IP Library › Granted Patent US 12,416,016
Granted Patent B2
US 12,416,016 · App. 16/975,545 · Granted Sep 16, 2025

Adeno-associated virus (AAV) vectors, AAV vectors having reduced capsid deamidation and uses therefor

Inventors: James M. Wilson (Philadelphia, PA); April Tepe (Columbia, MD); Kevin Turner (Newtown Square, PA); Joshua Joyner Sims (Philadelphia, PA); Qiang Wang (Philadelphia, PA)
C12N15/86C07K14/005C12N2750/14121C12N2750/14122C12N2750/14143
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Quick Facts
Patent No.
US 12,416,016
App. No.
16/975,545
Granted
Sep 16, 2025
Kind
B2
Abstract

A recombinant adeno-associated virus (rAAV) vector comprising an AAV capsid having a heterogeneous population of vp1 proteins, a heterogeneous population of vp2 protein and a heterogeneous population of vp3 proteins. The capsid contains modified amino acids as compared to the encoded VP1 amino acid sequence, the capsid containing highly deamidated asparagine residues at asparagine-glycine pair, and further comprising multiple other, less deamidated asparagine and optionally glutamine residues.

Claims (42)

1. A recombinant adeno-associated virus (rAAV) which comprises an AAVrh79 capsid comprising AAVrh79 vp1 proteins, AAVrh79 vp2 proteins, and AAVrh79 vp3 proteins comprising glutamic acid (E) at position 67 in the AAVrh79 vp1 proteins and arginine (R) at position 169 in the AA Vrh79 vp1 and AAVrh79 vp2 proteins, wherein the AAVrh79 vp1 proteins contain amino acid modifications comprising at least 50% to 100% deamidated asparagines (N) in asparagine-glycine pairs in each of positions N57, N263, N385 and N514 relative to SEQ ID NO: 2, as determined by mass spectrometry, the AAVrh79 vp2 proteins contain amino acid modifications comprising at least 50% to 100% deamidated asparagines (N) in asparagine-glycine pairs in each of positions N263, N385 and N514 relative to SEQ ID NO: 2, as determined by mass spectrometry, and the AAVrh79 vp3 proteins contain amino acid modifications comprising at least 50% to 100% deamidated asparagines (N) in asparagine-glycine pairs in each of positions N57, N263, N385, and N514 relative to SEQ ID NO: 2, as determined by mass spectrometry, wherein the deamidated asparagines are deamidated to an aspartic acid, an isoaspartic acid, an interconverting aspartic acid/isoaspartic acid pair, or combinations thereof,

wherein the rAAV further comprises a vector genome in the AAVrh79 capsid, the vector genome comprising a nucleic acid molecule comprising AAV inverted terminal repeat (ITR) sequences and a non-AAV nucleic acid sequence encoding a product operably linked to sequences which direct expression of the product in a host cell.

2. The rAAV according to claim 1 , wherein the capsid further comprises deamidated glutamine(s) which are deamidated to (α)-glutamic acid, γ-glutamic acid, an interconverting (α)-glutamic acid/γ-glutamic acid pair, or combinations thereof.

3. The rAAV according to claim 1 , wherein the AAVrh79 capsid comprises subpopulations having one or more of:

(a) at least 75% of asparagines (N) in asparagine-glycine pairs located at position 57 of the vp1 proteins are deamidated, based on the numbering of SEQ ID NO:2;

(b) at least 75% of N in asparagine-glycine pairs in position 263 of the vp1, vp2 and vp3 proteins are deamidated, based on the residue numbering of the amino acid sequence of SEQ ID NO: 2,

(c) at least 70% of N in asparagine-glycine pairs in position 385 of the vp1, vp2 and vp3 proteins are deamidated, based on the residue numbering of the amino acid sequence of SEQ ID NO: 2; and/or

(d) at least 85% of N in asparagine-glycine pairs in position 514 of the vp1, vp2 and vp3 proteins are deamidated, based on the residue numbering of the amino acid sequence of SEQ ID NO: 2.

4. The rAAV according to claim 1 , wherein the rAAVrh79 capsid comprises a subpopulation of vp1 in which 75% to 100% of the N at position 57 of the vp1 proteins are deamidated, as determined using mass spectrometry.

