Novel simian t-cell lymphotropic virus

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.

We 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.   
     
     
         2 . An isolated antibody that binds to the isolated polypeptide of  claim 1 . 
     
     
         3 . The isolated antibody of  claim 2 , wherein the antibody is labeled. 
     
     
         4 . The antibody according to  claim 3 , wherein the antibody is radiolabeled, fluorescently-labeled, biotin-labeled, enzymatically-labeled, or chemically-labeled. 
     
     
         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.   
     
     
         6 . 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). 
     
     
         7 . 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.   
     
     
         8 . 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. 
     
     
         9 . 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. 
     
     
         10 . 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. 
     
     
         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.   
     
     
         12 . The method according to  claim 7 , wherein the probe is labeled. 
     
     
         13 . The method according to  claim 12 , wherein the probe is radiolabeled, fluorescently-labeled, biotin-labeled, enzymatically-labeled, or chemically-labeled. 
     
     
         14 . 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.   
     
     
         15 . The method of  claim 5 , wherein the sample is a biological sample. 
     
     
         16 . The method of  claim 15 , wherein the biological sample is obtained from a primate. 
     
     
         17 . The method of  claim 16 , wherein the primate is a non-human primate. 
     
     
         18 . 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. 
     
     
         19 . 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.