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 .
DETAILED ACTION
Acknowledgement is hereby made of receipt and entry of the communication filed on Jul. 9, 2024. Claims 1-20 are pending and currently examined.
Specification – Sequence Compliance
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 through 1.825 for the reason(s) as follows:
The specification does not contain sequence identifiers (SEQ ID NO:) in all locations where sequences are disclosed, see Fig. 3. To correct this, the sequences in figures can be referred to in either the figure or the Brief Description of Drawings. If the prior filed Sequence Listing does not contain updated sequences, Applicant is also required to submit a replacement Sequence Listing that includes all updated sequences.
Full compliance with the sequence rules is required in response to this Office Action. A complete response to this office action should include both compliance with the sequence rules and a response to the Office Action set forth below. Failure to fully comply with both these requirements in the time period set forth in this Office Action will be held non-responsive.
Claim Objection
Claims 1, 2 and 4-9 are objected to for the following abnormalities:
1) These claims use the word “aminoacid” or “amino acids” which should be correctly spelled as “amino acid” or “amino acids”.
2) Claim 2 and 4-9 are depended claims, with claim 2 reciting “A mutated SARS-CoV-2 spike protein as claimed in claim 1” and claims 4-9 reciting “A variant as claimed in claim 3”. Applicant should change the phrases to “The mutated SARS-CoV-2 spike protein according to claim 1” and “The variant according to claim 3”, respectively.
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.
Claims 1-20 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1 recites “A mutated SARS-CoV-2 spike protein, wherein at least one of the aminoacids isoleucine or leucine at a position corresponding to aminoacid 818, 821, 822, 841, 844, 861, 864 and 865 of the wild type SARS-CoV-2 protein sequence (SEQ ID NO: 1) is replaced by alanine.” This claim is not clear in at least the following two aspect.
First, the claim specifies a “mutated SARS-CoV-2 spike protein” with only one attached limiting structural feature, i.e., substituting the isoleucine or leucine residue with alanine at one or more positions of 818, 821, 822, 841, 861, 864 and 865 of the wild type S protein (SEQ ID NO: 1). The claim does not specify whether the “mutated SARS-CoV-2 spike protein” contains other mutations relative to a “wild type”. The specification does not provide a clear definition for the term “mutated SARS-CoV-2 spike protein”, it is thus not clear what the boundary for this term is. E.g., it is not clear how much difference a protein may have from a wild-type SARS-CoV-2 spike protein for it to be called a “mutated SARS-CoV-2 spike protein”, and how much difference is too much. E.g., it is not clear if the spike protein of a SARS-CoV-1 which is about 76% identical to the spike of a wild-type SARS-CoV-2 or a mutated form thereof can be considered as a “mutated SARS-CoV-2 spike protein”.
Secondly, claim 1 recites “the wild type SARS-CoV-2 protein sequence (SEQ ID NO: 1)”. By using the parenthesis, it is not clear what the relation between the “the wild type SARS-CoV-2 protein sequence” and the sequence of SEQ ID NO: 1 is. E.g., it is not clear if SEQ ID NO: 1 is “the wild type SARS-CoV-2 protein sequence”, or it is just one example of it.
Claim 3 recites “A variant of a mutated SARS-CoV-2 spike protein, wherein at least one of the aminoacids isoleucine or leucine at a position corresponding to aminoacid 818, 821, 822, 841, 844, 861, 864 and 865 of the wild type SARS-CoV-2 protein sequence (SEQ ID NO: 1) are replaced by alanine, or a variant of a mutated SARS-CoV-2 spike protein selected from SEQ ID NO: 2, 28, 29, 30, or 31.”
First, similar to claim 1, by using the parenthesis, it is not clear what the relation between the “the wild type SARS-CoV-2 protein sequence” and the sequence of SEQ ID NO: 1 is.