5. The rAAV according to claim 1 , wherein the rAAVrh79 capsid comprises subpopulations of vp1 proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 263, based on the numbering of SEQ ID NO:2, are deamidated as determined using mass spectrometry.

6. The rAAV according to claim 1 , wherein the rAAVrh79 capsid comprises subpopulations of vp1 proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 385, based on the numbering of SEQ ID NO:2, are deamidated as determined using mass spectrometry.

7. The rAAV according to claim 1 , wherein the rAAVrh79 capsid comprises subpopulations of vp1 proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 514, based on the numbering of SEQ ID NO:2, are deamidated.

8. The rAAV according to claim 1 , wherein the nucleic acid sequence encoding the vp1 proteins, vp2 proteins and/or vp3 proteins is SEQ ID NO: 1, or a nucleic acid sequence at least 80% to at least 99% identical to SEQ ID NO: 1 which encodes the amino acid sequence of SEQ ID NO:2.

9. The rAAV according to claim 8 , wherein the nucleic acid sequence is at least 80% to 97% identical to SEQ ID NO: 1.

10. The rAAV according to claim 1 , wherein the rAAVrh79 capsid comprises subpopulations of vp1 proteins, vp2 proteins and/or vp3 proteins which further comprise 1% to about 40% deamidation in at least one or more of positions N94, N254, N305, N410, N479, N653, or combinations thereof.

11. The rAAV according to claim 1 , wherein the rAAVrh79 capsid comprises subpopulations of vp1 proteins, vp2 proteins and/or vp3 proteins which further comprise one or more modifications consisting of: acetylated lysine, phosphorylated serine and/or threonine, isomerized aspartic acid, oxidized tryptophan and/or methionine, or an amidated amino acid.

12. The rAAV according to claim 1 , wherein the AAV ITR sequences are a 5′ ITR and a 3′ ITR from AAV2.

13. A composition comprising an AAV according to claim 1 and a pharmaceutical carrier, excipient and/or diluent.

14. A production cell in vitro comprising the rAAV according to claim 1 .

15. An rAAV production system useful for producing an rAAV according to claim 1 in a production cell, wherein the production system comprises:

(a) an AAV capsid nucleic acid sequence encoding the amino acid sequence of SEQ ID NO:2;

(b) a nucleic acid molecule suitable for packaging into the AAV capsid, said nucleic acid molecule comprising at least one AAV inverted terminal repeat (ITR), a functional rep gene and a non-AAV nucleic acid sequence encoding a gene product operably linked to sequences which direct expression of the product in a host cell; and

(c) sufficient AAV rep functions and helper functions to permit packaging of the nucleic acid molecule into the AAV capsid.

16. The system according to claim 15 , wherein the nucleic acid sequence of (a) comprises at least SEQ ID NO: 1, or a nucleic acid sequence at least 70% to at least 99% identical to SEQ ID NO: 1 which encodes the amino acid sequence of SEQ ID NO:2.

17. The system according to claim 15 , wherein the production cell culture comprises human embryonic kidney 293 cells.

18. The system according to claim 15 , wherein the AAV rep is from AAV2.

19. The rAAV according to claim 1 , wherein the AAVrh79 capsid comprises less than 1% deamidation at positions other than N57, N263, N365 and/or N514.

20. The rAAV according to claim 1 , wherein the AAVrh79 vp1 proteins contain amino acid modification comprising at least 70% to 100% deamidated asparagines (N) in asparagine-glycine pairs in each of positions N57, N263, N385 and N514 relative to SEQ ID NO: 2, as determined by mass spectrometry, the AAVrh79 vp2 proteins contain amino acid modification comprising at least 70% to 100% deamidated asparagines (N) in asparagine-glycine pairs in each of positions N263, N385 and N514 relative to SEQ ID NO: 2, as determined by mass spectrometry, and the AAVrh79 vp3 proteins contain amino acid modifications comprising at least 70% to 100% deamidated asparagines (N) in asparagine-glycine pairs in each of positions N263, N385, and N514 relative to SEQ ID NO: 2, as determined by mass spectrometry.

