title: Performance of genotypic tools for prediction of tropism in HIV-1 subtype C V3 loop sequences.
abstract: Currently, there is no consensus on the genotypic tools to be used for tropism analysis in HIV-1 subtype C strains. Thus, the aim of the study was to evaluate the performance of the different V3 loop-based genotypic algorithms available. We compiled a dataset of 645 HIV-1 subtype C V3 loop sequences of known coreceptor phenotypes (531 R5-tropic/non-syncytium-inducing and 114 X4-tropic/R5X4-tropic/syncytium-inducing sequences) from the Los Alamos database (http://www.hiv.lanl.gov/) and previously published literature. