# US 6,699,663 B1 · Molecular sequence of swine retrovirus

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- Number: US 6,699,663 B1
- Document ID: US6699663B1
- Status: Granted
- Kind: B1
- Application number: 09/661,858
- Filed: 2000-09-14
- Granted: 2004-03-02
- Earliest claimed: 1995-12-14
- Assignees: The General Hospital Corporation
- Inventors: Jay A. Fishman
- Web page: https://patentgrep.com/patent/US6699663B1

## CPC

- C12N 15/8509: {for producing genetically modified animals, e.g. transgenic}
- C07K 14/005: from viruses
- C12N 7/00: Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof (preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00)
- C12N 15/86: Viral vectors
- C12Q 1/6888: for detection or identification of organisms
- C12Q 1/702: {for retroviruses}
- A01K 2217/05: Animals comprising random inserted nucleic acids (transgenic)
- A01K 2217/075: inducing loss of function, i.e. knock out
- A01K 2227/108: Swine
- A01K 2267/02: Animal zootechnically ameliorated
- A01K 2267/025: Animal producing cells or organs for transplantation
- C12N 2740/10021: Viruses as such, e.g. new isolates, mutants or their genomic sequences
- C12N 2740/10022: New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
- C12N 2740/10043: viral genome or elements thereof as genetic vector
- C12N 2740/13021: Viruses as such, e.g. new isolates, mutants or their genomic sequences
- C12N 2740/13022: New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
- C12N 2740/13043: viral genome or elements thereof as genetic vector
- C12N 2740/15043: viral genome or elements thereof as genetic vector
- C12Q 2600/156: Polymorphic or mutational markers
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- 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)
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- A01K: ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS

## Abstract

Purified nucleic acid which can specifically hybridize with the sequence of swine retroviruses.

## Claims

### Claim 1

A purified nucleic acid molecule at least 85% identical to a molecule selected from the group consisting of SEQ ID NO:1, the fully complementary sequence of SEQ ID NO:1, SEQ ID NO:2, the fully complementary sequence of SEQ ID NO:2, SEQ ID NO:3, the fully complementary sequence of SEQ ID NO:3.

### Claim 2 (depends on 1)

The purified nucleic acid molecule of claim 1 that is SEQ ID NO:1.

### Claim 3 (depends on 1)

The purified nucleic acid molecule of claim 1 that is the fully complementary sequence of SEQ ID NO:1.

### Claim 4 (depends on 1)

The purified nucleic acid molecule of claim 1 that is SEQ ID NO:2.

### Claim 5 (depends on 1)

The purified nucleic acid molecule of claim 1 that is the fully complementary sequence of SEQ ID NO:2.

### Claim 6 (depends on 1)

The purified nucleic acid molecule of claim 1 that is SEQ ID NO:3.

### Claim 7 (depends on 1)

The purified nucleic acid molecule of claim 1 that is the fully complementary sequence of SEQ ID NO:3.

### Claim 8

A purified nucleic acid molecule selected from the group consisting of:
(a) nucleotides 2-1999 of SEQ ID NO:1;
(b) nucleotides 2452-4839 of SEQ ID NO:1;
(c) nucleotides 4871-8060 of SEQ ID NO:1;
(d) nucleotides 598-2169 of SEQ ID NO:2;
(e) nucleotides 2320-4737 of SEQ ID NO:2;
(f) nucleotides 4738-6722 of SEQ ID NO:2;
(g) nucleotides 585-2156 of SEQ ID NO:3;
(h) nucleotides 2307-5741 of SEQ ID NO:3; and
(i) nucleotides 5620-7533 of SEQ ID NO:3.

### Claim 9 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 2-1999 of SEQ ID NO:1.

### Claim 10 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 2452-4839 of SEQ ID NO:1.

### Claim 11 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 4871-8060 of SEQ ID NO:1.

### Claim 12 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 598-2169 of SEQ ID NO:2.

### Claim 13 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 2320-4737 of SEQ ID NO:2.

### Claim 14 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 4738-6722 of SEQ ID NO:2.

### Claim 15 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 585-2156of SEQ ID NO:3.

### Claim 16 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 2307-5741 of SEQ ID NO:3.

### Claim 17 (depends on 8)

The purified nucleic acid molecule of claim 8 that is nucleotides 5620-7533 of SEQ ID NO:3.