21. A recombinant adeno-associated virus (rAAV) which comprises an AAVrh79 capsid comprising AAVrh79 vp1 proteins, AAVrh79 vp2 proteins, and AAVrh79 vp3 proteins produced by expression of a nucleic acid sequence which encodes the amino acid sequence of 1 to 738 of SEQ ID NO: 2,

wherein the rAAV further comprises a vector genome in the AAVrh79 capsid, the vector genome comprising a nucleic acid molecule comprising AAV inverted terminal repeat (ITR) sequences and a non-AAV nucleic acid sequence encoding a product operably linked to sequences which direct expression of the product in a host cell.

22. The rAAV according to claim 21 , wherein the AAVrh79 capsid comprising AAVrh79 vp1 proteins, AAVrh79 vp2 proteins, and AAVrh79 vp3 proteins is produced by expression from SEQ ID NO: 1.

23. A composition comprising an AAV according to claim 21 and a pharmaceutical carrier, excipient and/or diluent.

24. A method of generating a recombinant AAV comprising an AAV capsid comprising the steps of culturing a host cell containing:

(a) a nucleic acid sequence encoding an AAVrh79 vp1 capsid protein having amino acids 1 to 738 of SEQ ID NO: 2, wherein the AAVrh79 vp1 coding sequence is operably linked to regulatory sequences which permit expression of AAVrh79 vp1 proteins, AAVrh79 vp2 proteins and AAVrh79 vp3 proteins in the cultured host cell;

(b) a functional rep gene;

(c) a nucleic acid molecule which is a vector genome having a nucleic acid sequence comprising an AAV 5′ inverted terminal repeats (ITRs), an expression cassette comprising a non-AAV nucleic acid sequence encoding a product, and an AAV 3′ ITR sequence and a transgene; and

(d) sufficient helper functions to permit packaging of the vector genome into the AAV capsid.

25. A cultured host cell comprising a recombinant nucleic acid molecule comprising:

(a) a nucleic acid sequence encoding an AAVrh79 vp1 capsid protein having amino acids 1 to 738, of SEQ ID NO: 2, wherein the AAVrh79 vp1 coding sequence is operably linked to regulatory sequences which permit expression of AAVrh79 vp1 proteins, AAVrh79 vp2 proteins and AAVrh79 vp3 proteins in the cultured host cell;

(b) a functional rep gene;

(c) a nucleic acid molecule which is a vector genome having a nucleic acid sequence comprising an AAV 5′ inverted terminal repeat (ITR), an expression cassette comprising a non-AAV nucleic acid sequence encoding a product, and an AAV 3′ ITR sequence and a transgene; and

