Characterizing the relationship between HIV-1 genotype and phenotype: prediction-based classification
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Updated: Oct 2, 2026

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
Published on: December 1, 2011
1Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA. foulkes@sdac.harvard.edu
Abstract:
This paper establishes a framework for understanding the complex relationships between HIV-1 genotypic markers of resistance to antiretroviral drugs and clinical measures of disease progression. A new classification scheme based on the probabilities of how new patients will respond to antiretroviral therapy given the available data is proposed as a method for distinguishing among groups of viral sequences. This approach draws from existing cluster analysis, discriminant analysis, and recursive partitioning techniques and requires a model relating genotypic characteristics to phenotypic response. A data set of 2,746 sequences and the corresponding Indinavir 50% inhibitory concentrations are described and used for illustrative purposes.
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