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 .
Claims 19-38 are pending. Claim 38 is withdrawn. Claims 19-37 are under examination.
Election/Restrictions
Applicant’s election without traverse of Group I and the species B. subtilis, sialic acid, alpha 2,3 sialic acid, coronaviral virolectin and Coronaviridae and Reoviridae in the reply filed on 2/8/26 is acknowledged.
Claim 38 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 2/8/26.
Information Disclosure Statement
The information disclosure statement filed 3/17/24 has been considered and an initialed copy is enclosed.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1), 1.835(a)(2), or 1.835(b)(2) is missing, defective or incomplete.
Required response - Applicant must:
• Provide a substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 of carrying out his invention.
Claim 19-37 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
The claims are drawn to an endospore-forming microorganism of the genus Bacillus wherein said microorganism displays viral decoy receptors on its surface and preparations thereof.
The claims requires a large and variant genus of Bacillus species. The common structure of the genus of Bacillus is that they display viral decoy receptors on their surfaces. Members of this genus includes but strains of B. subtilis, B. licheniformis, B. paralicheniformis, B. amyloliquefaciens, B. velezensis, B. pumilus, B. megaterium and B. coagulans. Furthermore, the genus encompasses variants of DSM 33855, DSM 33856, DSM 33857 and DSM 33858.
The claims require that members of this genus are able to bind to at least two viruses, selected from the families Orthomyxoviridae, Paramyxoviridae, Coronaviridae, Reoviridae, Noroviridae, Picornaviridae, Adenoviridae, Anelloviridae, Asfarviridae, Baculoviridae, Circoviridae, Geminiviridae, Hepadnaviridae, Iridoviridae, Nanoviridae, Nimaviridae, Nudiviridae, Papillomaviridae, Parvoviridae, Polyomaviridae, Flaviviridae, Bunyaviridae, Filoviridae, Arenaviridae and Poxviridae.
Members of the genus are highly variant because each member displays a different viral decoy receptor on its surface.
Members of this genus also possess at least one further characteristic selected from the group consisting of: an ability to grow in large-scale bioreactors; an ability to multiply and produce viral decoy receptors in situ; an ability to grow in the presence of bile; an ability to form endospores; an ability to produce at least one enzyme selected from cellulase, xylanase and protease; a sensitivity with respect to at least 8 different antibiotics; an ability to grow and produce lactic acid under anaerobic conditions; an ability to inhibit the growth of at least one pathogenic bacteria selected from the group consisting of: E. coli, Vibrio parahaemolyticus and Staphylococcus aureus subsp. aureus.
The specification also requires that they are naturally occurring or spontaneous mutants and are able to inhibit the growth of at least one pathogenic bacterial selected from the group consisting of: Clostridium perfringens, Streptococcus suis and Enterococcus cecorum.
The specification teaches that viral decoy receptor producing microorganisms can be screened for wherein viral particles or their receptor-binding moieties are immobilized on a carrier and microorganisms are subsequently analyzed for their ability to bind to the viral particles or receptor-binding moieties on the carrier.
Applicants screened a library of about 200 Bacillus strains w for adsorption of virolectins i.e. PEDV-GDU S1-Fc-loaded pA-LS nanoparticles or purified RAV VP8*-LS.
Only 27 were identified to be able to bind to viral PEDV particles and by showing that PEDV particles were not able to bind to the desialylated neuraminidase-treated Bacillus strains, it could be shown that binding takes place to sialic acid or to sialic acid containing binding sites on the Bacillus strains. The identified binding strains were of the species Bacillus subtilis, Bacillus velezensis, Bacillus pumilus and Bacillus megaterium. 16 of those 27 strains were able to bind in addition to viral VP8* particles. Of the identified strains, four were selected, because they exhibited some further positive characteristics which identified them as particularly suitable for feed applications. The selected strains were DSM 33855, DSM 33856, DSM 33857 and DSM 33858. Of the four deposited strains, three are of the species B. subtilis (DSM 33855, DSM 33856 and DSM 33858), while one belongs to the species B. velezensis (DSM 33857).
The disclosure of a few species of Bacillus which bind the tested viral antigen from two viruses PEDV and rotavirus group A representative variants of three porcine P-genotypes, P[7] strain OSU (ATCC VR-892), p[6] strain Z84, and P[19] strain Mm7, does not place Applicants in possession of the genus of endospore forming Bacillus displaying viral decoy receptors on it surface.
The disclosure of assays for screening for endospore forming Bacillus that display viral decoy receptors and any of the functional traits recited in the claims does not put Applicants in possession of the highly variant genus of Bacillus species that display viral decoy receptors. The written description requirement is separate and distinct from the enablement requirement (See also Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 920-23, 69 USPQ2d 1886, 1890-93 (Fed. Cir. 2004)) and adequate written description requires more than a mere reference to a potential method for identifying candidate polypeptides. The purpose of the written description requirement is broader than to merely explain how to ‘make and use’ [the invention] Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1560, 19 USPQ2d 1111, 1114 (Fed. Cir. 1991).
Being an endospore forming Bacillus does not immediately predict viral decoy receptor on the surface of a Bacillus. For instance, a library of about 200 Bacillus strains was screened batchwise for adsorption of virolectins (PEDV-GDU S1-Fc-loaded pA-LS nanoparticles or purified RAV VP8*-LS) and out of these only 27 were identified to be able to bind to viral PEDV particles.
The 27 naturally occurring Bacillus that were bound by PEDV via sialic acid or sialic acid binding sites on the bacteria are not representative of the genus of bacillus display viral decoy receptors. A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that "only describe[d] one type of structurally similar antibodies" that "are not representative of the full variety or scope of the genus.").
There is substantial variation due to the plethora of Bacillus species and their strain and the high variation in possible viral decoy structures compounded by the high number of different viruses and viral strains.
In the instant case, Applicants have reduced to practice 27 Bacillus that bind the only two viruses tested PEDV and Rotavirus, wherein these viruses bind via sialic acid or sialic acid containing structure of the bacteria. The 27 strains are not representative of the full variation set forth in the claims
Although the number of the described species appears high quantitatively, the described species are all of the similar type i.e. they bind to the PEDV and bind to PEDV rotavirus strains on the Bacilllus and do not qualitatively represent other types of Bacillus encompassed by the genus. See Ariad, 598 F.3d at 1351[*1301] ("[No] brightline rules governf] the number of species that must be disclosed to describe a genus claim, as this number necessarily changes with each invention, and it changes with progress in a field."). Abbvie Deutschland GmbH & Co. v. Janssen Biotech, Inc., 759 F.3d 1285, 1301, 111 U.S.P.Q.2d 1780, 1790, 2014 BL 183329, 13 (Fed. Cir. 2014)
With the written description of a genus, however, merely drawing a fence around a perceived genus is not a description of the genus. One needs to show that one has truly invented the genus i.e. that one has conceived and described sufficient representative species encompassing the breath of the genus. Otherwise, one has only a research plan, leaving it to others to explore the unknown contours of the claimed genus. See Ariad, 598 F.3d at 1353 (The written description requirement guards against claims that “merely recite a description of the problem to be solved while claiming all solutions to it and …cover any compound later actually invented and determined to fall within the claim’s functional boundaries.”). See Abbvie Deutschland GmbH & Co. v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 U.S.P.Q.2d 1780, 1790, 2014 BL 183329, 12 (Fed. Cir. 2014).
In view of the above, considerations, the claims do not comply with the written description requirement.
Claims 22 and 33-36 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The application lacks complete deposit information for the bacterial strains DSM 33855, DSM 33856, DSM 33857 and DSM 33857. Because it is not clear that these bacteria were known and publicly available or can be reproducibly isolated from nature without undue experimentation and because the claims requires these bacteria, a suitable deposit for patent purposes is required. Exact replication of these bacteria is an unpredictable event.