(d) sufficient helper functions to permit packaging of the vector genome into an AAV capsid.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Apr 20, 2021
From: WILSON, JAMES M.; TEPE, APRIL; TURNER, KEVIN; SIMS, JOSHUA JOYNER; WANG, QIANG
To: THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA
Reel/Frame 055971/0791 →
Continuity (15)
Provisional Application 62722382 · Aug 24, 2018
Provisional Application 62722388 · Aug 24, 2018
Provisional Application 62703673 · Jul 26, 2018
Provisional Application 62703670 · Jul 26, 2018
Provisional Application 62677474 · May 29, 2018
Provisional Application 62667585 · May 29, 2018
Provisional Application 62677471 · May 29, 2018
Provisional Application 62667881 · May 7, 2018
Provisional Application 62667888 · May 7, 2018
Provisional Application 62667587 · May 6, 2018
Provisional Application 62663797 · Apr 27, 2018
Provisional Application 62663788 · Apr 27, 2018
Provisional Application 62635968 · Feb 27, 2018
Provisional Application 62635964 · Feb 27, 2018
Related Publication 20210123073A1 · Apr 29, 2021
References Cited (145)
US 5139941A · Muzyczka et al. · 1992 [cited by applicant]
US 6057152A · Samulski et al. · 2000 [cited by applicant]
US 6200560B1 · Couto et al. · 2001 [cited by applicant]
US 6204059B1 · Samulski et al. · 2001 [cited by applicant]
US 6221349B1 · Couto et al. · 2001 [cited by applicant]
US 6268213B1 · Samulski et al. · 2001 [cited by applicant]
US 6491907B1 · Rabinowitz · 2002 [cited by applicant]
US 6660514B1 · Zolotukhin et al. · 2003 [cited by applicant]
US 6951753B2 · Shenk et al. · 2005 [cited by applicant]
US 7094604B2 · Snyder et al. · 2006 [cited by applicant]
US 7125717B2 · Carter · 2006 [cited by applicant]
US 7172893B2 · Rabinowitz · 2007 [cited by applicant]
US 7201898B2 · Monahan et al. · 2007 [cited by applicant]
US 7229823B2 · Samulski et al. · 2007 [cited by applicant]
US 7439065B2 · Ferrari et al. · 2008 [cited by applicant]
US 7442373B2 · Morrow et al. · 2008 [cited by applicant]
US 7456683B2 · Takano et al. · 2008 [cited by applicant]
US 7588772B2 · Kay et al. · 2009 [cited by applicant]
US 20060136184A1 · Gustafsson et al. · 2006 [cited by applicant]
US 20070036760A1 · Wilson et al. · 2007 [cited by applicant]
US 20090197338A1 · Vandenberghe et al. · 2009 [cited by applicant]
US 20110294218A1 · Chatterjee et al. · 2011 [cited by applicant]
US 20130045186A1 · Gao et al. · 2013 [cited by applicant]
US 20140032186A1 · Gustafsson et al. · 2014 [cited by applicant]
US 20150315612A1 · Wilson et al. · 2015 [cited by applicant]
US 20170159027A1 · Wilson et al. · 2017 [cited by applicant]
JP 2007507223 · 2007 [cited by applicant]
JP 2008538286 · 2008 [cited by applicant]
WO WO2003042397 · 2003 [cited by applicant]
WO WO2005033321 · 2005 [cited by applicant]
WO WO2006110689 · 2006 [cited by applicant]
WO WO2011126808 · 2011 [cited by applicant]
WO WO2017075119 · 2017 [cited by applicant]
WO WO2017100674 · 2017 [cited by applicant]
WO WO2017100676 · 2017 [cited by applicant]
WO WO2017160360 · 2017 [cited by applicant]
WO WO2017180854 · 2017 [cited by applicant]
WO WO2017181113 · 2017 [cited by applicant]
WO WO2018035059 · 2018 [cited by applicant]
WO WO2018160582 · 2018 [cited by applicant]
WO WO2018160585A2 · 2018 [cited by applicant]
Yang et al., Mass Spectrometric Analysis of Asparagine Deamidation and Aspartate Isomerization in Polypeptides. Electrophoresis, 2010. 31:1764. [cited by examiner]
Wakankar et al., Formulation Considerations for Proteins Susceptible to Asparagine Deamidation and Aspartate Isomerization. Journal of Pharmaceutical Sciences, 2006. 95(11):2321-2336. [cited by examiner]
Li et al., Effects of Acidic N+1 Residues on Asparagine Deamidation Rates in Solution and in the Solid State. Journal of Pharmaceutical Sciences, 2006. 94(3):666-675. [cited by examiner]
Pierson et al. Resolving Adeno-Associated Viral Particle Diversity With Charge Detection Mass Spectrometry. Analytical Chemistry, 2016. 88: 6718-6725. [cited by examiner]
Adachi et al., Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing, Nature Communications, vol. 5(3075), 2014. [cited by applicant]
Aydemir et al., Mutants at the 2-Fold Interface of Adeno-associated Virus Type 2 (AAV2) Structural Proteins Suggest a Role in Viral Transcription for AAV Capsids, Journal Virology, vol. 90(16):7196-7204, Aug. 2016. [cited by applicant]
