? Understanding the genetic basis of drug resistance is essential for using genotypic drug resistance testing to help physicians select optimal therapy for their patients, for designing new antiviral drugs, and for monitoring the spread of drug-resistant viruses. We plan to identify patterns of protease, reverse transcriptase (RT), and perhaps envelope, and integrase mutations developing in HIV-1 isolates from persons receiving antiretroviral therapy. We will use these patterns to create panels of prototypical infectious biological and molecular clones with high-level resistance to each drug class to assist scientists investigating the biophysical and biochemical basis of drug resistance. To determine whether drug resistance can be explained solely by mutations in the molecular targets of drug therapy, we will compare the susceptibility of biological clones obtained directly from a patient sample with those of recombinant molecular clones in which only the target of therapy has been contributed by the biological clone. We will also compare the susceptibility of recombinant and non-recombinant biological clones from subtype A, C, D, F, G, A/E, and A/G isolates with common patterns of drug-resistance mutations. To examine the role of newly identified treatment-associated RT and protease mutations, we will compare the susceptibility and replication of pairs of clones that are isogenic except for mutation at the position of interest. We hypothesize that HIV-1 isolates with high-level class resistance consist of complex mixtures of clones with related but distinct patterns of drug-resistance mutations. The extent of drug resistance in such isolates is likely to be lower than the cumulative amount of drug resistance in the clones that comprise the isolate. Drugs that are only partially active against isolates with high-level class resistance may not be effective for salvage therapy because these isolates may harbor subpopulations that will require only one or two additional mutations to become highly cross-resistant to a new drug. We will examine the susceptibility of clones from high-level class-resistant isolates to drugs in pre-clinical and clinical development and will culture these clones in the presence of increasing concentrations of these drugs to select viruses with high level cross-resistance for use in drug development efforts. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI046148-06
Application #
6989121
Study Section
AIDS Discovery and Development of Therapeutics Study Section (ADDT)
Program Officer
Ussery, Michael A
Project Start
1999-08-01
Project End
2008-11-30
Budget Start
2005-12-01
Budget End
2006-11-30
Support Year
6
Fiscal Year
2006
Total Cost
$351,541
Indirect Cost
Name
Stanford University
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
Varghese, Vici; Mitsuya, Yumi; Fessel, W Jeffrey et al. (2013) Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1. Antimicrob Agents Chemother 57:4290-4299
Balamane, Maya; Varghese, Vici; Melikian, George L et al. (2012) Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine. Antimicrob Agents Chemother 56:4522-4
Blanco, Jose-Luis; Varghese, Vici; Rhee, Soo-Yon et al. (2011) HIV-1 integrase inhibitor resistance and its clinical implications. J Infect Dis 203:1204-14
Reuman, Elizabeth C; Margeridon-Thermet, Severine; Caudill, Harrison B et al. (2010) A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. Bioinformatics 26:2929-32
Varghese, Vici; Wang, Elijah; Babrzadeh, Farbod et al. (2010) Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation. PLoS One 5:e10992
Reuman, Elizabeth C; Rhee, Soo-Yon; Holmes, Susan P et al. (2010) Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations. J Antimicrob Chemother 65:1477-85
Reuman, Elizabeth C; Bachmann, Michael H; Varghese, Vici et al. (2010) Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector. Antimicrob Agents Chemother 54:934-6
Varghese, Vici; Liu, Tommy F; Rhee, Soo-Yon et al. (2010) HIV-1 integrase sequence variability in antiretroviral naïve patients and in triple-class experienced patients subsequently treated with raltegravir. AIDS Res Hum Retroviruses 26:1323-6
Varghese, Vici; Shahriar, Rajin; Rhee, Soo-Yon et al. (2009) Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors. J Acquir Immune Defic Syndr 52:309-15
Shafer, Robert W (2009) Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. J Infect Dis 199:610-2

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