High concordance between the position-specific scoring matrix and geno2pheno algorithms for genotypic interpretation of HIV-1 tropism: V3 length as the major cause of disagreement

Abstract

The agreement between the position-specific scoring matrix (PSSM) and geno2pheno as tools for genotypic interpretation of HIV-1 tropism using 800 clinical specimens was assessed. There was an overall concordance of 88%. Disagreement was found mostly in specimens with short V3 lengths (<35 amino acids). Thus, consideration of V3 lengths should improve the predictability of HIV-1 tropism using genotypic algorithms. Copyright © 2011, American Society for Microbiology. All Rights Reserved.