Bish et al., Adeno-associated virus (AAV) serotype 9 provides global cardiac gene transfer superior to AAV1, AAV6, AAV7, and AAV8 in the mouse and rat, Human Gene Therapy, vol. 19(12): 1359-68, Dec. 2008. [cited by applicant]
Calcedo et al., Worldwide epidemiology of neutralizing antibodies to adeno- associated viruses, The Journal of Infectious Diseases, vol. 199(3):381-90, Feb. 2009. [cited by applicant]
Calcedo R., Wilson JM., AAV Natural Infection Induces Broad Cross-Neutralizing Antibody Responses to Multiple AAV Serotypes in Chimpanzees, Human Gene Therapy, vol. 27(2):79-82, May 2016. [cited by applicant]
Carrillo-Tripp et al., VIPERdb2: an enhanced and web API enabled relational database for structural virology, Nucleic Acids Reaserch, vol. 37:D436-42, Jan. 2009. [cited by applicant]
Chen et al., Biodistribution of AAV8 vectors expressing human low-density lipoprotein receptor in a mouse model of homozygous familial hypercholesterolemia, Human Gene Therapy Clinical Development, vol. 24(4):154-60, De… [cited by applicant]
Chicoine et al., Plasmapheresis eliminates the negative impact of AAV antibodies on microdystrophin gene expression following vascular delivery, Molecular Therapy, vol. 22(2):338-47, Feb. 2014. [cited by applicant]
Delano et al., PyMOL: An Open-Source Molecular Graphics Tool, vol. 40:82-92, 2002. [cited by applicant]
Ellis et al., A survey of ex vivo/in vitro transduction efficiency of mammalian primary cells and cell lines with Nine natural adeno-associated virus (AAV1-9) and one engineered adeno-associated virus serotype, Virology… [cited by applicant]
Falese et al., Strategy to detect pre-existing immunity to AAV gene therapy, Gene Therapy, vol. 24(12):768-778, Dec. 2017. [cited by applicant]
Fisher et al., Transduction with recombinant adeno-associated virus for gene therapy is limited by leading-strand synthesis., Journal of Virology, vol. 70:520-532, Jan. 1996. [cited by applicant]
Flatmark et al., Deamidations in recombinant human phenylalanine hydroxylase. Identification of labile asparagine residues and functional characterization of Asn --> Asp mutant forms, The Journal of biological chemistry… [cited by applicant]
Flotte et al., Phase 2 clinical trial of a recombinant adeno-associated viral vector expressing al-antitrypsin: interim results, Human Gene Therapy, vol. 22(10):1239-47, Oct. 2011. [cited by applicant]
Foust et al., Intravascular AAV9 preferentially targets neonatal neurons and adult astrocytes, Nature Biotechnology, vol. 27(1):59-65, Jan. 2009. [cited by applicant]
Gao et al., Adeno-associated viruses undergo substantial evolution in primates during natural infections, Proc. Natl. Acad. Sci. U.S.A, vol. 100 (10):6081-6086, May 2003. [cited by applicant]
Gao et al., Novel adeno-associated viruses from rhesus monkeys as vectors for human gene therapy, Proc Natl Acad Sci USA, vol. 99(18):11854-9, Sep. 2002. [cited by applicant]
Geiger T., Clarke S., Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation, Journal of Biological Chemistry, … [cited by applicant]
George et al., Spk-8011: Preliminary Results from a Phase ½ Dose Escalation Trial of an Investigational AAV-Mediated Gene Therapy for Hemophilia a, Blood, vol. 130(Suppl 1):604, Dec. 2017. [cited by applicant]
Giles et al., Deamidation of Amino Acids on the Surface of Adeno-Associated Virus Capsids Leads to Charge Heterogeneity and Altered Vector Function, Molecular Theory, vol. 26:2848-2862, Oct. 2019. [cited by applicant]
Gonzalez-Quintela et al., Serum levels of immunoglobulins (IgG, IgA, IgM) in a general adult population and their relationship with alcohol consumption, smoking and common metabolic abnormalities, Clinical and Experimen… [cited by applicant]
Govindasamy et al., Structural Insights into Adeno-Associated Virus Serotype 5, Journal Virology, vol. 87(20):11187-99, Oct. 2013. [cited by applicant]
Greig et al., Non-Clinical Study Examining AAV8.TBG.hLDLR Vector-Associated Toxicity in Chow-Fed Wild-Type and LDLR+/− Rhesus Macaques, Human Gene Therapy Clinical Development, vol. 28(1):39-50, Mar. 2017. [cited by applicant]
