# US 2014/0186383 A1 · Novel simian t-cell lymphotropic virus

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- Number: US 2014/0186383 A1
- Document ID: US20140186383A1
- Status: Published application
- Kind: A1
- Application number: 14/013,947
- Filed: 2013-08-29
- Published: 2014-07-03
- Earliest claimed: 2007-05-21
- Assignees: The Johns Hopkins University; The Government of the U.S.A as Represented by the Secretary of the Department of He
- Applicants: Johns Hopkins University; The Government of the U.S.A. as Represented by the Secretary of the Department of He
- Inventors: William M. Switzer; Walid Heneine; Thomas M. Folks; Nathan D. Wolfe; Donald S. Burke; David M. Sintasath
- Web page: https://patentgrep.com/patent/US20140186383A1

## CPC

- C07K 14/005: from viruses
- A61P 31/12: Antivirals
- A61P 37/04: Immunostimulants
- C07K 16/112: Retroviridae (F), e.g. leukemia 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
- G01N 33/56983: {Viruses}
- C12N 2740/14021: Viruses as such, e.g. new isolates, mutants or their genomic sequences
- C12N 2740/14022: New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
- C12N 2740/14043: viral genome or elements thereof as genetic vector
- Y02A 50/30: Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
- 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)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

Disclosed are the simian T-cell lymphotropic virus type 3 subtype D (STLV-3 subtype D), isolated nucleic acid molecules encoding STLV-3 subtype D polypeptides, such as STLV-3 subtype D envelope, protease, polymerase, tax, rex, and capsid polypeptides, isolated polypeptides encoded by such nucleic acids. Methods are also disclosed for detecting STLV-3 subtype D, for example by detecting a STLV-3 subtype D nucleic acid or polypeptide in the sample. Accordingly, probes, primers, and antibodies for use in detecting STLV-3 subtype D nucleic acids or polypeptides are disclosed. Therapeutic compositions which include isolated nucleic acid molecules encoding a STLV-3 subtype D polypeptides or isolated polypeptides encoded by such nucleic acid molecules are also disclosed.

## Claims

### Claim 1

An isolated simian T-cell lymphotropic virus type 3 West African subtype D (STLV-3 subtype D) polypeptide, comprising:
an amino acid sequence encoded by a nucleic acid sequence at least 95% identical to one of: nucleotides 747-2009 of SEQ ID NO: 1; nucleotides 1961-2494 of SEQ ID NO: 1; nucleotides 2416-5061 of SEQ ID NO: 1; nucleotides 5054-6535 of SEQ ID NO: 1; SEQ ID NO: 25; or SEQ ID NO: 26;
wherein the STLV-3 subtype D (simian T-cell lymphotropic virus type 3 West African subtype D) polypeptide encoded by the nucleic acid sequence at least 95% identical to nucleotides 747-2009 of SEQ ID NO: 1 is a capsid protein; nucleotides 1961-2494 of SEQ ID NO: 1 is a protease; nucleotides 2416-5061 of SEQ ID NO: 1 is a polymerase; nucleotides 5054-6535 of SEQ ID NO: 1 is an envelope protein; SEQ ID NO: 25 is a tax polypeptide; and SEQ ID NO: 26 is a rex polypeptide.

### Claim 2 (depends on 1)

An isolated antibody that binds to the isolated polypeptide of claim 1.

### Claim 3 (depends on 2)

The isolated antibody of claim 2, wherein the antibody is labeled.

### Claim 4 (depends on 3)

The antibody according to claim 3, wherein the antibody is radiolabeled, fluorescently-labeled, biotin-labeled, enzymatically-labeled, or chemically-labeled.

### Claim 5

A method for detecting a simian T-cell lymphotropic virus type 3 subtype D (STLV-3 subtype D) in a sample, comprising:
amplifying a STLV-3 subtype D nucleic acid from the sample, using two or more oligonucleotide primers between 15 and 50 nucleotides in length that hybridize under very high stringency conditions to a STLV-3 subtype D nucleic acid sequence set forth as SEQ ID NO: 1 to produce amplified STLV-3 subtype D nucleic acids; and
detecting the amplified STLV-3 subtype D nucleic acids, wherein the presence of the amplified STLV-3 subtype D nucleic acids indicates the presence of the STLV-3 subtype D virus in the sample.

