DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
2. Applicant's election with traverse of Group I: claims 1, 4-8, 10-11, 13-14, and 16 in the reply filed on 18 March 2026 is acknowledged. The traversal is on the grounds that Groups I and II share a common feature and that Group III includes all features of Group II. This is not found persuasive because the common feature does not define a contribution over the prior art, and thus is not a special technical feature. Applicant has not established that the claimed invention would provide a contribution over the cited prior art in the Restriction Requirement mailed on 19 December 2025. Additionally, Applicant also applies a different standard to traverse the restriction requirement, as search burden is irrelevant to National Phase (371) applications. Thus, the requirement is still deemed proper and is therefore made FINAL.
Claims 2-3, 17-23 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 19 December 2025.
Claim Status
3. Claims 2-3, 17-23 are withdrawn and claims 9, 12, 15, and 24 are canceled. Claims 1, 4-8, 10-11, 13-14, and 16 are under consideration.
Priority
4. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. Therefore, the effective filing date of the claims is 27 January 2021.
Information Disclosure Statement
5. The information disclosure statement (IDS) submitted on 08 November 2023 was filed after the mailing date of the Instant Application on 17 July 2023. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
6. The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
7. Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
8. The use of the term “ELISpot” (page 27, ¶ 1-3), which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Note that “ELISpot” is merely an example and all improper uses of trademarks in the specification should be identified by Applicant and properly addressed.
Claim Objections
9. Applicant is advised that should claim 10 be found allowable, claim 13 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claim Rejections - 35 USC § 112(b)
10. 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.
11. Claims 1, 4-8, 10-11, 13-14, and 16 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.
Regarding claim 1, “producing a pool” is unclear. This could be interpreted to be either a mixture of protein fragments or a digitalized list of fragments. Examiner is interpreting this to be a digitalized list.
Claims 4-8, 10-11, 13-14, and 16, which depend on claim 1, are similarly rejected.
Regarding claim 1, “encompassing at least 80% of the sequence of the microbial protein” in a) and c(ii) is unclear because this could be interpreted that the library has 80% of the reference sequence or that each fragment has an 80% identity to the reference sequence. Examiner is interpreting this to be that the library has at least 80% of the reference sequence.
Claims 4-8, 10-11, 13-14, and 16, which depend on claim 1, are similarly rejected.
Regarding claim 1, it is unclear if everything after “and” in c(ii) is applicable to c(i) and c(ii) or just c(ii).
Claims 4-8, 10-11, 13-14, and 16, which depend on claim 1, are similarly rejected.
The term “emerging” in claim 4 is a relative term which renders the claim indefinite. The term “emerging” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The specification does provide a definition on page 10, but it does not alleviate the indefiniteness of the term.
See Ex parte Miyazaki, 89 USPQ2d 1207 (BPAI 2008) ("[R]ather than requiring that the claims are insolubly ambiguous, we hold that if a claim is amenable to two or more plausible claim constructions, the USPTO is justified in requiring the applicant to more precisely define the metes and bounds of the claimed invention by holding the claim unpatentable under 35 U.S.C. §112, second paragraph, as indefinite.").
Claim Rejections - 35 USC § 101
12. Claims 1, 4-8, 10-11, 13-14, and 16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The claims recite “identifying”, “determining”, and “preparing a pool of fragments”. This judicial exception is not integrated into a practical application and the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons set forth below. See MPEP 2106 for analysis framework.
The instant claims are drawn to a method with steps of “identifying”, “determining”, and “preparing a pool of fragments”. As such, the instant claims are drawn to a process, which is statutory category of matter (Step 1: Yes).
The instant claims are drawn to a judicial exception of an abstract idea, the entirety of the instant claims can be done on a computer or using a program. The step of identifying, determining, or preparing could be performed by a human using mental steps or basic critical thinking using the output of such a computer or program, which are types of activities that have been found by the courts to represent abstract ideas (e.g., the mental comparison in Ambry Genetics, or the diagnosing an abnormal condition by performing clinical tests and thinking about the results in Grams). Thus, the claim is directed to at least one exception, which may be termed as an abstract idea (Step 2A, Prong 1: Yes). The instant claims are drawn solely to a judicial exception which is not integrated into a practical application because the claimed invention is not used to provide a particular treatment or prophylaxis for a disease or medical condition. Further, the claimed invention does not apply or use the judicial exception in a meaningful way and there is no inventive concept in the claims. Generally linking the use of the judicial exception to a particular technological environment or field of use, is not indicative of integration into a practical application (see MPEP 2106.05(h) and Example 29, Claim 2 (Diagnosing and Treating Julitis) of the Subject Matter Eligibility Examples: Life Sciences found at https://www.uspto.gov/sites/default/files/documents/ieg-may-2016-ex.pdf)). Therefore, the instant claims do not recite any additional elements that integrate the exception into a practical application (Step 2A, Prong 2: No).
The instant claims are drawn to a judicial exception and do not recite any additional elements that amount to significantly more than the judicial exception (Step 2B: No).
In view of the foregoing, the instant claims do not constitute patent eligible subject matter under 35 U.S.C. § 101.
