Methods of assessing hiv integrase inhibitor therapy

Abstract

The present invention relates to methods and products for the evaluation of HIV treatment. The methods are based on evaluating molecular events at the HIV integrase resulting in altered therapeutic efficacy of the investigated compounds. The methods rely on providing an integrase gene and evaluating either through genotyping or phenotyping said integrase gene. The present invention relates to the fields of diagnostics, drug screening, pharmacogenetics and drug development.

1 . to  8 . (canceled)  
     
     
         9 . A method of constructing a genotypic and phenotypic database of IN sequences, comprising 
 i) obtaining samples of HIV RNA comprising the IN gene or a portion thereof;    ii) reverse-transcribing and amplifying said HIV RNA with primers specific for the IN region of the HIV genome to obtain an amplicon comprising the IN gene or a portion thereof;    iii) determining the nucleotide sequence of the amplicon or portions thereof;    iv) generating a plasmid comprising the wild-type HIV sequence with a deletion in the IN region of the HIV genome characterized in that said deletion is generated using nucleic acid amplification;    v) preparing recombinant virus by homologous recombination or ligation between the amplicon and a plasmid comprising the wild-type HIV sequence with a deletion in the IN region;    vi) determining the relative replicative capacity of the recombinant virus in the presence of anti-HIV drugs compared to an HIV virus with a wild-type IN gene sequence.    
     
     
         10 . A method of constructing a genotypic and phenotypic database of IN sequences, comprising 
 i) obtaining samples of HIV DNA comprising the IN gene or a portion thereof;    ii) amplifying said HIV DNA with primers specific for the IN region of the HIV genome to obtain an amplicon comprising the IN gene or a portion thereof;    iii) determining the nucleotide sequence of the amplicon or portions thereof;    iv) generating a plasmid comprising the wild-type HIV sequence with a deletion in the IN region of the HIV genome characterized in that said deletion is generated using nucleic acid amplification    v) preparing recombinant virus by homologous recombination or ligation between the amplicon and a plasmid comprising the wild-type HIV sequence with a deletion in the IN region;    vi) determining the relative replicative capacity of the recombinant virus in the presence of anti-HIV drugs compared to an HIV virus with a wild-type IN gene sequence.    
     
     
         11 . A database comprising genotypic and phenotypic data of the HIV integrase, wherein the database further provides a correlation between genotypes and between genotypes and phenotypes, wherein the correlation is indicative of efficacy of a given drug regimen.  
     
     
         12 . to  17 . (canceled)