### Claim 6 (depends on 5)

The method according to claim 5, wherein amplifying the STLV-3 subtype D nucleic acid comprises amplifying with polymerase chain reaction (PCR), real-time PCR, reverse transcriptase-polymerase chain reaction (RT-PCR), real-time reverse transcriptase-polymerase chain reaction (rt RT-PCR), ligase chain reaction, or transcription-mediated amplification (TMA).

### Claim 7 (depends on 5)

The method according to claim 5, further comprising:
contacting the sample with a probe comprising a nucleic acid sequence at least 15 nucleotides in length that hybridizes under very high stringency conditions to the amplified STLV-3 subtype D nucleic acid sequence set forth as SEQ ID NO: 1; and
detecting hybridization between the amplified STLV-3 subtype D nucleic acid and the probe, wherein the detection of hybridization indicates the presence of the STLV-3 subtype D virus in the sample.

### Claim 8 (depends on 5)

The method according to claim 5, wherein the two or more oligonucleotide primers comprise a first and second primer, wherein the first primer comprises SEQ ID NO: 21 and the second primer comprises SEQ ID NO: 22.

### Claim 9 (depends on 5)

The method according to claim 5, wherein the two or more oligonucleotide primers comprise a first and second primer, wherein the first primer comprises SEQ ID NO: 23 and the second primer comprises SEQ ID NO: 24.

### Claim 10 (depends on 5)

The method according to claim 5, wherein the two or more oligonucleotide primers are two pairs of primers, wherein the first pair of primers comprises a first primer comprising SEQ ID NO: 21 and a second primer comprising SEQ ID NO: 22, and the second pair of primers comprises a third primer comprising SEQ ID NO: 23 and a fourth primer comprising SEQ ID NO: 24.

### Claim 11

A method for detecting a simian T-cell lymphotropic virus type 3 West African subtype D (STLV-3 subtype D) virus in a sample, comprising:
contacting the sample with at least one probe comprising a nucleic acid sequence at least 15 nucleotides in length that hybridizes under very high stringency conditions to a STLV-3 subtype D nucleic acid sequence set forth as SEQ ID NO: 1; and
detecting hybridization between the STLV-3 subtype D nucleic acid and the probe, wherein the detection of hybridization indicates the presence of the STLV-3 subtype D virus in the sample.

### Claim 12 (depends on 7)

The method according to claim 7, wherein the probe is labeled.

### Claim 13 (depends on 12)

The method according to claim 12, wherein the probe is radiolabeled, fluorescently-labeled, biotin-labeled, enzymatically-labeled, or chemically-labeled.

### Claim 14 (depends on 2)

A method for detecting a STLV-3 subtype D polypeptide in a sample, comprising:
contacting the sample with the antibody of claim 2; and
detecting binding of the antibody to a STLV-3 subtype D polypeptide in the sample, wherein binding of the antibody to the polypeptide indicates the presence of the STLV-3 subtype D polypeptide.

### Claim 15 (depends on 5)

The method of claim 5, wherein the sample is a biological sample.

### Claim 16 (depends on 15)

The method of claim 15, wherein the biological sample is obtained from a primate.

### Claim 17 (depends on 16)

The method of claim 16, wherein the primate is a non-human primate.

### Claim 18 (depends on 1)

A method for generating an immune response in a subject to a STLV-3 subtype D virus, comprising administering to the subject a therapeutically effective amount of the isolated polypeptide of claim 1, thereby generating the immune response to the STLV-3 subtype D virus.

### Claim 19 (depends on 1)

A method for treating or preventing STLV-3 subtype D viral infection in a subject; comprising administering to the subject a therapeutically effective amount of the isolated polypeptide of claim 1, thereby treating or preventing the STLV-3 subtype D viral infection in the subject.