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 .
Claim Status
2. This Office Action is in response the amendment filed 16 April 2025, wherein claims 1, 3-5, 12-14, 17, and 19 were amended and claims 16 and 20 were canceled.
Claims 1-15 and 17-19 are under consideration.
Information Disclosure Statement
3. 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.
Claim Interpretation
4. It is interpreted that the SEQ ID NOs require the full length of the sequence as listed without any additions/mutations/substitutions in between but can have base pairs before/after.
Objections Withdrawn
Specification
5. The objection to the specification for SEQ ID NO: 3 having no information is withdrawn in view of Applicant’s amendments.
6. The objection to the specification for the table numbers being out of order is withdrawn in view of Applicant’s amendments.
7. The objection to the specification for containing embedded hyperlinks and/or other form of browser-executed code is withdrawn in view of Applicant’s amendments.
8. The objection to the specification for use of trade name or trademarks without proper identifier is withdrawn in view of Applicant’s amendments.
Claim Objections
9. The objections to claims 4-5, 12-13, and 19 are withdrawn in view of Applicant’s amendments.
Rejections Withdrawn
Claim Rejections – 35 USC § 112
10. The rejections of claims 1-17 and 19-20 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite are withdrawn in view of Applicant’s amendments.
11. Applicant’s arguments, see page 9 of Applicant’s remarks, filed 16 April 2026, with respect to the rejection of claim 18 under 35 U.S.C. 112(b) for the use of “concern” being relative, have been fully considered and are persuasive. The rejection of claim 18 under 35 U.S.C. 112(b) has been withdrawn.
Claim Rejections – 35 USC § 101
12. Under further consideration, the rejection of claims 1-13 and 15-20 under 35 U.S.C. 101 have been withdrawn for not reading on a mental process. Examiner notes that the judicial exception that should have been considered was a natural correlation, however the addition of probes overcomes this natural correlation (Step 2A, Prong 1: No).
Claim Rejections – 35 USC § 102
13. The rejection of claims 1-8, 12-13, and 18-19 under 35 U.S.C. 102(a)(1) as being anticipated by Smyth (medRxiv, 26 July 2021) (See IDS filed 17 January 2025) is withdrawn in view of Applicant’s amendments.
Claim Rejections – 35 USC § 103
14. The rejection of claims 9-11 under 35 U.S.C. 103 as being unpatentable over Smyth (supra) and further in view of Meinke (US 20240293531 A1; 06 April 2021) (See PTO-892 mailed 16 December 2025) is withdrawn in view of Applicant’s amendments.
15. The rejection of claims 15-16 under 35 U.S.C. 103 as being unpatentable over Smyth (supra) and further in view of Smyth2 (Nat. Commun., 03 February 2022, 13, 635) (See IDS filed 17 January 2025) is withdrawn in view of Applicant’s amendments.
16. The rejection of claim 17 under 35 U.S.C. 103 as being unpatentable over Smyth (supra) and Smyth2 (supra), and further in view of Wohlstadter (US 20210349104 A1; EFD 30 April 2021) (See PTO-892 mailed 16 December 2025) is withdrawn in view of Applicant’s amendments.
17. The rejection of claim 20 under 35 U.S.C. 103 as being unpatentable over Smyth (supra) and further in view of Dergham (J. Clin. Med., 18 June 2021, 10(12), 2696) (See PTO-892 mailed 16 December 2025) is withdrawn in view of Applicant’s amendments.
Objections Maintained
Drawings
18. Examiner notes that Applicant has filed a petition for color drawings on 16 April 2026. Since no petition decision has been made, the objection is maintained.
New Objections
Specification
19. The specification is objected to because Table 3 is indiscernible.
20. The specification is objected to because the SEQ ID NO’s on pages 61-62, 64, and 73-74 should be in parentheses.
Claim Objections
21. Claim 1 is objected to because of the following informalities:
“wherein the RT-PCR primers pairs” in line 8 should read “wherein the RT-PCR primer pairs”
“SEQ ID NO: 25 and SEQ ID NO: 26 or SEQ ID NO: 16 and SEQ ID NO: 7” should be rewritten using a) and b) to list each option for clarity.
A comma should be added after “stool” in line 11.
“the” should be added before “antigenic variants” in line 12.
“SARS-CoV-2” should be added to claim 1 as the primers will not work with other types of viruses.
Appropriate correction is required.
22. Claim 17 is objected to because of the following informalities: the nucleic acid sequences are identical to the sequence identifiers inside the parentheses and should be deleted. The claim should read “wherein the nested primers are SEQ ID NO: 17 and SEQ ID NO: 18.”. Appropriate correction is required.