Secondly, besides the term “mutated SARS-CoV-2 spike protein” which is already not clear, claim 3 further recites a “variant of a mutated SARS-CoV-2 spike protein” making the claim even more unclear. The specification defines the term “variant” as following (see page 10, para 2):
According to the present invention, by "variant" of the mutated SARS-CoV-2 spike protein it is meant a protein having an aminoacid sequence which differs from the sequence of the mutated SARS-CoV-2 spike protein as described above, in that it contains one or more substitutions, deletions or insertions of aminoacids. Said substitutions, deletions or insertions of aminoacids may be in any position except a position corresponding to aminoacid 818, 821, 822, 841, 844, 861, 864 and 865 of SEQ ID NO: 1. Preferably, said substitutions, deletions or insertions do not interfere with the conformation and the antigenic properties of the mutated SARS-CoV-2 spike protein according to the present invention. More preferably, said substitutions, deletions or insertions improve the antigenic properties and/or stability of the mutated SARS-CoV-2 spike protein. Preferably, the variant has a sequence with an aminoacid identity with the corresponding mutated SARS-CoV-2 spike protein as described above of at least 80%, 85%, 90%, 95%, 98%, 99%.
This definition does not attach any limiting structural and/or property requirements for the “variant of the mutated SARS-CoV-2 spike protein” except for the amino acid on a position corresponding to amino acid 818, 821, 822, 841, 844, 861, 864 and 865 of SEQ ID NO: 1. On the contrary, the definition explicitly introduces additional one or more substitutions, deletions or insertions of amino acids.
Additionally, claim 3 recites “or a variant of a mutated SARS-CoV-2 spike protein selected from SEQ ID NO: 2, 28, 29, 30, or 31”. It is not clear which one, the variant or the mutated SARS-CoV-2 spike protein, has the recited sequence. If Applicant intends to claim a variant having the recited sequence, Applicant must clarify by proper amendment. E.g., Applicant may consider language “or a variant of a mutated SARS-CoV-2 spike protein, wherein the variant comprises SEQ ID NO: 2, 28, 29, 30, or 31”.
Claims 7-9 are directed to a “variant as claimed in claim 3” further specifying additional point mutations at positions according to SEQ ID NO: 1. As indicated above, the “variant” of claim 3 is unclear and can vary significantly from the wild-type SARS-CoV-2 according to SEQ ID NO: 1. With substitutions, deletions, and insertions of unspecified amount of amino acid sequences in the claimed “variant”, it is unclear how to identify the claimed additional modifications in the “variant” and to correlate them to SEQ ID NO: 1.
Claim 9 recites a list of amino acid mutations without a conjunction word, “or” or “and”, to link the recited mutations. Therefore, it is not clear whether all or part of the mutations are required.
Claims 10, 13, 14, 16, 19 and 20 all recite “a variant of a mutated SARS-CoV-2 spike protein selected from SEQ ID NO: 2, 28, 29, 30, or 31”. As indicated in the discussion about claim 3, it is not clear which one, the variant or the mutated SARS-CoV-2 spike protein, has the recited sequence. If Applicant intends to claim a variant having the recited sequence, Applicant must clarify by proper amendment. E.g., Applicant may consider language “or a variant of a mutated SARS-CoV-2 spike protein, wherein the variant comprises SEQ ID NO: 2, 28, 29, 30, or 31”.
Claim 18 recites “preferably selected from adeno or pox viruses”. It is not clear if this limitation is required, or only exemplary.
In general, the claims use the terms “mutated SARS-CoV-2 spike protein” and “variant of a mutated SARS-CoV-2 spike protein” and try to distinguish the two terms. However, Applicant has not provided descriptions in the specification that can distinguish the two terms. As indicated above, the term “variant” of a mutated protein is defined to refer to a polypeptide that contains additional substitutions, deletions or insertions of the mutated protein. Such substitutions, deletions, and insertions are still mutations. Since the “mutated SARS-CoV-2 spike protein” of claim 1 does not exclude mutations in addition to the specified amino acid substitutions, there is no evidence that the claimed “variant” can be any different to the “mutated SARS-CoV-2 spike protein” in general, unless such “variant of a mutated SARS-CoV-2 spike protein” is changed too much that it can no longer be called a “mutated SARS-CoV-2 spike protein” according to claim 1, which by itself not clear. Applicant must provide clarification and/or proper amendment to avoid an interpretation of “mutated SARS-CoV-2 spike protein” or “variant of a mutated SARS-CoV-2 spike protein” as reading on a polypeptide that is not related to the SARS-CoV-2 spike protein.
Claim Rejections - 35 USC § 102
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.
Claims 1, 3, 4, 13, 14, 16 and 17 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Nguyen et al. (J. Virol., 95:e02304-20, March, 2021; submitted in IDS filed on Oct. 2, 2025).
