Mutational profile in hiv-1 gag cleavage site correlated with phenotypic drug resistance

Abstract

The invention concerns novel mutations or mutational profiles of HIV-1 protease cleavage sites (CS) in the Gag region correlated with a phenotype causing alterations in sensitivity to anti-HIV drugs. The present invention also relates to the use of genotypic characterization of a target population of HIV and the subsequent association, i.e. correlation, of this information to phenotypic interpretation in order to correlate virus mutational profiles with drug resistance. The invention further relates to methods of utilizing the mutational profiles of the invention in databases, drug development, i.e., drug design, and drug modification, therapy and treatment design and clinical management.

1 . A computer system directed by software wherein the software correlates the presence of at least one mutation in the human immunodeficiency virus type 1 (HIV-1) protease cleavage sites in the gag region and a change in susceptibility of at least one strain of HIV to a protease inhibitor, in particular to the darunavir/ritonavir combination, characterized in that the software uses at least one record corresponding to a correlation between at least one mutation E428G in said gag cleavage site, and treatment with at least a protease inhibitor, in particular the darunavir/ritonavir combination. 
   
   
       2 . A method of evaluating the effectiveness of a protease inhibitor, in particular the darunavir/ritonavir combination, as an antiviral therapy for a patient infected with at least one mutant HIV strain comprising:
 (i) collecting a sample from an HIV-infected patient;   (ii) determining whether the sample comprises a nucleic acid sequence encoding HIV gag-pol having at least one mutation E428G in the gag gene;   (iii) correlating the presence of said at least one mutation of step (ii) to a change in effectiveness of said protease inhibitor.   
   
   
       3 . A method of identifying a drug effective against mutant HIV gag-pol, comprising:
 (i) providing a nucleic acid sequence comprising HIV gag-pol comprising at least one mutation E428G in the gag gene;   (ii) recombining said nucleic acid sequence comprising HIV of step (i) into a proviral nucleic acid sequence deleted for said sequence to generate a recombinant HIV virus;   (iii) determining a phenotypic response to said drug for said recombinant virus; and   (iv) identifying a drug effective against mutant HIV based on the phenotypic response of step (iii).   
   
   
       4 . A method of identifying a drug effective against mutant HIV gag-pol, comprising:
 (i) providing a HIV gag-pol comprising at least one mutation E428G in the gag gene;   (ii) determining the activity of said drug on said HIV gag-pol;   (iii) determining the activity of said drug on wild type HIV gag-pol;   (iv) determining the ratio of the activity determined in step (iii) over the activity determined in step (ii);   (v) identifying an effective drug against mutant HIV based on the ratio of step (iv).   
   
   
       5 . A method for evaluating a change in viral drug susceptibility, comprising:
 (i) collecting a sample from an HIV-infected patient;   (ii) determining whether the sample comprises a HIV gag-pol having at least one mutation E428G in the gag gene;   (iii) correlating the presence of said at least one mutation of step (ii) to a change in viral drug susceptibility.   
   
   
       6 . A method of evaluating a change in viral drug susceptibility, comprising:
 (i) providing an HIV comprising a gag-pol containing at least one mutation E428G in the gag gene;   (ii) determining a phenotypic response of said virus to said drug; and   (iii) correlating the phenotypic response of step (ii) to a change in viral drug susceptibility.   
   
   
       7 . A method for evaluating a change in drug effectiveness against mutant HIV gag-pol, comprising:
 (i) providing a HIV gag-pol comprising at least one mutation E428G in the gag gene;   (ii) determining the activity of said drug on said mutant HIV gag-pol;   (iii) determining the activity of said drug on wild type HIV gag-pol and;   (iv) determining the ratio of the activity determined in step (iii) over the activity determined in step (ii);   (v) identifying an effective drug against mutant HIV based on the ratio of step (iv).   
   
   
       8 . A vector for performing phenotypic analysis comprising an HIV sequence having at least one mutation E428G in the HIV gag gene. 
   
   
       9 . An isolated and purified HIV gag-pol sequence having at least one mutation E428G in the gag gene, wherein said at least one mutation in said sequence correlates to a fold change in susceptibility towards a HIV protease inhibitor, in particular the darunavir/ritonavir combination.