Means and methods for monitoring protease inhibitor antiretroviral therapy and guiding therapeutic decisions in the treatment of HIV/AIDS

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said patient a nucleic acid encoding HIV protease having a mutation at codon 82 and a secondary mutation at a codon selected from the group consisting of codons 33, 23, 32, 53, 37, 71, 61, 11, and 46, wherein the presence of said protease-encoding nucleic acid in said biological sample indicates a difference in said HIV protease's susceptibility to amprenavir relative to a reference HIV protease, thereby assessing the effectiveness of protease antiretroviral therapy.

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said HIV-infected patient a nucleic acid encoding an HIV protease that comprises a mutation at codon 82 and a secondary mutation at a codon selected from the group consisting of codons 55, 53, 23, 33, and 39, wherein the presence of said protease-encoding nucleic acid in said biological sample indicates a difference in said HIV protease's susceptibility to a protease inhibitor relative to a reference HIV protease, thereby assessing the effectiveness of protease antiretroviral therapy.

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said patient a nucleic acid encoding HIV protease having a mutation at codon 82 and a secondary mutation at a codon selected from the group consisting of codons 33, 23, 53, and 11, wherein the presence of said protease-encoding nucleic acid in said biological sample indicates a decrease in said HIV protease's susceptibility to a protease inhibitor relative to a reference HIV protease, thereby indicating a decrease in the effectiveness of protease antiretroviral therapy.

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said HIV-infected patient a nucleic acid encoding an HIV protease that comprises a mutation at codon 82 and a secondary mutation at a codon selected from the group consisting of codons 32 and 46;

• the group consisting of codons 13 and 61;
• or the group consisting of codons 32 and 39, wherein the presence of said protease-encoding nucleic acid in said biological sample indicates an increase in said HIV protease's susceptibility to a protease inhibitor relative to a reference HIV protease, thereby indicating an increase in the effectiveness of protease antiretroviral therapy.

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said HIV-infected patient a nucleic acid encoding an HIV protease that comprises a mutation at codon 90 and a secondary mutation at a codon selected from the group consisting of codons 53, 95, 13, 74, 55, 85, 62, 66, 33, 64, 23, and 58, wherein the presence of said protease-encoding nucleic acid in said biological sample indicates a difference in said HIV protease's susceptibility to amprenavir relative to a reference HIV protease, thereby assessing the effectiveness of protease antiretroviral therapy.

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said patient a nucleic acid encoding HIV protease having a mutation at codon 90 and a secondary mutation at a codon selected from the group consisting of codons 89, 53, 33, 92, 95, 58, 62, 74, 15, 47, 66, 32, 55, 53, 13, and 69, wherein the presence of said protease-encoding nucleic acid in said biological sample in comparison indicates a difference in said HIV protease's susceptibility to amprenavir relative to a reference HIV protease, thereby assessing the effectiveness of protease antiretroviral therapy.

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said HIV-infected patient a nucleic acid encoding an HIV protease that comprises a mutation at codon 90 and a secondary mutation at a codon selected from the group consisting of codons 53, 95, 55, 85, 66, 33, 23, and 58, wherein the presence of said protease-encoding nucleic acid in said biological sample indicates a difference in said HIV protease's susceptibility to a protease inhibitor relative to a reference HIV protease, thereby assessing the effectiveness of protease antiretroviral therapy.

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said patient a nucleic acid encoding HIV protease having a mutation at codon 90 and a secondary mutation at a codon selected from the group consisting of codons 89, 53, 33, 92, 95, 58, 66, and 55, wherein the presence of said protease-encoding nucleic acid in said biological sample indicates a decrease in said HIV protease's susceptibility to a protease inhibitor relative to a reference HIV protease, thereby indicating a decrease in the effectiveness of protease antiretroviral therapy.

A method of assessing the effectiveness of protease antiretroviral therapy of a patient infected with HIV, said method comprising detecting in a biological sample from said HIV-infected patient a nucleic acid encoding an HIV protease that comprises a mutation at codon 90 and a secondary mutation at a codon selected from the group consisting of codons 64, 77, and 93;

• the group consisting of codons 13 and 74;
• or the group consisting of codons 74, 15, and 69, wherein the presence of said protease-encoding nucleic acid in said biological sample indicates an increase in said HIV protease's susceptibility to a protease inhibitor relative to a reference HIV protease, thereby indicating an increase in the effectiveness of protease antiretroviral therapy.