claims 1-10 and 12-15 are currently pending. Of those, claims 1 and 3 are currently amended, and no claims are new. Claims 13-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 20 May 2025. Claim 11 is cancelled. Claims 1-10 and 12 will be examined on the merits herein.
Response to Arguments
The Applicants’ arguments filed 11 Nov 2025 are acknowledged. For clarity, in this action, said arguments will be referred to as “Remarks” and the Non-Final Office Action mailed 23 Jun 2025 will be referred to as “NFOA.”
Priority
The NFOA found that claims 1-10 and 12 have support in priority document PCT/US2021/046055, but do not have support in priority document 63/066,020 (see NFOA par. 4-10 for the detailed determination of support). Therefore, the effective filing date for claims 1-10 and 12 is 15 Aug 2021. Applicant did not dispute this finding in the Remarks by pointing out earlier support for the claimed invention.
Objection(s) and Rejection(s) Withdrawn
The rejection of claim 8 under 35 U.S.C. 112(d) (NFOA par. 13-14) is withdrawn in view of the claim amendment and arguments.
The rejections of claims 3, 5-6, and 11 under 35 U.S.C. 112(b) (NFOA par. 15-18) are withdrawn in view of the claim amendments (claims 3, 5-6), and in view of the arguments and further consideration (claim 11, which is now in claim 1).
The rejection of claims 1-12 under 35 U.S.C. 112(a) for written description (NFOA par. 19-31) and enablement (NFOA par. 32-45) are withdrawn in view of the amendments to no longer require the method’s product to function as a vaccine and the amendment to mix a bacteria suspension with the lyophilization buffer instead of mixing the bacteria.
New Rejection(s)
Claim Rejections - 35 USC § 102
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 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 1-10 and 12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Thalen et al. (13 Sep 2020; hereafter Thalen; made of record in IDS filed 25 May 2023). This reference may be eligible for a 102(b)(1)(A) exception, as Thalen appears to be the same person as an inventor on the instant application. However, the “reasonable explanation of the presence of additional authors” required in MPEP 2155.01 should explain the author contribution section of the paper, which states that Thalen and other authors were together responsible for “conceptualization” of the study (pg. 14 par. 7).
Regarding claim 1-4, 7-10, 12, Thalen teaches a stable lyophilization formulation of Bordetella pertussis strain BPZE1 (see claims 1-4). Thalen teaches that the bacteria are harvested at the target OD600 of 1.1–1.4 (pg. 2 Section 2.2), then mixing cultures with lyophilization buffer that has been cooled to 4°C in a 1:1 ratio, lyophilizing the bacteria and capping the vial and collecting the lyophilized Bordetella bacteria (pg. 2-3 Section 2.3). Thalen teaches that the lyophilization buffer can comprise 5% or 10% of the cryoprotectant sugars trehalose and sucrose (pg. 5 Table 3, see claims 1, 7) and that the buffer can further comprise glutamate (pg. 5 Table 3, see claims 8-9). Thalen teaches hold times between harvest and the start of lyophilization that are less than 36 and 48 hours; specifically, hold times of 6, 16, 26, 28, 31, and 32 hours (pg. 6 par. 5, Table 4 on pg. 7; see claims 1 and 10). Thalen also teaches that the protocol chosen for clinical development has a step of concentrating the culture to an OD600 of 5.0, followed by diluting the bacterial suspension 1:1 with cold lyophilization buffer (pg. 6 par. 4, see claim 12).
Regarding claims 5-6, Thalen also teaches “At the 8-L bioreactor scale, the suspension at OD600 of 0.5 showed little clumping, but poor survival after lyophilization compared to OD600s of >1.0.” (pg. 4 par. 3). An OD600 of 0.5 is between 0.4 and 1.0 and less than 1.0. Applicant argued in the Remarks (pg. 9) that non-optimal embodiments are included in the scope of the claim elements, and Thalen does not teach that each and every bacteria in the lyophilized sample with poor survival is killed, so the sub-optimal method with poor Bordetella survival still meets the claim limitation of “making lyophilized live attenuated Bordetella bacteria”.