These claims encompass a mutated SARS-CoV-2 spike protein or variant thereof, wherein at least one of the amino acids isoleucine or leucine at at least one of positions corresponding to amino acids 818, 821, 822, 841, 844, 861, 864 and 865 of the wild type SARS-CoV-2 protein sequence (SEQ ID NO: 1) is replaced by alanine.
Nguyen teaches that the authors studied the contribution of several SARS-CoV-2 S glycoprotein features to its functions in mediating the virus entry into host cells and cytopathic effect (syncytium formation), focusing on those that differ among related coronaviruses. Acquisition of the furin cleavage site by the SARS-CoV-2 S glycoprotein decreased virus stability and infectivity but greatly enhanced syncytium-forming ability. Notably, the D614G change found in globally predominant SARS-CoV-2 strains increased infectivity, modestly enhanced responsiveness to the ACE2 receptor and susceptibility to neutralizing sera, and tightened association of the S1 subunit with the trimer. Apparently, these two features of the SARS-CoV-2 S glycoprotein, the furin cleavage site and D614G, have evolved to balance virus infectivity, stability, cytopathicity and antibody vulnerability. See Abstract.
Fig. 1 of Nguyen shows various mutants of the SARS-CoV-2 S protein used in the study. See below:
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Nguyen teaches that the putative fusion peptide of the SARS-CoV-2 S2 glycoprotein (residues 816 to 834) has been identified by analogy with the SARS-CoV-1 S gp. Changes in the fusion peptide and a more C-terminal S2 region in SARS-CoV-1 S gp have been suggested to result in fusion-defective mutants (58–60). The authors introduced analogous changes into the putative fusion peptide of the SARS-CoV-2 S gp (L821A and F823A) and also made a change (F888R) in the downstream region implicated in SARS-CoV-1 S gp function. The L821A and F823A mutants were processed slightly less efficiently than the wild-type S gp. Compared to the wild-type S gp, the F888R mutant exhibited a lower ratio of the S1 gp in cell lysates relative to the S1 gp in cell supernatants, suggesting a decrease in the association of S1 with the S trimer (Fig. 3A and 5). Modest decreases in the level of S glycoproteins on lentivirus particles were observed for all three mutants. L821A and F823A retained the ability to mediate cell-cell fusion, although the syncytia formed were smaller than those induced by the wild-type S gp (Fig. 4B and 5). F888R was severely compromised in the ability to mediate cell-cell fusion; however, this ability was recovered when TMPRSS2 was coexpressed with ACE2 in the target cells (Fig. 5). The infectivity of viruses pseudotyped with these three mutants was greatly decreased, relative to viruses with wild-type S gp (Fig. 5). In summary, these S2 ectodomain changes exert pleiotropic effects, ultimately compromising virus infectivity. See pages 9 and 11.
Of these mutants, the S2 ectodomain mutant L821A reads on the mutated SARS-CoV-2 spike protein or variant thereof, as claimed.
Regarding claim 13, it does not specify what the “one or more additional sequences” are. Therefore, any of the sequences of a mutated/variant SARS-CoV-2 S protein can be considered as an additional sequence to another region of the same protein.
Claims 14 and 16-17 are drawn to an mRNA and DNA, respectively, encoding for a mutated SARS-CoV-2 spike protein of claim 1, an immunogenic fragment thereof, or a variant thereof. Fig 3 of Nguyen teaches expressing SARS-CoV-2 S gp variants by transfecting host cells with plasmids encoding the S gp variants. See lagend of Fig. 3. Such expression processes inherently involve DNA (plasmid) and mRNA encoding the mutant S gp proteins.
Accordingly, Nguyen discloses various mutants of the SARS-CoV-2 spike glycoprotein (S gp), including one mutant containing the leucine to alanine mutation at position 821 (L821A) as claimed. Therefore, Nguyen anticipates claims 1, 3, 4, 13, 14, 16 and 17.
Claim Rejections - 35 USC § 103
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 of this title, 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.
Claims 1, 3, 4, 9, 10, 11, 13, 14, 16 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Nguyen et al. (J. Virol., 95:e02304-20, March, 2021; submitted in IDS filed on Oct. 2, 2025), as applied above, and Madu et al. (JOURNAL OF VIROLOGY, Aug. 2009, Vol. 83, No. 15, p. 7411–7421).