Grieger & Samulski, Adeno-associated virus as a gene therapy vector: Vector development, production and clinical applications, Advances in Biochemical Engineering/Biotechnology, vol. 99:119-145, Oct. 2005. [cited by applicant]
Grimm et al., Titration of AAV-2 particles via a novel capsid ELISA: packaging of genomes can limit production of recombinant AAV-2, Gene Therapy, vol. 6:1322-1330, Aug. 1999. [cited by applicant]
Gurda et al., Capsid Antibodies to Different Adeno-Associated Virus Serotypes Bind Common Regions Journal Virology, vol. 87(16):9111-24, Aug. 2013. [cited by applicant]
Gurda et al., Mapping a neutralizing epitope onto the capsid of adeno-associated virus serotype 8, Journal Virology, vol. 86(15):7739-51, Aug. 2012. [cited by applicant]
Harrington et al., Neutralizing Antibodies Against Adeno-Associated Viral Capsids in Patients with mut Methylmalonic Acidemia, Human Gene Therapy, vol. 27(5):345-53, May 2016. [cited by applicant]
Henderson et al., Primary structure of human carbonic anhydrase C, The Journal of Biological Chemistry, vol. 251:5457-5463, Sep. 1976. [cited by applicant]
Houde et al., Post-translational Modifications Differentially Affect IgG1 Conformation and Receptor Binding, Molecular Cell Proteomics, vol. 9.8:1716-1728, Aug. 2010. [cited by applicant]
Huang et al., Characterization of the Adeno-Associated Virus 1 and 6 Sialic Acid Binding Site, Journal of Virology, vol. 90(11):5219-30, Jun. 2016. [cited by applicant]
Huttner et al., Genetic modifications of the adeno-associated virus type 2 capsid reduce the affinity and the neutralizing effects of human serum antibodies, Gene Therapy, vol. 10(26):2139-47, Nov. 2003. [cited by applicant]
Kleywegt, G., Crystallographic refinement of ligand complexes, Acta Crystallogr D Biol Crystallogr, vol. 63(Pt 1):94-100, Jan. 2007. [cited by applicant]
Kornegay et al., Widespread Muscle Expression of an AAV9 Human Mini-dystrophin Vector After Intravenous Injection in Neonatal Dystrophin-deficient Dogs, Molecular Therapy, vol. 18(8): 1501-8, Aug. 2010. [cited by applicant]
Leem et al., ABodyBuilder: Automated antibody structure prediction with data-driven accuracy estimation, Mabs, vol. 8(7):1259-1268, Oct. 2016. [cited by applicant]
Lock et al., Absolute determination of single-stranded and self-complementary adeno-associated viral vector genome titers by droplet digital PCR, Human Gene Therapy Methods, vol. 25(2):115-25, Apr. 2014. [cited by applicant]
Lock et al., Rapid, simple, and versatile manufacturing of recombinant adeno-associated viral vectors at scale, [cited by applicant]
McCarty et al., Self-complementary recombinant adeno-associated virus (scAAV) vectors promote efficient transduction independently of DNA synthesis, Gene Therapy, vol. 8(16):1248-1254, Aug. 2001. [cited by applicant]
Mendell et al., Single-Dose Gene-Replacement Therapy for Spinal Muscular Atrophy, New England Journal of Medicine, vol. 377(18):1713-22, Nov. 2017. [cited by applicant]
Murray et al., Characterization of the capsid protein glycosylation of adeno-associated virus type 2 by high-resolution mass spectrometry, Journal of Virology, vol. 80(12):6171-6, Jun. 2006. [cited by applicant]
Nam et al., Structure of adeno-associated virus serotype 8, a gene therapy vector, Journal of Virology, vol. 81(22):12260-71, Nov. 2007. [cited by applicant]
Nebija et al., Quality Control and Stability Studies with the Monoclonal Antibody, Trastuzumab: Application of 1D- vs. 2D-Gel Electrophoresis, International Journal of Medical Studies, vol. 15(4):6399-411, Apr. 2014. [cited by applicant]
Parthasarathy, S., Murthy, MR., Analysis of temperature factor distribution in high-resolution protein structures, Protein Science : a Publication of the Protein Society, vol. 6:2561-7, Dec. 1997. [cited by applicant]
Rao et al., Specificity and affinity of natural product cyclopentapeptide inhibitors against A. fumigatus, human, and bacterial chitinases, Chemistry & Biology, vol. 12(1):65-76, Jan. 2005. [cited by applicant]
Raupp et al., The Threefold Protrusions of Adeno-Associated Virus Type 8 Are Involved in Cell Surface Targeting as Well as Postattachment Processing, [cited by applicant]
Robinson, Ne., Robinson, AB., Molecular clocks, [cited by applicant]