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.
Claims 1-2, 5-10, and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Karataev et al. (RU-2709657-C2, published 2019; hereafter Karataev; original Russian text made of record in IDS 25 May 2023, full-text English machine translation made of record with PTO-892 mailed 23 June 2025) in view of Shimizu (US-4456588-A, published 1982; PTO-892) and Searles et al. (2001; hereafter Searles; PTO-892), as evidenced by Ramikissoon et al. (2020; hereafter Ramikissoon; PTO-892), Stevenson et al. (2016; hereafter Stevenson; PTO-892), and Radkowska et al. (2017; hereafter Radkowska; PTO-892).
Regarding claims 1-2, 7-8, Karataev teaches a lyophilization method for an attenuated Bordetella pertussis bacteria (Abstract). Karataev teaches that the attenuated Bordetella pertussis bacteria with mutations in the ptx and dnt gene (Abstract), such as the B. pertussis 4MKS strain, which “contain[s] a mutation in the regulatory region of the ptx gene, two mutations in the region that determines the enzymatic (toxic) activity of CT, and a knockout (inactivating) mutation in the coding region of the dnt gene” (pg. 3 par. 4).
The lyophilization method is disclosed in Example 1 (pg. 6) and includes: Harvesting Bordetella bacteria from solid media and suspending bacteria “in appropriate protective media to a concentration of 109 -1010 microbial cells /ml according to the optical turbidity standard” (pg. 6 par. 7). Ramikissoon provides evidence that for Bordetella pertussis cells “OD600 = 1.0 (approximately 109 cfu/ml)” (Ramikissoon pg. 3 par. 2), so the OD600 range described in Karataev includes OD600 of approximately 1.0. So this meets the claim limitation “harvesting Bordetella bacteria from a culture at an OD600 between 0.4 and 1.6 to yield a harvested Bordetella bacteria suspension”.
The protective media used include sucrose 10% + gelatin 1% (10% cryoprotective sugar, gelatin is nutrient substrate, pg. 6 par. 4), and one of ordinary skill in the art would understand this media to be at room temperature (approx. 20-22°C) in the absence of a teaching to use it at some other temperature.
Karataev teaches lyophilizing the bacteria in a freeze-dryer, then capping under vacuum and collecting the bacteria (pg. 6 par. 8-9). Karataev teaches “The first stage - freezing the culture - was carried out in a refrigerator at a temperature of - 45 to -80 °C for 3-15 hours” (pg. 6 par. 8), but does not teach what cooling rate the samples experienced. The bacterial survival values are shown in Table 1 and “a statistically significant decrease in CFU is observed” (pg. 6 par. 11), but bacteria survive to “make lyophilized live attenuated Bordetella bacteria” as required by the claim.
Regarding claims 5-6, Karataev teaches using an amount of 109 microbial cells /ml that is approximately OD600 = 1.0, as evidenced by Ramikissoon.
Regarding claim 10, Karataev teaches that the first stage of freezing the culture prior to carrying out freeze-drying (i.e. the hold time between harvest and lyophilization) was 3-15 hours if performed in a freezer, or 10-30 minutes if performed in liquid nitrogen (pg. 6 par. 8); in both cases, the hold step is less than 36 or 48 hours.
Regarding claim 12, Karataev teaches “a concentration of 109 -1010 microbial cells /ml according to the optical turbidity standard” (pg. 6 par. 7). The amount of bacteria after resuspension is more than OD600 = 1.0, as evidenced by Ramikissoon (pg. 3 par. 2). Stevenson provides additional evidence for converting between organisms/mL and OD600 values. Stevenson Figure 2 shows that an OD curve for 1 µm sized beads has the same OD600-to-concentration value as disclosed in Ramikissoon for Bordetella cells, and Stevenson Figure 2 shows that 1×1010 objects/ml has an OD600 less than 6.
