Mutational profiles in HIV-1 protease and reverse transcriptase correlated with phenotypic drug resistance

A method of evaluating the effectiveness of an HIV-1 antiviral therapy of an HIV-1 infected patient comprising:

• (i) collecting a sample from an HIV-1 infected patient;
• (ii) detecting in said sample each of the following nucleic acids:
• a) a first nucleic acid encoding an HIV-1 reverse transcriptase comprising:
• 1) at least one mutation chosen from the group consisting of 88E, 101H, 101N, 101P, 101Q, 101T, 103H, 103S, 179I, 179E, 181V, 190E, 190S and 190T;
• or
• 2) a combination of mutations 103R and 179D,
• in which the presence of said first nucleic acid correlates with resistance to a Non-Nucleoside Reverse Transcriptase Inhibitor (NNRTI);
• b) a second nucleic acid encoding an HIV-1 reverse transcriptase comprising at least one mutation chosen from the group consisting of 69S-[S-S], 184G, 215V, 44D, 44A, and 118I,
• in which the presence of said second nucleic acid correlates with resistance to a Nucleoside Reverse Transcriptase Inhibitor (NRTI);
• and
• c) a third nucleic acid encoding an HIV-1 protease comprising:
• 1) mutation 88T;
• or
• 2) a combination of mutations 33F and 90M,
• in which the presence of said third nucleic acid correlates with resistance to a Protease Inhibitor (PI);
• whereby the presence of each of the nucleic acids in step (ii) individually correlates with the effectiveness of said HIV-1 antiviral therapy.