# US 9,719,070 B2 · Methods of predicting ancestral virus sequences and uses thereof

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- Number: US 9,719,070 B2
- Document ID: US9719070B2
- Status: Granted
- Kind: B2
- Application number: 15/291,470
- Filed: 2016-10-12
- Published: 2017-02-23
- Granted: 2017-08-01
- Earliest claimed: 2013-10-11
- Assignees: Massachusetts Eye and Ear Infirmary; The Schepens Eye Research Institute, Inc.
- Applicants: Massachusetts Eye and Ear Infirmary; Schepens Eye Research Institute
- Inventors: Luk H. Vandenberghe; Eric Zinn
- Web page: https://patentgrep.com/patent/US9719070B2

## CPC

- C07K 14/075: Adenoviridae
- C12N 7/00: Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof (preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00)
- A61K 39/00: Medicinal preparations containing antigens or antibodies (materials for immunoassay G01N33/53)
- A61P 27/02: Ophthalmic agents
- A61P 37/04: Immunostimulants
- A61P 43/00: Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
- C07K 14/00: Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K 14/005: from viruses
- C07K 16/22: against growth factors {; against growth regulators}
- C12N 15/86: Viral vectors
- A61K 2039/525: {Virus}
- A61K 2039/6075: {Viral proteins}
- C07K 2317/24: containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
- C07K 2317/76: Antagonist effect on antigen, e.g. neutralization or inhibition of binding
- C12N 2750/14121: Viruses as such, e.g. new isolates, mutants or their genomic sequences
- C12N 2750/14122: New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
- C12N 2750/14123: Virus like particles [VLP]
- C12N 2750/14141: Use of virus, viral particle or viral elements as a vector
- C12N 2750/14142: virus or viral particle as vehicle, e.g. encapsulating small organic molecule
- C12N 2750/14143: viral genome or elements thereof as genetic vector
- C12N 2750/14171: Demonstrated in vivo effect
- Y02A 90/10: Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

Methods are described for predicting ancestral sequences for viruses or portions thereof. Also described are predicted ancestral sequences for adeno-associated virus (AAV) capsid polypeptides. The disclosure also provides methods of gene transfer and methods of vaccinating subjects by administering a target antigen operably linked to the AAV capsid polypeptides.

## Claims

### Claim 1

An adeno-associated virus (AAV) capsid polypeptide having at least 95% sequence identity to the amino acid sequence shown in SEQ ID NO: 23.

### Claim 2 (depends on 1)

The AAV capsid polypeptide of claim 1, wherein the AAV capsid polypeptide or a virus particle comprising the AAV capsid polypeptide:
exhibits a lower seroprevalence than does an AAV2 capsid polypeptide or a virus particle comprising an AAV2 capsid polypeptide, and wherein the AAV capsid polypeptide or a virus particle comprising the AAV capsid polypeptide exhibits about the same or a lower seroprevalence than does an AAV8 capsid polypeptide or a virus particle comprising an AAV8 capsid polypeptide; and/or
is neutralized to a lesser extent by human serum than is an AAV2 capsid polypeptide or a virus particle comprising an AAV2 capsid polypeptide, and wherein the AAV capsid polypeptide or a virus particle comprising the AAV capsid polypeptide is neutralized to a similar or lesser extent by human serum than is an AAV8 capsid polypeptide or a virus particle comprising an AAV8 capsid polypeptide.

### Claim 3 (depends on 1)

The AAV capsid polypeptide of claim 1, wherein the AAV capsid polypeptide is purified.

### Claim 4 (depends on 1)

The AAV capsid polypeptide of claim 1, wherein the polypeptide has at least 99% sequence identity to the amino acid sequence shown in SEQ ID NO: 23.

### Claim 5 (depends on 1)

The AAV capsid polypeptide of claim 1, wherein the polypeptide has 100% sequence identity to the amino acid sequence shown in SEQ ID NO: 23.

### Claim 6 (depends on 1)

A virus particle comprising the AAV capsid polypeptide of claim 1.

### Claim 7 (depends on 6)

The virus particle of claim 6, further comprising a transgene.