New Rejections
23. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Rejections - 35 USC § 112(b)
24. Claims 1-15 and 17-20 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, it is unclear what the control is for comparison when “identifying sequence differences in the variable regions” in line 13. One could envision the control being the sequence of the original SARS-CoV-2 strain or the sequence of the most common SARS-CoV-2 strain at the time of filing. 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.").
Claims 2-15 and 17-20, which are dependent on claim 1, are similarly rejected.
The term “cryptic” in claim 1 is a relative term which renders the claim indefinite. The term “cryptic” is not defined by the claim, the specification defines the term as “rarely observed in contemporaneous clinical samples” (Page 9, ¶ 3), which is also a relative term, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claims 2-15 and 17-20, which are dependent on claim 1, are similarly rejected.
Claim 4 is rejected for claiming the limitation of amino acid positions within a protein sequence without providing an appropriate frame of reference for said sequence. Said frame of reference can be provided by referencing a sequence disclosed within the application (i.e. a sequence with a SEQ ID NO: identifier) or by referencing a start position for said sequence (i.e. “…wherein said nucleotide is at position X from the starting ATG of the open reading frame…” or “…wherein said amino acid is at position X from the starting methionine of the protein…”).
Claim Rejections - 35 USC § 112(d)
25. 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.
26. Claims 2-4 are 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. The claims recite SARS-CoV-2 and that the variable regions are in the SARS-CoV-2 spike or membrane protein, further specifying the RBD or first 19 amino acids of the membrane protein. This does not further limit claim 1 as the primers recited will only bind these regions on SARS-CoV-2. 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 so long as no duplicates are made, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 103
27. 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.
28. 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.
29. Claims 1-8, 12, 15, and 17-19 are rejected under 35 U.S.C. 103 as being unpatentable over Smyth (medRxiv, 26 July 2021) (See IDS filed 17 January 2025) in view of Seo (US 11020475 B1; Application filed 26 October 2020), Rychlik (Nucleic Acids Research, 1989, 17(21): 8543-8551), and Buck (Biotechniques, 1999, 27(3): 528-536).
Regarding claims 1-4 and 19, Smyth teaches “Wastewater was collected from the inflow at 14 NYC wastewater treatment plants and RNA isolated according to our previously published protocol.” (Wastewater Sample Processing and RNA Extraction, ¶ 1) and “To monitor New York City (NYC) for the presence of novel variants, we amplified regions of the SARS-CoV-2 Spike protein gene from RNA acquired from all 14 NYC wastewater treatment plants (WWTPs) and ascertained the diversity of lineages from these samples using high throughput sequencing. Here we report the detection and increasing frequencies of novel SARS-CoV-2 lineages not recognized in GISAID’s EpiCoV database.” (Abstract). Smyth further teaches “Our targeted sequencing strategy entailed iSeq 100 and MiSeq sequencing of PCR-amplified regions of the SARS-CoV-2 Spike protein gene, particularly the receptor binding domain (RBD).” (Main, ¶ 1). In summary, Smyth collected wastewater, extracted the RNA, amplified the RBD region using PCR, sequenced the Spike protein region of SARS-CoV-2, and used a database to determine which lineages were previously unidentified, as claimed.
Smyth teaches using nested primers with PCR (Table 1), but does not teach the specific primer pairs of SEQ ID NO: 25 and 26 or SEQ ID NO: 16 and 7. However, Seo teaches SEQ ID NO: 3, which is the surface glycoprotein (Columns 51-56) of wild-type SARS-CoV-2 (CoV-2-CNUHV03) (Column 18). The surface glycoprotein is the Spike protein.
SEQ ID NO: 3 (‘Db’) has a 100% sequence identity to SEQ ID NO: 16 (‘Qy’):
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The SEQ ID NO: 3 (‘Db’) also has a 100% sequence identity to SEQ ID NO: 7 (‘Qy’):
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Since the reference sequence is given, making these primers would have been obvious to one of ordinary skill before the time of filing. Rychlik teaches it is routine and predictable to make
primers for DNA amplification wherein primers are designed to a known oligonucleotide sequence.
Rychlik teaches criteria to design/choose suitable primers for DNA amplification (see whole document
and Abstract). Buck expressly provides evidence of the equivalence of primers. Specifically, Buck invited
primer submissions from a number of labs (39) (Pg. 532, Column 3), with 69 different primers being
submitted (Pg. 530, Column 1). Buck also tested 95 primers spaced at 3 nucleotide intervals along the
entire sequence at issue, thereby testing more than 1/3 of all possible 18 met primers on the 300 base
pair sequence (Pg. 530, Column 1). When Buck tested each of the primers selected by the methods of
the different labs, Buck found that every single primer worked (Pg. 533, Column 1). Further, every single control primer functioned as well (Pg. 533, Column 1). Buck expressly states "The results of the empirical
sequencing analysis were surprising in that nearly all of the primers yielded data of extremely high
quality (Pg. 535, Column 2)." Therefore, Buck provides direct evidence that all primers would be
expected to function, and in particular, all primers selected according to the ordinary criteria. This
clearly shows that every primer would have a reasonable expectation of success.