Relevance of Nguyen is set forth above. Briefly, Nguyen teaches a study on the characterization of mutants of the SARS-CoV-2 spike glycoprotein (S pg). Nguyen discloses various mutants of the SARS-CoV-2 spike glycoprotein (S gp), including one mutant containing the leucine to alanine mutation at position 821 (L821A), which reads on an embodiment of the claimed invention. However, Nguyen is silent on certain other mutations specified in the claims. The current 103 rejection addresses more mutations specified in the claims that are not taught in Nguyen.
Madu teaches that many viral fusion proteins are primed by proteolytic cleavage near their fusion peptides, and that, while the coronavirus (CoV) spike (S) protein is known to be cleaved at the S1/S2 boundary, this cleavage site is not closely linked to a fusion peptide. Madu teaches a study characterizing the proteolytic cleavage site identified in the severe acute respiratory syndrome CoV (SARS-CoV) S2 domain (R797). The authors investigated whether this internal cleavage of S2 exposes a viral fusion peptide. They show that the residues immediately C-terminal to the SARS-CoV S2 cleavage site SFIEDLLFNKVTLADAGF are very highly conserved across all CoVs. Mutagenesis studies of these residues in SARS-CoV S, followed by cell-cell fusion and pseudotyped virion infectivity assays, showed a critical role for residues L803, L804, and F805 in membrane fusion. Mutation of the most N-terminal residue (S798) had little or no effect on membrane fusion. Biochemical analyses of synthetic peptides corresponding to the proposed S2 fusion peptide also showed an important role for this region in membrane fusion and indicated the presence of a-helical structure. They propose that proteolytic cleavage within S2 exposes a novel internal fusion peptide for SARS-CoV S, which may be conserved across the Coronaviridae. See Abstract.
Madu teaches that the SARS-CoV S2 fusion peptides SFIEDLLFNKVTLADAGFMKQYGCGKKKK, SFIEDLLFGCGKKKK, and SFIEDAAAGCGKKKK were synthesized using solid-phase techniques by New England Peptide (Gardner, MA). The GCGKKKK linker was included to promote liposome association. See page 7412, right column, para 5.
Here, the above peptide immediately C-terminal to the S2 cleavage site of the SARS-CoV S glycoprotein, SFIEDLLFNKVTLADAGF, also exist in the SARS-CoV-2 S glycoprotein, and contains the Isoleucine 818 (I818), Leucine 821 (L821) and Leucine 822 (L822) according to SEQ ID NO: 1. See boldfaced letters below:
SARS-CoV 1 SFIEDLLFNKVTLADAGF 18
SFIEDLLFNKVTLADAGF
SARS-CoV-2 1 SFIEDLLFNKVTLADAGF 18
Fig. 7 of Madu summarizes results of a study on mutating each amino acid residues in this region. See below:
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Here, the mutations I800A, L803A and L804A, based on the SAR-CoV S amino acid numbering, are equivalent to I818A, L821A, and L822A of the instant claims, based on the amino acid numbering of the SARS-CoV-2 S protein. Fig. 7 shows that all of these three mutations affect cell-cell fusion.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the current invention to combine the teachings of Nguyen and Madu to arrive at the invention as claimed. One would have been motivated to do so to test the effects of the mutations taught in Madu to the SARS-CoV-2 S protein.
Regarding claim 9, Nguyen teaches the mutation of D614G. See discussion in the 102 rejection above. One of skill in the art would have found it obvious to combine the D614G and the leucine/isoleucine to alanine mutation disclosed in Nguyen and Madu to find out the combined effect of such double mutations.
Claim 12 specifies an immunogenic fragment of claim 10, further containing at least two non-overlapping sequences selected from regions of SEQ ID NO: 1. Since the claim does not specify structural limitations of the “immunogenic fragment”, such as “fragment” reads on any portion of a mutated SARS-CoV-2 S protein according to claim 10. One of skill in the art would have found it obvious to make deletion or truncation mutations to the mutant S proteins that contain the claimed Isoleucine/leucine to alanine mutations to study combined effects, as done in Nguyen shown in Fig. 1 above. The resulting mutant S proteins would contain the claimed features of claim 12 and can be considered as an “immunogenic fragment”.
Claims 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Nguyen et al. (J. Virol., 95:e02304-20, March, 2021; submitted in IDS filed on Oct. 2, 2025) and Madu et al. (JOURNAL OF VIROLOGY, Aug. 2009, Vol. 83, No. 15, p. 7411–7421), as applied above, in view of McIntyre et al. (Aust Prescr. 2021 Feb;44(1):19-25).