### Claim 18

A purified nucleic acid sequence at least 15 base pairs in length selected from a polynucleotide sequence, the polynucleotide sequence selected from the group consisting of SEQ ID NO:1, the fully complementary sequence of SEQ ID NO:1, SEQ ID NO:2, the fully complementary sequence of SEQ ID NO:2, SEQ ID NO:3, and the fully complementary sequence of SEQ ID NO:3, and further characterized by having less than 70% homology with the corresponding region in human, mouse and primate retroviral sequences, wherein the last five 3′ bases are unique to the selected sequence.

### Claim 19 (depends on 18)

The purified nucleic acid sequence of claim 18 wherein the sequence is selected from SEQ ID NO:1.

### Claim 20 (depends on 18)

The purified nucleic acid sequence of claim 18, wherein the sequence is selected from the fully complementary sequence of SEQ ID NO:1.

### Claim 21 (depends on 18)

The purified nucleic acid sequence of claim 18, wherein the sequence is selected from SEQ ID NO:2.

### Claim 22 (depends on 18)

The purified nucleic acid sequence of claim 18, wherein the sequence is selected from the fully complementary sequence of SEQ ID NO:2.

### Claim 23 (depends on 18)

The purified nucleic acid sequence of claim 18, wherein the sequence is selected from SEQ ID NO:3.

### Claim 24 (depends on 18)

The purified nucleic acid sequence of claim 18, wherein the sequence is selected from the fully complementary sequence of SEQ ID NO:3.

### Claim 25

A purified nucleic acid sequence selected from the group consisting of SEQ ID NO:4 through SEQ ID NO:74.

### Claim 26

A purified nucleic acid molecule at least 20 nucleotides in length that hybridizes under stringent conditions to a molecule selected from the group consisting of SEQ ID NO:1, the fully complementary sequence of SEQ ID NO:1, SEQ ID NO:2, the fully complementary sequence of SEQ ID NO:2, SEQ ID NO:3, the fully complementary sequence of SEQ ID NO:3.

### Claim 27

A method of determining the copy number or size of a porcine retrovirus, comprising:
contacting a target nucleic acid from the donor, recipient, or a graft, with a second nucleic acid selected from the group of: a sequence which can specifically hybridize to the sequence of SEQ ID NO:1, or its complement of the same length; a sequence which can specifically hybridize to the sequence of SEQ ID NO:2, or its complement of the sane length; a sequence which can specifically hybridize to the sequence of SEQ ID NO:3, or its complement of the same length; a nucleic acid which can specifically hybridize to a sense or antisense sequence which encodes a gag protein, said sense or antisense sequence being selected from the group consisting of gag-encoding nucleotides of SEQ ID NO:1, gag-encoding nucleotides of SEQ ID NO:2, and gag-encoding nucleotides of SEQ ID NO:3; a nucleic acid which can specifically hybridize to a sense or antisense sequence from nucleotides 2452-4939 or nucleotides 3112-4683 of SEQ ID NO:1, nucleotides 598-2169 of SEQ ID NO:2, or nucleotides 585-2156, of SEQ ID NO:3; a nucleic acid which can specifically hybridize to sense or antisense sequence which encodes a pol protein, said sense or antisense sequence being selected from the group consisting of pol-encoding nucleotides of SEQ ID NO:1, pol-encoding nucleotides of SEQ ID NO:2, and pol-encoding nucleotides of SEQ ID NO:3; a nucleic acid which can specifically hybridize to a sense or antisense sequence from a nucleotides 4871-8060 of SEQ ID NO:1, nucleotides 2320-4737 of SEQ ID NO:2, or nucleotides 2307-5741 of SEQ ID NO:3; a nucleic acid which can specifically hybridize to a sense or antisense sequence which encodes an env protein, said sense or antisense sequence being selected from the group consisting of env-encoding nucleotides of SEQ ID NO:1, env-encoding nucleotides of SEQ ID NO:2, and env-encoding nucleotides of SEQ ID NO:3; a nucleic acid which can specifically hybridize to a sense or antisense sequence from nucleotides 2-1999 or nucleotides 86-1999 of SEQ ID NO:], nucleotides 4738-6722 of SEQ ID NO:2, or nucleotides 1820-7533 of SEQ ID NO:3,
wherein the target nucleic acid is from a human recipient.