Karataev does not teach mixing the bacteria and lyophilization buffer at a ratio between 5:1 and 1:5 by volume and does not teach wherein the lyophilization step comprises a pre-crystallization hold step wherein the mixture of the Bordetella bacteria suspension and the lyophilization buffer is held at 0.1 to 100C above the crystallization temperature of the lyophilization buffer for 0.5-10 hours prior to further cooling, as in claim 1. Karataev does not teach the nutrient substrate is glutamate, as in claim 9.
Regarding claim 1, Shimizu teaches a similar lyophilization method for Bordetella comprising: growing B. bronchisceptica, “The grown cells are collected and suspended in a sterilized phosphate buffered saline (pH 7.0) in a concentration of 1.5×109 organisms/ml. The cell suspension is admixed well with an equiamount of a drying protecting agent (a mixture of 10% skim milk and 5% yeast extract, which is sterilized at 110° C. for 10 minutes) to give a final bulk”, and the final bulk is lyophilized (Example 4). So, Shimizu teaches harvesting Bordetella bacteria from culture to yield a bacteria suspension, mixing with a lyophilization buffer in equal amounts (1:1 ratio), and lyophilizing the bacterial suspension. The bacteria remain live after lyophilization, “When the product is dissolved in a solvent (10 ml), the solution contains sufficiently satisfactory amount of live bacteria, more than 108 organisms/ml.” (Example 4). Regarding claims 8-9, yeast extract contains glutamate as evidenced by Radkowska (“…yeast extracts… all contain significant amounts of glutamic acid…” Abstract), so the lyophilization buffer comprises the nutrient substrate glutamate. Regarding claim 10, Shimizu does not teach that there is any delay between harvesting and lyophilization. Regarding claim 12, the Shimizu teaching “The grown cells are collected and suspended in a sterilized phosphate buffered saline” would be read by one of ordinary skill in the art as a step of centrifuging the cells to remove the BG media that the cells were grown in (i.e. a step of concentrating the harvested Bordetella bacteria suspension prior to the mixing step), before resuspending it in PBS.
Regarding claim 1, Searles investigates ice crystal formation during lyophilization cooling. Searle defines “Primary nucleation is the initial (heterogeneous) ice nucleation event” (pg. 861 col. 1 par. 1), which corresponds to the instant crystallization temperature (“the crystallization temperature is determined by slowly cooling the buffer and noting the temperature at which the onset of crystallization occurs” [instant specification 0079]). Searle teaches the nucleation/crystallization temperatures of the samples tested in Table 2, and the samples chosen include samples comprising bacteria. Searles measured pre-nucleation cooling rates as low as 0.05 °C/min, as well as 0.2 °C/min (Abstract, Figure 4). With these cooling rates, the sample will be held within the range of 0.1°C to 10°C for a duration between 0.5 and 10 hours (calculation performed as 9.9°C range ÷ 0.05 or 0.2°C/min rate ÷ 60 min/hr). For 0.05 °C/min the samples are held in the temperature range for 3.3 hours, and for 0.2°C/min the samples are held in the temperature range for 0.825 hours. Searles teaches “The effect of the pre-nucleation vial- (and shelf-) cooling rate [on the primary drying rate] is small compared with the overall impact of the nucleation temperature, as shown in Figure 3” (Figure 4 legend).