Claim 18 is directed to a viral vector containing the DNA as claimed in claim 16. Claim 19 is directed to a method comprising administering to a subject a mutated SARS-CoV-2 spike protein, a variant thereof, or an mRNA, a DNA or a viral vector expressing the mutated spike protein or variant thereof. Claim 20 is directed to a vaccine composition containing a mutated SARS-CoV-2 spike protein, a variant thereof, or an mRNA, a DNA or a viral vector expressing the mutated spike protein or variant thereof.
Relevance of Nguyen and Madu is set forth above. However, they are silent on a viral vector or using the mutated Spike protein as a vaccine antigen.
McIntyre teaches that as of mid-December 2020, more than 200 COVID‑19 vaccine candidates are in development and 11 have entered phase III clinical trials globally. All generate immunity to the viral spike glycoprotein. Three vaccine candidates have agreements for procurement and use in Australia if efficacy and safety requirements are met – one protein-based vaccine, one vaccine using a simian-derived adenovirus vector and one messenger RNA (mRNA) vaccine. The latter two vaccines have published interim analyses and efficacy results of their phase III trials. The messenger RNA vaccine is being rolled out in the UK, USA and Canada. See Abstract.
Fig. 2 of McIntyre presents approaches being used to develop SARS-CoV-2 vaccines, including conventional approaches (protein subunit vaccines, virus like particle vaccine, and whole virus vaccines) and novel approaches (nucleic acid vaccines - DNA vaccine and mRNA vaccine, and viral vector vaccines).
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the current invention to combine the teachings of Nguyen, Madu and McIntyre to arrive at the invention as claimed. One would have been motivated to do so to study the potential of the SARS-CoV-2 spike protein mutants suggested by the combined teachings of Nguyen and Madu as vaccine immunogens. There is a reasonable expectation of success that the vaccine potential of the mutant S proteins can be evaluated on the various vaccine platforms taught in McIntyre.
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Nguyen et al. (J. Virol., 95:e02304-20, March, 2021; submitted in IDS filed on Oct. 2, 2025) and Madu et al. (JOURNAL OF VIROLOGY, Aug. 2009, Vol. 83, No. 15, p. 7411–7421) in view of McIntyre et al. (Aust Prescr. 2021 Feb;44(1):19-25), as applied above, and further in view of Anderson et al. (Nucleic Acids Research, 2010, 38(17): 5884–5892).
Claim 15 is directed to an mRNA encoding the mutated SARS-CoV-2 spike protein or variant thereof specified in claim 14, further specifying that uridine residues are replaced with a modified nucleoside selected from a list of uridine analogs.
Relevance of Nguyen, Madu and McIntyre is set forth above. However, they are silent on replacing the uridines in an mRNA by a uridine analog as claimed.
Anderson teaches that in vitro transcribed messenger RNA (mRNA) has many advantages as a vehicle for gene delivery. Transfection of mRNA is very efficient, and rapid expression of the encoded protein can be achieved. Unlike viral vectors or plasmid DNA, cell-delivered mRNA does not introduce the risk of insertional mutagenesis. Previous studies have shown that RNA can activate a number of innate immune receptors, including Toll-like receptor (TLR)3, TLR7, TLR8 and retinoic acid-inducible gene I (RIG-I). However, activation of these receptors can be avoided by incorporating modified nucleosides, e.g. pseudouridine or 2-thiouridine (s2U), into the RNA. See Introduction. Anderson further teaches that previous studies have shown that the translation level of in vitro transcribed messenger RNA (mRNA) is enhanced when its uridines are replaced with pseudouridines. See Abstract.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the current invention to introduce a pseudouridine (e.g., 2-thiouridine) into mRNA molecules in an mRNA vaccine suggested by the combined teachings of Nguyen, Madu and McIntyre. One would have been motivated to do so to make use of the advantages of the pseudouridines in mRNA based on the teachings of Anderson.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIANXIANG (NICK) ZOU whose telephone number is (571)272-2850. The examiner can normally be reached on Monday - Friday, 8:30 am - 5:00 pm, EST. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MICHAEL ALLEN, on (571) 270-3497, can be reached. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/NIANXIANG ZOU/
Primary Examiner, Art Unit 1671
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