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 .
Election/Restrictions
Applicant's election with traverse of Group II (claims 15, 17, 19, 22-23, 25 and 75) in the reply filed on 9/11/2025 is acknowledged. The traversal is on the ground(s) that Groups V and VI include the limitations of Group II claims. This is not found persuasive.
Group II claims are directed to a fusion protein. Group V claims are directed to a polynucleotide and do not require the presence of the fusion protein. Thus, these two groups do not share a common feature or structure. Group VI claims are directed to a method of using the fusion protein of Group II. As outlined below, the cited prior art renders the claimed fusion protein obvious. Accordingly, the elected fusion protein does not make a contribution over the prior art.
The requirement is still deemed proper and is therefore made FINAL.
Withdrawn Rejections
The rejection of claim 19 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, has been withdrawn in view of applicant’s amendments to the claim to recite “the sequence” instead of “a sequence”.
The rejection of claims 15, 19, 23 and 25 under 35 U.S.C. 103 as being unpatentable over Graham et al. (U.S. Patent No. 10960070), and Bosch et al. (Journal of Virology, July 2004, 78(14):7369–7378) has been withdrawn in view of applicant’s amendments to the claims to recite SARS-CoV-2.
The rejection of claim 17 under 35 U.S.C. 103 as being unpatentable over Graham et al. (U.S. Patent No. 10960070), Bosch et al. (Journal of Virology, July 2004, 78(14):7369–7378) and Escriou et al. (U.S. Patent Application No. 20230021583; effectively filed 2/13/2020) has been withdrawn in view of applicant’s amendments to the claims to recite SARS-CoV-2.
Claim Objections
Claim 17 is objected to because of the following informalities: Claim 17 recites “wherein the the S protein”. Appropriate correction is required.
Claims 84 and 85 are objected to because of the following informalities: Applicant is advised that should claim 84 be found allowable, claim 85 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).
New Rejections Necessitated by Amendment
Claim Rejections - 35 USC § 112
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.
Claims 88 and 89 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.
Claim 88 is directed to a fusion protein comprising an S protein ectodomain from SARS-CoV-2, a trimerization domain, and a fluorescent protein, where the trimerization domain and the fluorescent protein are linked via a flexible peptide linker comprising 1-15 amino acids. Then the claim further recites that the fusion protein comprises another a fluorescent protein, where the trimerization domain and the fluorescent protein are linked via a flexible peptide linker. It is not clear how the two fluorescent proteins are linked to the trimerization domain. Accordingly, one of ordinary skill in the art will not know the metes and bounds of the claim.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 15, 19, 23, 25 and 84-87 are rejected under 35 U.S.C. 103 as being unpatentable over Graham et al. (WO 2021/163365; effectively 2/11/2020), and further in view of Bosch et al. (Journal of Virology, July 2004, 78(14):7369–7378) and Bergeron et al. (Biotechnology and Bioengineering, 2009, 102(5):1316-1322).
The instant claims are directed to a fusion protein, which comprises from the N-terminal to the C-terminal: a S protein ectodomain sequence of SARS-CoV-2, a trimerization domain sequence, and a fluorescent protein; wherein the trimerization domain sequence and the fluorescent protein are linked by a flexible peptide linker.
Graham et al. teaches that the ectodomain portion of the SARS-CoV-2 S protein mediates virus attachment to the host receptor and cell fusion. Graham et al. further teaches that the ectodomain of the SARS-CoV-2 S protein (or a prefusion stabilized S protein) can be linked to a T4 Fibritin trimerization domain. In this regard, Graham et al. teaches that “the C-terminal residue of the ectodomains of the protomers in the recombinant SARS-CoV-2 S ectodomain trimer can be linked to a trimerization domain to promote trimerization of the protomers, and to stabilize the membrane proximal aspect of the protomers in a trimeric configuration” (see page 22, lines 8-18). Graham et al. also teaches the use of linkers, such as glycine, serine, or glycine-serine linkers between the S1 and S2 portions of the S protein and between the ectodomain and the trimerization domain (see page 22, lines 24-26; page 24, lines 40-41; and claims 8, 14, and 17).
Bergeron et al. teaches glycine-serine linkers consisting of one repeat (GGGGS)1, two repeats (GGGGS)2, and four repeats (GGGGS)4.
Bosch et al. teaches a fusion protein comprising the S protein of a coronavirus and GFP (green fluorescent protein) at the C-terminal end (see Figure 1A below).
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Bosch et al. found that the S-GFP chimeric protein induced the formation of fluorescent syncytia, indicating that it was synthesized and folded properly, trimerized, and transported to the plasma membrane, where it exhibited the two key S protein functions, i.e., interaction with virus receptor molecules and membrane fusion.
