Adeno-Associated-Virus Rep Sequences, Vectors and Viruses

Abstract

The invention provides adeno-associated virus (AAV) replication (Rep) sequences. In one embodiment, the invention provides nucleotide sequences encoding a chimeric protein, wherein the encoded chimeric protein contains a wild type AAV Rep inhibitory amino acid sequence, and wherein the nucleotide sequences contain a scrambled and/or deoptimized polynucleotide sequence encoding the wild type AAV Rep inhibitory amino acid sequence. The invention provides vectors, cells, and viruses containing the invention's sequences. Also provided are methods for detecting portions of the AAV Rep inhibitory amino acid sequence, which reduce replication and/or infection and/or productive infection by viruses. The invention's compositions and methods are useful for site-specific integration and/or expression of heterologous sequences by recombinant adeno-associated virus (rAAV) vectors and by rAAV virus particles, such as hybrid viruses (e.g., Ad-AAV) comprising such vectors. The invention's compositions and methods find application in, for example, gene therapy and/or vaccines.

We claim: 
     
         1 . A method for reducing one or more symptoms of disease in a mammalian subject, comprising administering a therapeutically effective amount of the vector of claim  46  to a mammalian subject in need of therapy. 
     
     
         2 . The method of  claim 1 , further comprising detecting the presence of at least a portion of the vector in a cell of the treated subject. 
     
     
         3 . The method of  claim 1 , wherein the recombinant nucleotide sequence further comprises a heterologous polynucleotide sequence operably linked to a first adeno-associated virus inverted terminal repeat (AAV ITR). 
     
     
         4 . The method of  claim 3 , wherein the heterologous polynucleotide sequence comprises a therapeutic sequences. 
     
     
         5 . The method of  claim 3 , wherein the therapeutic sequences encodes one or both of a disease associated polypeptide and an antigen polypeptide. 
     
     
         6 . The method of  claim 5 , wherein the therapeutic sequence encodes an antigen polypeptide, and the method further comprises detecting an immune response by the subject to the antigen polypeptide.