Stanford University HIV Drug Resistance Database - A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

Publications

HIV-1 Protease and Reverse Transcriptase Mutation Patterns Responsible for Discordances Between Genotypic Drug Resistance Interpretation Algorithms

Jaideep Ravela, Bradley J. Betts, Francoise Brun-Vézinet, Anne-Mieke Vandamme, Diane Descamps, Kristel Van Laethem, Kate Smith, Jonathan M. Schapiro, Dean Winslow, Caroline Reid, Robert W. Shafer

ABSTRACT

Several rules-based algorithms have been developed to interpret HIV-1 genotypic resistance tests. To assess the concordance of these algorithms and to identify sequences causing inter-algorithm discordances, we applied four publicly available algorithms to the sequences of isolates from 2045 individuals in Northern California. Drug resistance interpretations were classified as S for susceptible, I for intermediate, and R for resistant. Of 30,675 interpretations (2045 sequences x 15 drugs), 4.4% were completely discordant, with at least one algorithm assigning an S and another an R; 29.2% were partially discordant, with at least one algorithm assigning an S and another an I, or at least one algorithm assigning an I and another an R; and 66.4% displayed complete concordance, with all four algorithms assigning the same interpretation. Discordances between nucleoside reverse transcriptase (RT) inhibitor interpretations usually resulted from several simple, frequently occurring mutational patterns. Discordances between protease inhibitor interpretations resulted from a larger number of more complex mutational patterns. Discordances between non-nucleoside RT inhibitor interpretations were uncommon and resulted from a small number of individual drug-resistance mutations. Determining the clinical significance of these mutational patterns responsible for inter-algorithm discordances will improve inter-algorithm concordance and the accuracy of genotypic resistance interpretation.


Data Section:

To download the file with the 2045 sequences click here
To download PR drug interpretation scores worksheet click here
To download NRTI drug interpretation scores worksheet click here
To download NNRTI drug interpretation scores worksheet click here
To download the summary of the PR patterns found click here
To download the summary of the NRTI patterns found click here
To download the summary of the NNRTI patterns found click here
To download all the overall Kappa values click here
To download all the Kappa values by drug click here