Bosch et al. teaches that the fluorescent S-GFP is a convenient tool to study coronaviral cell entry (see the Abstract). Bosch et al. states that the “S-GFP protein that we constructed in the present study for our ongoing analysis of coronavirus structure and assembly provides us now with a virus, the fluorescent properties of which may allow us to investigate cell entry of coronaviruses by using time-lapsed imaging fluorescence microscopy”.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the trimerized SARS-CoV-2 S protein of Graham et al. and include a reporter molecule, such as the GFP, at the C-terminal end as taught by Bosch et al. One would have been motivated to do so given the suggestion by Bosch et al. that S-GFP chimeric proteins are useful tools for studying coronaviral cell entry and given the teachings of Graham et al. regarding the ectodomain portion of the SARS-CoV-2 S protein [the S protein mediates virus attachment to the host receptor and cell fusion]. Additionally, one of ordinary skill in the art would be motivated to use SARS-CoV-2-GFP trimers as tools to study SARS-CoV-2 S protein interactions with its receptor molecules on host cells, membrane fusion and cell entry, as SARS-CoV-2 is a newer coronavirus. There would have been a reasonable expectation of success given that Bosch et al. successfully linked GFP to the coronavirus S protein.
As for the use of linkers, Graham et al. teaches the use of glycine, serine and glycine-serine linkers between peptides of their S protein constructs. Bergeron et al. teaches glycine-serine linkers consisting of one repeat (GGGGS)1, two repeats (GGGGS)2, and four repeats (GGGGS)4.
Given teachings of Graham et al. and Bergeron et al. regarding linkers and given the state of the art regarding the use of linkers (e.g., prevent steric hindrances between proteins), it would be obvious and routine for one of ordinary skill in the art before the effective filing date of the claimed invention to place, as necessary, known serine, glycine or glycine-serine linkers, such as the linkers of Bergeron et al., between S1 and S2, between the S protein and the trimerization domain, and between the trimerization domain and the GFP protein. One would be motivated to do so and there would be a reasonable expectation of success given the teachings and finding of Graham et al. and Bergeron et al.
Regarding claim 19, Graham et al. teaches that the trimerization domain can be the T4 Fibritin trimerization domain GYIPEAPRDGQAYVRKDGEWVLLSTF (see page 18, lines 26-34), which comprises instant SEQ ID NO: 40.
Regarding claim 23, Graham et al. teaches that the recombinant coronavirus S ectodomain linked to the nanoparticle subunit can include an N - terminal signal peptide that is cleaved during cellular processing (see page 20, lines 32-36 and page 35, lines 1-4).
Regarding claim 25, Graham et al. teaches a trimer (a multimer) comprising the recombinant protomers (see page 2, lines 6-9) and page 6, line 33 to page 7, line 1).
Regarding claims 84-85, Graham et al. teaches the linker can be a gly-ser linker, for example, a 10 amino acid glycine-serine peptide linker (see page 23, lines 37-38).
Regarding claims 86 and 87, Bergeron et al. teaches glycine-serine linkers consisting of one repeat (GGGGS)1, two repeats (GGGGS)2, and four repeats (GGGGS)4.
Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Graham et al. (WO 2021/163365; effectively 2/11/2020), Bosch et al. (Journal of Virology, July 2004, 78(14):7369–7378) and Bergeron et al. (Biotechnology and Bioengineering, 2009, 102(5):1316-1322) as applied to claims 15, 19, 23, 25 and 84-87 above, and further in view of Escriou et al. (U.S. Patent Application No. 20230021583; effectively filed 2/13/2020).
The instant claim is directed to the fusion protein of claim 15 where the S protein ectodomain sequence is set forth in SEQ ID NO: 21 or a sequence having a sequence identity of at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% as compared to the sequence set forth in SEQ ID NO:21.
The teachings of Graham et al. and Bosch et al. are outline above and incorporated herein. While Graham et al. and Bosch et al. teach a coronavirus S protein, neither reference teaches instant SEQ ID NO: 21. However, Escriou et al. teaches a coronavirus S protein sequence that contains instant SEQ ID NO: 21 (see SEQ ID NO: 43 of Escriou et al.). The sequence of Escriou et al. is 93.4% identical to instant SEQ ID NO: 21 overall (see the alignment below) and 99% identical to amino acids 16-1207 of instant SEQ ID NO: 21.