Therefore, it would have been obvious to one of ordinary skill before the effective filing date to take the method of Smyth and further use the primers made obvious by Seo, Rychlik, and Buck to arrive at the method as claimed. 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 claims 5-8 and 18, Smyth further teaches “To test if the WNY lineages have gained resistance to neutralizing antibodies, we obtained three clinically approved neutralizing monoclonal antibodies representing these 3 classes, LY-CoV016 (etesevimab, Class 1)43, LY-CoV555 (bamlanivimab, Class 2)44, and REGN10987 (imdevimab, Class 3)45, and tested their ability to neutralize the WNY lineages. All four of the WNY lineages displayed complete resistance to LY-CoV555, despite the parent lineage remaining potently sensitive to this antibody (Fig.3). The WNY 1 and 2 remained at least partially sensitive to LY-CoV016 and REGN10987, but WNY 3 and 4 appeared to be completely resistant to all three neutralizing antibodies (Fig. 3).” (Lineages Detected from Wastewater Are Resistant to Some Neutralizing Antibodies, ¶ 2) and “Transfections of 10cm dishes of 293FT cells were performed 5 mg each of heavy and light chain vectors and 40 mg polyethyleneimine (PEI).” (Monoclonal antibody synthesis, ¶ 1). Smyth further teaches “Thus, the characteristics of these variant lineages provide them the capacity to be an increased threat to human health.” (Lineages Detected from Wastewater Are Resistant to Some Neutralizing Antibodies, ¶ 3). In summary, Smyth teaches an antibody neutralization assay (Antibody Neutralization Assay, ¶ 1) to test the viruses and generated monoclonal antibodies that were somewhat capable of recognizing and neutralizing the variants. One of ordinary skill would be concerned with the variants that were found to be resistant to the existing neutralizing antibodies. In addition, the prior art clearly demonstrates that it would be desirable to have a neutralizing antibody against the variants and generating new antibodies against the variants would be obvious. Notably, the Board of Patent Appeals and Interferences has taken the position that once an antigen has been isolated, the manufacture of monoclonal antibodies against it is prima facie obvious. See Ex parte Ehrlich, 3 USPQ 2d 1011 (PTO BPAI, 1987) and Ex parte Sugimoto, 14 USPQ 2d 1312 (PTO BPAI, 1990).
Regarding claims 12 and 15, Seo’s SEQ ID NO: 3 (‘Db’) has a 100% match to SEQ ID NO: 6 (‘Qy’):
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SEQ ID NO: 3 (‘Db’) also has a 100% match to SEQ ID NO: 7 (‘Qy’):
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The obviousness of primers is discussed by Rychlik and Buck supra. It would further be obvious to add this second set of primers, as Smyth teaches nested primers. The addition of another set of primers allows for a more specific amplification region. The bounds of the second primer pair (SEQ ID NOs: 6 and 7) are within the bounds of the first primer pair (SEQ ID NOs: 16 and 7). After amplification with the first primer pair, the resulting amplified region on the Spike protein would be greater than 1.5 kb.
Regarding claim 17, Seo’s SEQ ID NO: 3 (‘Db’) has a 100% match to SEQ ID NO: 17 (‘Qy’):
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SEQ ID NO: 3 (‘Db’) also has a 100% match to SEQ ID NO: 18 (‘Qy’):
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The obviousness of primers is discussed by Rychlik and Buck supra. It would further be obvious to add this second set of primers, as Smyth teaches nested primers. The bounds of the second primer pair (SEQ ID NOs: 17 and 18) are within the bounds of the first primer pair (SEQ ID NOs: 16 and 7) and so this second pair would predictably function in the assay of Smyth.
30. Claims 9-11 are rejected under 35 U.S.C. 103 as being unpatentable over Smyth (supra), Seo (supra), Rychlik (supra), and Buck (supra) as applied to claims 1-8, 12, 15 and 17-19 above, and further in view of Meinke (US 20240293531 A1; 06 April 2021) (See PTO-892 mailed 16 December 2025).
Regarding claims 9-11, Smyth, Seo, Rychlik, and Buck make claim 1 obvious as discussed supra. All discussions thereon incorporated here. None of the references teach an inactivated vaccine using more than one of the antigenic variants. However, Meinke teaches “The SARS-CoV-2 particles in the vaccine composition may be derived from any known strain of SARS-CoV-2, or variants thereof. […] As described herein, the inactivation process may result in modification (e.g. alkylation or acylation) and/or fragmentation of viral RNA, and thus it will be understood that the inactivated viral particles may not comprise an intact RNA sequence as defined herein, but rather are derived from native viral particles which do comprise such a sequence.” (¶ [0070]) and “In some embodiments, the inactivated SARS-CoV-2 particles are combined with other inactivated SARS-CoV-2 particles in the vaccine (other=other sequence).” (¶ [0081]). Adding more than one variant would allow for more broadly-protecting SARS-CoV-2 vaccine.
