Complete genome sequence of a simian immunodeficiency virus from a red-capped mangabey

Abstract

The nucleotide sequence and deduced amino acid sequences of the complete genome of a simian immunodeficiency virus isolate from a red-capped mangabey are disclosed. The invention relates to the nucleic acids and peptides encoded by and/or derived from these sequences and their use in diagnostic methods and as immunogens.

What is claimed is:  
     
         1 . A nucleic acid comprising the nucleotide sequence of the genome of the simian immunodeficiency virus isolate SIVrcm shown in SEQ ID NO:1 or a complementary sequence thereof.  
     
     
         2 . The nucleic acid of  claim 1 , wherein said nucleic acid comprises a nucleotide sequence of at least 12 contiguous bases of said nucleic acid or a complementary sequence thereof.  
     
     
         3 . The nucleic acid of  claim 1 , wherein said nucleic acid comprises a nucleotide sequence of a LTR of said nucleic acid or a complementary sequence thereof.  
     
     
         4 . The nucleic acid of  claim 1 , wherein said nucleic acid encodes a polypeptide selected from the group consisting of Gag, Pol, Vif, Vpr, Env, Tat, Rev, Nef and Vpx of SIVrcm.  
     
     
         5 . The nucleic acid of  claim 1 , wherein said nucleic acid has a nucleotide sequence which is derived from SEQ ID NO:1.  
     
     
         6 . A vector comprising the nucleic acid of  claim 1 .  
     
     
         7 . A cell comprising the nucleic acid of  claim 1 .  
     
     
         8 . A cell comprising the vector of  claim 6 .  
     
     
         9 . A composition comprising the nucleic acid of  claim 1  and a physiologically acceptable carrier.  
     
     
         10 . A method for producing a polypeptide encoded by the nucleic acid of  claim 1 , comprising the step of growing a cell comprising the nucleic acid of  claim 1  under conditions such that the encoded polypeptide is produced.  
     
     
         11 . The method of  claim 10 , wherein said polypeptide comprises a contiguous sequence of at least 13 amino acids.  
     
     
         12 . A composition comprising the polypeptide produced by the method of  claim 10  and a physiologically acceptable carrier.  
     
     
         13 . A method for producing a polypeptide encoded by the nucleic acid of  claim 1 , comprising the step of growing a cell comprising a vector, said vector comprising the nucleic acid of  claim 1 , under conditions such that the encoded polypeptide is produced.  
     
     
         14 . The method of  claim 13 , wherein said polypeptide comprises a contiguous sequence of at least 13 amino acids.  
     
     
         15 . A composition comprising the polypeptide produced by the method of  claim 13  and a physiologically acceptable carrier.  
     
     
         16 . A method of inducing serum antibodies that bind at least one polypeptide encoded by the nucleic acid of  claim 1 , said method comprising: administering to a mammal, in a physiologically acceptable carrier, an amount of said encoded polypeptide sufficient to elicit production of said antibodies.  
     
     
         17 . An anti-SIVrcm antibody made by the method of  claim 16 .  
     
     
         18 . A composition comprising an antibody according to  claim 17  and a physiologically acceptable carrier.  
     
     
         19 . A method for detecting the presence of SIVrcm in a sample comprising contacting said sample with the antibody of  claim 17  under conditions that allow the formation of an antibody-antigen complex and detecting said complex.  
     
     
         20 . A kit for detecting the presence of SIVrcm in a sample comprising an antibody of  claim 17 .  
     
     
         21 . A method of inducing serum antibodies that bind at least one polypeptide encoded by the nucleic acid of  claim 1 , said method comprising: administering to a mammal, in a physiologically acceptable carrier, the nucleic acid of  claim 1  encoding said polypeptide and which produces an immunologically sufficient amount of the encoded polypeptide to elicit said antibodies.  
     
     
         22 . An antibody to SIVrcm made by the method of  claim 21 .  
     
     
         23 . A composition comprising an antibody according to  claim 22 , and a physiologically acceptable carrier.  
     
     
         24 . A method for detecting the presence of SIVrcm in a sample comprising contacting said sample with the antibody of  claim 22  under conditions that allow the formation of an antibody-antigen complex and detecting said complex.  
     
     
         25 . A kit for detecting the presence of SIVrcm in a sample comprising an antibody of  claim 22 .  
     
     
         26 . A method for detecting the presence of antibodies to SIVrcm in a sample comprising contacting said sample with a polypeptide encoded by the nucleic acid of  claim 1  under conditions that allow the formation of an antibody-antigen complex and detecting the complex.  
     
     
         27 . A method for detecting the presence of SIVrcm in a sample comprising contacting said sample with the nucleic acid of  claim 1  and detecting said nucleic acid bound to the genomic DNA, mRNA or cDNA of the SIVrcm virus.  
     
     
         28 . A kit for detecting the presence of SIVrcm in a sample comprising the nucleic acid of  claim 1 .  
     
     
         29 . A nucleic acid probe comprising a sequence of at least 19 contiguous nucleotides derived from the nucleic acid of  claim 1 , or the complementary sequence thereof.  
     
     
         30 . A composition comprising a nucleic acid according to  claim 29 .  
     
     
         31 . A method of detecting the presence of SIVrcm in a biological sample comprising: 
 a.) contacting the nucleic acid of the biological sample with the nucleic acid probe of  claim 29;  and    b.) detecting the presence or absence of complexes formed between said nucleic acid of the biological sample and said nucleic acid probe.    
     
     
         32 . A method of detecting the presence of SIVrcm in a biological sample comprising: 
 a). contacting said biological sample with at least two nucleic acid probes of  claim 29;     b). amplifying the RNA of the biological sample via reverse transcription-polymerase chain reaction to produce amplification products; and    c.) detecting the presence or absence of amplification products.    
     
     
         33 . A method for analyzing a first nucleotide sequence comprising comparing the nucleotide sequence of  claim 1  with said first sequence.