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 .
The response and claim amendments filed 5-21-2026 has been entered into the record. Claims 1-14, 16-18 and 23-25 are pending. Claims 15, 19-22 and 26-30 have been canceled.
Election/Restrictions
Applicant's election with traverse of Group I, combination of a)-f) in the reply filed on 5-21-2026 is acknowledged. The traversal is on the ground(s) that the is no search and examination burden to search and examine. This is not found persuasive because a search and examination of a) alone does not provide for art on any one of b)-f).
However, in view that the search of the combination of a)-f) did not provide for any art, the search and examination has been extended to the individual species. The species election is hereby withdrawn.
As the elected invention is not allowable, the withdrawn process claims have not been rejoined for examination at this time.
Claims 10-14, 16-18, 23-25 are withdrawn from consideration.
Information Disclosure Statement
The information disclosure statement filed 6-20-2025 has been considered. An initialed copy is enclosed.
Specification
The disclosure is objected to because of the following informalities: The specification at multiple instances recites a mutation at L341 which according to the sequence listing does not exist. The specification also recites M1-P33 which according to the sequence listing and Table 3 does not exist. While the amendment to the claims corrects the mutation position(s), the specification remains replete with incorrect positional information in the text.
A substitute specification including the claims is required pursuant to 37 CFR 1.125(a) because the specification at multiple instances recites a mutation at L341 which according to the sequence listing does not exist. While the amendment to the claims corrects the mutation position, the specification remains replete with incorrect positional information.
A substitute specification must not contain new matter. The substitute specification must be submitted with markings showing all the changes relative to the immediate prior version of the specification of record. The text of any added subject matter must be shown by underlining the added text. The text of any deleted matter must be shown by strike-through except that double brackets placed before and after the deleted characters may be used to show deletion of five or fewer consecutive characters. The text of any deleted subject matter must be shown by being placed within double brackets if strike-through cannot be easily perceived. An accompanying clean version (without markings) and a statement that the substitute specification contains no new matter must also be supplied. Numbering the paragraphs of the specification of record is not considered a change that must be shown.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claims 1-9 are rejected under 35 U.S.C. 112(a), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
The factors considered in the Written Description requirement are (1) level of skill and knowledge in the art, (2) partial structure, (3) physical and/or chemical properties, (4) functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the (5) method of making the claimed invention. While all of the factors have been considered, only those required for a prima facie case are set forth below.
Partial structure/correlation between structure and function
The specification defines “attenuated pathogenicity” means that infection with the Chlamydia cell of this invention results in reduced levels of hydrosalpinx and/or reduced levels of inflammatory cytokines (i.e., reduced inflammatory stimulation), relative to a Chlamydia cell lacking the substitutions, deletions and/or mutations described herein.” (specification page 13, lines 16-19). The claims recite isolated Chlamydia muridarum cells comprising a variety of mutations a)-f) as the elected embodiment, each alone and any combination thereof. The claims recite that the Chalmydia muridarum having the mutation(s) is of attenuated pathogenicity. The art teaches that the genome sequences of C. muridarum G13.32.1 and CMmCherryG5 are nearly identical with the exception of the gene coding for TC0412. Although mutations in this gene in C. trachomatis have been shown to alter the infectivity of C. trachomatis in the mouse genital tract, similar mutations in C. muridarum had no significant effects on either the infectivity or the pathogenicity in the genital tract infection model (see Zhu et al (Vaccine 36:2061-2068, 2018; page 2062, column 1, section 2.1). There is no evidence presented that any combination of mutations or the mutations individually provide for a phenotype of attenuated pathogenicity as determined by art accepted means. The specification as filed fails to provide a correlation of the claimed mutation(s) or any combination thereof in the claimed open reading frames with the function of attenuated pathogenicity as claimed. The specification teaches single mutations at the disclosed open reading frame points. The specification does not disclose a number of different mutations at those sites that provide for attenuated pathogenicity as claimed. Table 2 at page 41 lists general conservative substitutions but does not provide a Table of those that correlate with the function/phenotype of “attenuated pathogenicity”. The specification discloses a single variant having a very specific combination of mutations “G13”. The “G13” variant was not apparently tested for “attenuated pathogenicity”. The examples provide for oral administration compared to a control vehicle, but not in comparison to a non-mutated parental cell and as such cannot provide for a finding of “attenuated pathogenicity”. The courts have held that a sufficient number of representative species must be included “to demonstrate that the patentee possessed the full scope of the [claimed] invention.” Lizardtech, Inc. v. Earth Resource Mapping, Inc. 424 F.3d 1336, 1345, 76 USPQ2d 1724, 1732 (Fed. Cir. 2005). In the instant case, none of the mutations have been demonstrated to provide for attenuated pathogenicity as claimed.