Claim Rejections - 35 USC § 103
13. 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.
14. 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.
15. Claims 1, 4-8, 10-11, 13-14, and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Olvera (06 August 2020, Vaccines, 8(3): 444) (See IDS filed 08 November 2023) in view of Pitman (2006, Applied Mycology and Biotechnology).
Regarding claims 1, 4-8, 10-11, and 13-14, Olvera teaches “To accelerate immune studies in SARS-CoV-2 infection, we here describe a SARS-CoV-2 2020 consensus sequence (CoV-2-cons) which is based on more than 1700 viral genome entries in NCBI and encompasses all described SARS-CoV-2 open reading frames (ORF), including recently described frame-shifted and length variant ORF. Based on these sequences, we created curated overlapping peptide (OLP) lists containing between 1500 to 3000 peptides of 15 and 18 amino acids in length, overlapping by 10 or 11 residues, as ideal tools for the assessment of SARS-CoV-2-specific T cell immunity.” (Abstract). This list of overlapping peptides would then cover the full length protein, which would meet the claimed limitation of at least 80% coverage. Olvera further teaches “In an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences. […] (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment).” (2.3 Detection of Conserved Peptides Among Coronavirus) and “To identify previously reported epitopes in the conserved regions of coronaviruses (pan-coronavirus, betacoronaviruses, and human coronaviruses), and match them with the SARS-CoV-2 consensus sequence, searches for experimentally described epitopes were carried out in the Immune Epitope Database. The search criteria were as follows: “linear peptide; blast option: 90%; Host: Homo sapiens; Any MHC restriction; Positive assays only; All assays; Any disease”.” (2.4 Identification of Previously Described Epitopes in CoV-2 Conserved Regions).
In summary, Olvera teaches creating a consensus sequence based on all available SARS-CoV-2 sequences and curating a list of overlapping peptides (fragment library with at least 80% coverage) that can be 15 amino acids long and overlapping by 11 residues, as claimed. They then aligned the consensus sequence with other sequences from the coronavirus family to identify homologous proteins, including OC43, NL63, 229E, and HKU1, as claimed. These strains of coronavirus are endemic as they taught above to be “common cold species”, which is further supported by the Instant Specification (Page 33). They also searched for conserved coronavirus regions with a 90% match to the consensus sequence, which would read on ensuring that each homolog has at least 60% identity to the reference. Their list of identified sequences would read on a “pool of fragments”. At the time of this reference, SARS-CoV-2 was an emerging and pandemic-level pathogen starting in December 2019 (Introduction, ¶ 1).
Olvera does not teach the homologs must have at least 60% identity to the sequence.
However, Pitman teaches “As a general rule for homology modelling, the minimum percentage of amino acid sequence identity required between the target and template is 30%” (2.2 Identification of Template Structures). It would have been obvious to one of ordinary skill before the time of filing to take the method of Olvera and further decrease the standard percentage of identifying a homolog from 90% to 60% in order to identify a wider range of homologs that may elicit an immune response. The “any MHC restriction” search criteria used in Olvera also makes it obvious to look for epitopes that will elicit immune responses. The combination of familiar elements is likely to be obvious when it does no more than yield predictable results. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, A.). A rationale to support a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395 (2007) (see MPEP §§ 2143, A. and 2143.02).
Regarding claim 16, Olvera further teaches Table 3, which shows that they tested the spike, membrane (M), and nucleocapsid (N) proteins:
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883
866
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Regarding the interpretation of “a pool of fragments”, even if it were interpreted to be a physical mixture of protein fragments, it would still be rendered obvious by Olvera in view of Pitman. Olvera further teaches: “On the other hand, the existence of conserved sequences among beta- or even the whole coronavirus family suggests that T cell responses to these regions could provide broad protection and that the creation of a pan-coronavirus vaccine may be feasible. Such a vaccine could allow to prevent infection not only with SARS-CoV-2, but also with other, clinically relevant coronavirus like SARS-CoV-1 and MERS, and even with new coronaviruses jumping the species barrier to humans. However, the design of a pan-coronavirus vaccine will critically depend on the identification of epitopes shared among them. These pan-coronavirus epitopes are likely to exist in conserved sequences, but need to be experimentally validated.” (Discussion, ¶ 4). Therefore, it would have been obvious to one of ordinary skill before the time of filing to take the identified homologs between different coronaviruses and further add them to a vaccine in order to design a vaccine that will be effective against multiple types of coronaviruses. This would reduce the number of immunizations one would need for protection against multiple different coronaviruses. The combination of familiar elements is likely to be obvious when it does no more than yield predictable results. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, A.). A rationale to support a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395 (2007) (see MPEP §§ 2143, A. and 2143.02).
Conclusion
16. No claim is allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KRISTINA E LY whose telephone number is (571)272-5169. The examiner can normally be reached Monday - Thursday, 8:00 am - 5:00 pm EST.
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/KRISTINA E. LY/Examiner, Art Unit 1671 /Michael Allen/Supervisory Patent Examiner, Art Unit 1671
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