# Identity: 1191/1273 (93.6%)
# Similarity: 1191/1273 (93.6%)
SEQ21 1 ---------------VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHS 35
|||||||||||||||||||||||||||||||||||
SEQ43 1 MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHS 50
SEQ21 36 TQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNI 85
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 51 TQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNI 100
SEQ21 86 IRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNK 135
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 101 IRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNK 150
SEQ21 136 SWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGY 185
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 151 SWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGY 200
SEQ21 186 FKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT 235
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 201 FKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT 250
SEQ21 236 PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK 285
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 251 PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK 300
SEQ21 286 CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV 335
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 301 CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV 350
SEQ21 336 YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF 385
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 351 YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF 400
SEQ21 386 VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYN 435
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 401 VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYN 450
SEQ21 436 YLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPT 485
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 451 YLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPT 500
SEQ21 486 NGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTG 535
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 501 NGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTG 550
SEQ21 536 VLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP 585
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 551 VLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP 600
SEQ21 586 GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCL 635
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 601 GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCL 650
SEQ21 636 IGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLG 685
||||||||||||||||||||||||||||||||||.|||||||||||||||
SEQ43 651 IGAEHVNNSYECDIPIGAGICASYQTQTNSPGSAGSVASQSIIAYTMSLG 700
SEQ21 686 AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECS 735
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 701 AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECS 750
SEQ21 736 NLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF 785
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 751 NLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF 800
SEQ21 786 NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLI 835
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 801 NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLI 850
SEQ21 836 CAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM 885
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 851 CAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM 900
SEQ21 886 QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQD 935
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 901 QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQD 950
SEQ21 936 VVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGR 985
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 951 VVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGR 1000
SEQ21 986 LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM 1035
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 1001 LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM 1050
SEQ21 1036 SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT 1085
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 1051 SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT 1100
SEQ21 1086 HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKE 1135
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 1101 HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKE 1150
SEQ21 1136 ELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL 1185
||||||||||||||||||||||||||||||||||||||||||||||||||
SEQ43 1151 ELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL 1200
SEQ21 1186 QELGKYE------------------------------------------- 1192
|||||||
SEQ43 1201 QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSC 1250
SEQ21 1193 ----------------------- 1192
SEQ43 1251 GSCCKFDEDDSEPVLKGVKLHYT 1273
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the construct of Graham et al. and use known coronavirus S protein ectodomain sequences, such as the sequence taught by Escriou et al., and the result would be predictable [the ectodomain of the coronavirus S protein linked to a T4 Fibritin trimerization domain].
Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Response to Arguments
In the reply dated 3/20/2026, applicant argues that the objectives of Graham et al. are different from the objectives of the instant application, thus, one of ordinary skill in the art would not turn to Graham et al. for developing a probe for evaluating drugs to treat covid. Applicant’s arguments have been fully considered and not found persuasive.
The objective of Graham et al. is not relevant. As outlined above, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the trimerized SARS-CoV-2 S protein of Graham et al. and include a reporter molecule, such as the GFP, at the C-terminal. Such constructs can then be used as tools to study SARS-CoV-2 S protein interactions with its receptor molecules on host cells, membrane fusion and cell entry, as SARS-CoV-2 is a newer coronavirus. Bosch et al. teaches that the fluorescent S-GFP is a convenient tool to study coronaviral cell entry (see the Abstract). Bosch et al. states that the “S-GFP protein that we constructed in the present study for our ongoing analysis of coronavirus structure and assembly provides us now with a virus, the fluorescent properties of which may allow us to investigate cell entry of coronaviruses by using time-lapsed imaging fluorescence microscopy”.
Applicant next argues that modifying the stabilized protein of Graham et al. would defeat Graham’s objective. Applicant’s arguments have been considered and not found persuasive.
The rejection does not mention eliminating the stabilization of the S protein or the trimerization domain. The rejection discusses adding the GFP protein to the C-terminal end of Graham’s S protein/trimerization domain construct to create a tool to study SARS-CoV-2 S protein interactions with its receptor molecules on host cells, membrane fusion and cell entry (as suggested by Bosch et al.).
Allowable Subject Matter
A fusion protein containing: (1) an amino acid sequence consisting of amino acid residues 21 to 1502 of instant SEQ ID NO: 26; or (2) an amino acid sequence consisting of amino acid residues 21 to 1499 of instant SEQ ID NO: 27 is free of the prior art. Further, a search of the prior art did not identify a reference or set of references that teach or fairly suggest a kit comprising the fusion protein of claim 15 and a cell expressing a recombinant coronavirus receptor comprising a fluorescent protein, where the fluorescent protein contained in the fusion protein is detectably different from the fluorescent protein contained in the recombinant coronavirus receptor expressed by the cell. Accordingly, claims 22 and 75 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
No claim is 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 Nicole Kinsey White whose telephone number is (571)272-9943. The examiner can normally be reached M to Th 6:30 am to 6:00 pm.
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/NICOLE KINSEY WHITE/Primary Examiner, Art Unit 1672
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