Physical and chemical properties
The biological activity or activities of the open reading frames TC0168, TC0341, TC0342, TC0408, TC0412 and TC0708 are not set forth in the specification and not described in the prior art at the time of filing. The lack of activity or altered activity of each of these is not apparently disclosed in the prior art as correlating with an attenuated pathogenicity phenotype as defined. The specification does not disclose that mutations in one or more of the open reading frames provides for the phenotype of “attenuated pathogenicity” as claimed. The specification does not disclose that the mutations provide for attenuated pathogenicity as compared to a non-mutated parental strain as determined by standard art practices and as defined in the specification. The art does not provide the missing function/structure correlation.
Weighing all the factors, the breadth of the claims, the lack of correlation between structure and function of the individual mutations or the mutations as combined with attenuated pathogenicity, level of knowledge and skill in the art, one of ordinary skill in the art would not recognize from the disclosure that the applicant was in possession of the genus of Chlamydia muridarum mutants having attenuated pathogenicity. At best, it simply indicates that one should run tests on a wide spectrum of mutants in the hope that at least one of them have attenuated pathogenicity. Therefore, the written description requirement is prima facie not satisfied.
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.). The specification does not provide relevant identifying characteristics, including functional characteristics when coupled with known or disclosed correlation between function and structure. The courts have held that in these instances, the specification lacks written description see Enzo Biochem Inc. v. Gen-Probe Inc. 63 USPQ2D 1609 (CAFC 2002) and University of Rochester v. G.D. Searle & Co. 69 USPQ2D 1886 (CAFC 2004).
Free of the Prior Art
The claims are free of the prior art as the prior art does not teach or suggest the mutations as claimed in Chlamydia muridarum provide for the function of attenuated pathogenicity as defined in the specification.
Citation of Relevant Prior Art
Zhou et al (Infection and Immunity, 90(3):e00472-21, 2022) teaches Chalmydia deficient in pGP3 as an attenuated live oral vaccine. Zhou et al teach that the mutants were neither safe nor effective when delivered via the genital tracts, however oral inoculation with the pGP3-deficient mutant induced robust transmucosal immunity against both the infection and pathogenicity of wild-type C. muridarum in the genital tract. Demonstrating clear differences in activity by different routes of administration (see abstract).
Wang et al (Infection and Immunity, 86(2):e00630-17, 2018) teaches nonpathogenic colonization with Chlamydia in the gastrointestinal tracts as oral vaccination for inducing transmucosal protection. The transmucosal protection did not affect colonization of the gastrointestinal tract and was non-pathogenic to either the gastrointestinal or extra- gastrointestinal tissues. The transmucosal protective immunity did not restrict C. muridarum colonization of the gastrointestinal tract (see abstract). However, Wang et al also reported that Perry and Hughes have previously reported that C. muridarum spreads to extra-gastrointestinal tissues and this might reflect the different strains of C. muridarum used (see page 13, 1st full paragraph).
Zhou et al (FEMS Pathogens and Disease 77:1-8, 2019) teach a study of genes with select mutations by in vitro passage of Chlamydia muridarum strains. Zhou et al teach effects of various mutations on attenuation and pathogenic mechanism of Chlamydia (see abstract).
Phillips et al (Frontiers in Microbiology, 10, Article 70 pages 1-17, 2019) teach that although mouse model trails are useful, differences between host and infecting chmalydial strains are preventing vaccine formulations from mouse models to be translated into larger animals or intended hosts (see abstract).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Patricia Duffy whose telephone number is (571)272-0855. The examiner can normally be reached 8:00 am - 4 pm.
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/Patricia Duffy/Primary Examiner, Art Unit 1645
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