Rohou, A., Grigorieff, N., CTFFIND4: Fast and accurate defocus estimation from electron micrographs, Structural Biology, vol. 192(2):216-21, Nov. 2015. [cited by applicant]
Rose et al., Structural proteins of adenovirus-associated viruses, Journal of Virology, vol. 8(5):766-70, Nov. 1971. [cited by applicant]
Sawada-Hirai et al., Human anti-anthrax protective antigen neutralizing monoclonal antibodies derived from donors vaccinated with anthrax vaccine adsorbed, Journal of Immune Based Therapy Vaccines, vol. 2(1):5, May 2004. [cited by applicant]
Sommer et al., Quantification of adeno-associated virus particles and empty capsids by optical density measurement, Molecular Therapy, vol. 7:122-128, Jan. 2003. [cited by applicant]
Tse et al., Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion, Proc Natl Acad Sci USA, vol. 114(24):E4812-21, Jun. 2017. [cited by applicant]
Tseng et al., Adeno-Associated Virus Serotype 1 (AAV1)- and AAV5-Antibody Complex Structures Reveal Evolutionary Commonalities in Parvovirus Antigenic Reactivity, Journal of Virology, vol. 89(3):1794-808, Feb. 2015. [cited by applicant]
Tseng, Y., and Agbandje-McKenna, M., Mapping the AAV Capsid Host Antibody Response toward the Development of Second Generation Gene Delivery Vectors, Frontiers in Immunology, vol. 5:9, Jan. 2014. [cited by applicant]
Verma et al., Mechanistic Analysis of the Effect of Deamidation on the Immunogenicity of Anthrax Protective Antigen, Clinical and Vaccine Immunology, vol. 23(5):396-402, May 2016. [cited by applicant]
Wang et al., Impact of Pre-Existing Immunity on Gene Transfer to Nonhuman Primate Liver with Adeno-Associated Virus 8 Vectors, Human Gene Therapy, vol. 22(11):1389-1401, Nov. 2011. [cited by applicant]
Wobus et al., Monoclonal Antibodies against the Adeno-Associated Virus Type 2 (AAV-2) Capsid: Epitope Mapping and Identification of Capsid Domains Involved in AAV-2-Cell Interaction and Neutralization of AAV-2 Infection… [cited by applicant]
Xiao, C. and Rossmann, MG., Interpretation of electron density with stereographic roadmap projections, Journal of Structural Biology, vol. 158(2):182-7, 2007. [cited by applicant]
Xie et al., The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy, Proc Natl Acad Sci USA, vol. 99(16):10405-10, Aug. 2002. [cited by applicant]
Yan et al., AUTO3DEM—an automated and high throughput program for image reconstruction of icosahedral particles, Journal of Structural Biology, vol. 157(1):73-82, Jan. 2007. [cited by applicant]
Yan, BX. and Sun, YQ., Glycine residues provide flexibility for enzyme active sites, The Journal of Biological Chemistry, vol. 272(6):3190-4, Feb. 1997. [cited by applicant]
Yang, H. and Zubarev, R., Mass spectrometric analysis of asparagine deamidation and aspartate isomerization in polypeptides, Electrophoresis, vol. 31(11):1764-72, Jun. 2010. [cited by applicant]
Zanta-Boussif et al., Validation of a mutated PRE sequence allowing high and sustained transgene expression while abrogating WHV-X protein synthesis: application to the gene therapy of WAS, Gene Therapy, vol. 16:605-619… [cited by applicant]
Zhao et al., A Viral Deamidase Targets the Helicase Domain of RIG-I to Block RNA-induced Activation, Cell Host Microbe, vol. 20(6):770-84, Dec. 2016. [cited by applicant]
Zhao et al., Emerging Roles of Protein Deamidation in Innate Immune Signaling, Journal of Virology, vol. 90(9):4262-8, May 2016. [cited by applicant]
Zhong et al., Tyrosine-phosphorylation of AAV2 vectors and its consequences on viral intracellular trafficking and transgene expression Virology, vol. 381(2):194-202, Nov. 2008. [cited by applicant]
International Search Report and Written Opinion issued in International Patent Application No. PCT/US2019/019804, dated Jun. 20, 2019. [cited by applicant]
International Search Report and Written Opinion issued in International Patent Application No. PCT/US2019/019861, dated Jun. 14, 20219. [cited by applicant]
International Preliminary Report on Patentability issued in International Patent Application No. PCT/US2019/019804, dated Aug. 27, 2020. [cited by applicant]
International Preliminary Report on Patentability issued in International Patent Application No. PCT/US2019/019861, dated Sep. 3, 2020. [cited by applicant]