One of ordinary skill in the art at the time of filing would consider it prima facie obvious to modify the Karataev lyophilization method by making a 1:1 mixture of the Karataev cell suspension with the lyophilization buffer as in Shimizu and by testing slow pre-nucleation cooling rates such as 0.05 °C/min or 0.2 °C/min as in Searles in place of the undisclosed cooling rate from Karataev, thereby arriving at the claimed invention for claims 1-2 and 7-10, because the mixing ratio and initial cooling rates were disclosed in the art in Shimizu and Searles, respectively, and because there is no evidence in the specification, commensurate in scope to what is claimed, or in the art that these values are critical for success of making a live attenuated Bordetella bacteria. Both Karataev and Shimizu produce live lyophilized Bordetella bacteria (see par. 15 and 20), and Searles teaches that the cooling rate chosen does not have an effect on the drying rate (see par. 21). Therefore, the modifications can be made with a reasonable expectation of success because they only involve choosing known elements from successful lyophilization protocols in the art.
KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case all elements (i.e. harvesting Bordetella bacteria from culture at an OD600 of approximately 1.0 to make a bacterial suspension and a lyophilization buffer from Karataev, mixing a Bordetella bacterial suspension with a lyophilization buffer in a 1:1 ratio from Shimizu; lyophilizing the bacterial suspension with the buffer from both Karataev and Shimizu, the slow pre-nucleation cooling rate for lyophilization from Searles) were known in the art. In addition, combining these elements yields a method wherein each element merely performs the same function as it does separately; thus the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Also, one of ordinary skill in the art at the time of filing would also consider it prima facie obvious to harvest Bordetella at OD600 values just under 1.0, thereby arriving at the invention of claims 5-6. Karataev teaches using an amount of 109 microbial cells /ml that is approximately OD600 = 1.0, as evidenced by Ramikissoon. See MPEP 2144.05: “In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990) (The prior art taught carbon monoxide concentrations of "about 1-5%" while the claim was limited to "more than 5%." The court held that "about 1-5%" allowed for concentrations slightly above 5% thus the ranges overlapped.); In re Geisler, 116 F.3d 1465, 1469-71, 43 USPQ2d 1362, 1365-66 (Fed. Cir. 1997) (Claim reciting thickness of a protective layer as falling within a range of "50 to 100 Angstroms" considered prima facie obvious in view of prior art reference teaching that "for suitable protection, the thickness of the protective layer should be not less than about 10 nm [i.e., 100 Angstroms]." The court stated that "by stating that ‘suitable protection’ is provided if the protective layer is ‘about’ 100 Angstroms thick, [the prior art reference] directly teaches the use of a thickness within [applicant’s] claimed range."). See also In re Bergen, 120 F.2d 329, 332, 49 USPQ 749, 751-52 (CCPA 1941) (The court found that the overlapping endpoint of the prior art and claimed range was sufficient to support an obviousness rejection, particularly when there was no showing of criticality of the claimed range).” In this case, as in Woodruff, Geisler, and Bergen, the Karataev teaching that is approximately OD600 = 1.0 also allows for values slightly below 1.0, and thus the claimed range overlaps with the range disclosed in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Alternately, one of ordinary skill in the art at the time of filing would consider it prima facie obvious to further modify the lyophilization method as modified in par. 22-23 by centrifuging the bacteria and resuspending at a OD600 greater than 1.0 but less than 6.0, thereby arriving at the invention of claim 6, because Shimizu teaches concentrating bacteria and Karataev teaches using bacteria concentrations in of 109 -1010 microbial cells /ml, which corresponds to OD600 greater than 1.0 but less than 6.0 as evidenced by Ramikissoon and Stevenson.
KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case all elements (i.e. the individual elements making up the earlier modification, and the method step of concentrating bacteria from Shimizu, and the OD600 target to concentrate to from Karataev) were known in the art. In addition, combining these elements yields a method/composition wherein each element merely performs the same function as it does separately; thus the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMELIA NICOLE DICKENS whose telephone number is (571)272-0381. The examiner can normally be reached M-R 8:30-4:30, and every other F 8:30-4:30 (EDT/EST).
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/AMELIA NICOLE DICKENS/Examiner, Art Unit 1645
/DANIEL E KOLKER/Supervisory Patent Examiner, Art Unit 1645
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