Therefore, it would have been obvious to a person of ordinary skill before the effective filing date of the claimed invention to use the method made obvious by Smyth, Seo, Rychlik, and Buck and further use more than one identified antigenic variant in an inactivated viral vaccine, as discussed in Meinke. 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). One of ordinary skill in the art would have had a reasonable expectation of success for using the identified antigenic variants in an inactivated viral vaccine. There would have been a reasonable expectation of success given the underlying materials and methods are known, successfully demonstrated, and commonly used as evidenced by the applied prior art.
31. Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Smyth (supra), Seo (supra), Rychlik (supra), Buck (supra), and Meinke (supra), as applied to claims 9-11 above, and further in view of Tynan (US 20140093873 A1; Published 03 April 2014).
Regarding claim 13, Smyth, Seo, Rychlik, and Buck make claim 12 obvious as discussed supra. All discussions thereon incorporated here. Smyth further teaches that “The RBD region was amplified using Q5® High-Fidelity DNA Polymerase using primers that incorporate Illumina adaptors.” (iSeq sequencing, ¶ 1). Smyth’s Table 1 shows their MiSeq RBD nested primers, wherein the lowercase letters are the adaptor sequences:
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These primers have a 100% sequence identity to SEQ ID NOs: 8 and 9:
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None of the references teach SEQ ID NOs: 8 and 9, as written, in the same reference sequence with the other primer pairs. However, with the adaptor sequences removed, the remaining primers have a 100% match to Seo’s SEQ ID NO: 3 (‘Db’).
SEQ ID NO: 8 with the adaptor sequence removed (‘Qy’):
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SEQ ID NO: 9 with the adaptor sequence removed (‘Qy’):
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The obviousness of primers is discussed by Rychlik and Buck supra. It would further be obvious to add this third set of primers for greater specificity in the amplified region and these primers would predictably function in the assay of Smyth. Furthermore, Tynan teaches Table 11 with both adaptor sequences and “PCR primers were modified such that Illumina sequencing adapters could be added via universal tag sequences incorporated into the 5’ end of the SNP-specific PCR primers. Illumina tags were added using two separate PCR reactions (see Fig. 29 and Table 11 below)…” (¶ [0490]).
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Therefore, it would have been obvious to one of ordinary skill before the filing date to take the final set of nested primers and further add the Illumina sequencing adapters such that the resulting amplified regions can be read with the sequencer. 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).
32. Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Smyth (supra), Seo (supra), Rychlik (supra), Buck (supra), Meinke (supra), and Tynan (supra), as applied to claim 13 above, and further in view of Rauch (US 11596686 B2; CON to 03 February 2021).
Regarding claim 14, Smyth, Seo, Rychlik, and Buck make claim 1 obvious as discussed supra. All discussions thereon incorporated here. None of the references teach SEQ ID NOs: 25 and 26. However, Tynan teaches that SEQ ID NO: 11694 is a wild-type SARS-CoV-2 full-length Spike protein (Table 1; Column 38).
SEQ ID NO: 11694 (‘Db’) has a 100% sequence identity with SEQ ID NO: 25 (‘Qy’):
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SEQ ID NO: 11694 (‘Db’) has a 100% sequence identity with SEQ ID NO: 26 (‘Qy’):
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SEQ ID NO: 11694 (‘Db’) has a 100% sequence identity with SEQ ID NO: 8 with the adaptor sequence removed (‘Qy’):
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SEQ ID NO: 11694 (‘Db’) has a 100% sequence identity with SEQ ID NO: 18 (‘Qy’):
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The obviousness of primers is discussed by Rychlik and Buck supra. It would further be obvious to add a second set of primers. Tynan makes it obviousness to add the Illumina adaptor sequences.
Therefore, it would have been obvious to use these sequences in the method made obvious by Smyth, Seo, Rychlik, Buck, Meinke, and Tynan instead of primer pairs SEQ ID NOs: 16 and 7 and SEQ ID NOs: 17 and 18. The bounds of the second primer pair (SEQ ID NOs: 8 and 18) are within the bounds of the first primer pair (SEQ ID NOs: 25 and 26). There are multiple functional options that will arrive at predictable results in view of Rychilik and Buck. The simple substitution of one known element for another is likely to be obvious when predictable results are achieved. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, B.).
Conclusion
33. 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.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Michael Allen can be reached at (571) 270-3497. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KRISTINA E. LY/Examiner, Art Unit 1671 /Michael Allen/Supervisory Patent Examiner, Art Unit 1671
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