International Patent Application No. PCT/US2016/065970, filed Dec. 9, 2016. [cited by applicant]
International Patent Application No. PCT/US2016/065976, filed Dec. 9, 2016. [cited by applicant]
International Patent Application No. PCT/US16/66013, filed Dec. 9, 2016. [cited by applicant]
International Patent Application No. PCT/US2016/065974, filed Dec. 9, 2016. [cited by applicant]
U.S. Appl. No. 62/322,071, filed Apr. 13, 2016. [cited by applicant]
U.S. Appl. No. 62/226,357, filed Dec. 11, 2015. [cited by applicant]
U.S. Appl. No. 62/322,098, filed Apr. 13, 2016. [cited by applicant]
U.S. Appl. No. 62/266,341, filed Dec. 11, 2015. [cited by applicant]
U.S. Appl. No. 62/322,055, filed Apr. 13, 2016. [cited by applicant]
U.S. Appl. No. 62/266,347, filed Dec. 11, 2015. [cited by applicant]
U.S. Appl. No. 62/322,083, filed Apr. 13, 2016. [cited by applicant]
US Patent Application No. 62/26,351, filed Dec. 11, 2015. [cited by applicant]
Giles et al., The Biological and Functional Effects of Spontaneous Deamidation of the AAV Capsid on Gene Therapy Vectors, Molecular Therapy, vol. 22(1):S85, Abstract, May 2014. [cited by applicant]
Giles et al., Immunological and Biochemical Evaluation of the AAV Capsid to Advance Next-Generation Gene Therapy Vector Design, University of Pennsylvania ScholarlyCommons, p. 1-173, Jan. 2018. [cited by applicant]
Extended European Search Report dated Mar. 3, 2022 issued in corresponding European Patent Application No. 19760152.9. [cited by applicant]
Office Action dated Mar. 16, 2022 issued in corresponding Chilean Patent Application No. 2020-2201, with unofficial English translation provided by local agent. [cited by applicant]
Official Action dated Nov. 10, 2022 issued in corresponding Eurasian Patent Application No. 202092015, with unofficial English translation provided by local agent. [cited by applicant]
Office Action dated Feb. 22, 2023 issued in corresponding Japanese Patent Application No. 2020-545159, with unofficial English translation provided by local agent. [cited by applicant]
Office Action dated Sep. 20, 2023 issued in corresponding Japanese Patent Application No. 2020-545159, with unofficial English translation provided by local agent. [cited by applicant]
Office Action dated Dec. 14, 2023 issued in corresponding Canadian Patent Application No. 3,091,795. [cited by applicant]
Office Action dated Jul. 29, 2023 issued in corresponding Chinese Patent. Application No. 201980029022. 1, with unofficial English translation provided by local agent. [cited by applicant]
Substantive Examination Report dated Feb. 1, 2023 issued in related Chilean. Patent Application No. 202002201, with unofficial English translation provided by local agent. [cited by applicant]
Memorandum Opinion and Order, [cited by applicant]
Official Action dated Mar. 12, 2024 issued in corresponding Eurasian Patent Application No. 202092015, with unofficial English translation provided by local agent. [cited by applicant]
Office Action dated Jun. 20, 2024, issued in corresponding Chinese Patent Application No. 201980029022. 1, with unofficial English translation provided by local agent. [cited by applicant]
Notice to Grant Patent Right dated Nov. 8, 2024, issued in corresponding Chinese Patent Application No. 201980029022. 1, with unofficial English translation provided by local agent. [cited by applicant]
Notification of Readiness to Grant Patent dated Dec. 12, 2024, issued in corresponding Eurasian Patent Application No. 202092015, with unofficial English translation provided by local agent. [cited by applicant]
Examination Report dated Aug. 30, 2024, issued in corresponding Australian Patent Application No. 2019228504. [cited by applicant]
Substantive Examination Report dated Jul. 4, 2024, issued in corresponding Chilean Patent Application No. 202202498, with unofficial English translation provided by local agent. [cited by applicant]
Preliminary Rejection dated Jun. 26, 2024, issued in corresponding Korean Patent Application No. 10-2020-7027462, with unofficial English translation provided by local agent. [cited by applicant]
Office Action dated Aug. 30, 2024, issued in corresponding Mexican Patent Application No. MX/a/2020/008932, with unofficial English translation provided by local agent. [cited by applicant]