Applicant's referral to the deposit of the bacteria in the specification is an insufficient assurance that all required deposits have been made and all the conditions of 37 CFR §1.801-1.809 have been met.
If the deposit has been made under the provisions of the Budapest Treaty, filing of an affidavit or declaration by applicant or assignees or a statement by an attorney of record who has authority and control over the conditions of deposit over his or her signature and registration number stating that the deposit has been accepted by an International Depository Authority under the provisions of the Budapest Treaty, that all restrictions upon public access to the deposit will be irrevocably removed upon the grant of a patent on this application and that the deposit will be replaced if viable samples cannot be dispensed by the depository is required. This requirement is necessary when deposits are made under the provisions of the Budapest Treaty as the Treaty leaves this specific matter to the discretion of each State. Amendment of the specification to recite the date of deposit and the complete name and full street address of the depository is required.
If the deposits have not been made under the provisions of the Budapest Treaty, then in order to certify that the deposits comply with the criteria set forth in 37 CFR §1.801-1.809, assurances regarding availability and permanency of deposits are required. Such assurance may be in the form of an affidavit or declaration by applicants or assignees or in the form of a statement by an attorney of record who has the authority and control over the conditions of deposit over his or her signature and registration number averring:
(a) during the pendency of this application, access to the deposits will be afforded to the Commissioner upon request;
(b) all restrictions upon the availability to the public of the deposited biological material will be irrevocably removed upon the granting of a patent on this application;
(c) the deposits will be maintained in a public depository for a period of at least thirty years from the date of deposit or for the enforceable life of the patent of or for a period of five years after the date of the most recent request for the furnishing of a sample of the deposited biological material, whichever is longest; and
(d) the deposits will be replaced if they should become nonviable or non-replicable.
In addition, a deposit of biological material that is capable of self-replication either directly or indirectly must be viable at the time of deposit and during the term of deposit. Viability may be tested by the depository. The test must conclude only that the deposited material is capable of reproduction. A viability statement for each deposit of a biological material not made under the Budapest Treaty must be filed in the application and must contain:
1) The name and address of the depository;
2) The name and address of the depositor;
3) The date of deposit;
4) The identity of the deposit and the accession number given by the depository;
5) The date of the viability test;
6) The procedures used to obtain a sample if the test is not done by the depository; and
7) A statement that the deposit is capable of reproduction.
As a possible means for completing the record, applicant may submit a copy of the contract with the depository for deposit and maintenance of each deposit.
Applicant's attention is directed to In re Lundack, 773 F.2d. 1216, 227 USPQ 90 (CAFC 1985) and 37 CFR §1.801-1.809 for further information concerning deposit practice.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 32 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
When the one further characteristic is “an ability to form endospores”, this is already recited in claim 19.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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.
Claim(s) 19 and 23-25 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Almand et al. BMC Res Notes (2019) 12:607. https://doi.org/10.1186/s13104-019-4669-2 , 6 pages.
Claim 19: Almand et al disclose an endospore-forming microorganism, of the genus Bacillus wherein said microorganism displays histo blood group antigens (HBGA) viral decoy receptors on its surface and preparations thereof.
Claim 23: Almand et al disclose the viral decoy receptor is a compound comprising 1 to 10 sugar units, wherein the sugar unit is N-acetylgalactosamine. See table 1.
Claim 24: Almand et al disclose the viral decoy receptor comprises a glycan comprising N-acetylgalactosamine. See table 1.
Claim: 25: Almand et al disclose the viral decoy receptor is A/O Histo- blood group antigen (HBGA).
Status of Claims
Claims 19-37 are rejected. Claim 38 is withdrawn.
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/OLUWATOSIN A OGUNBIYI/Primary Examiner, Art Unit 1645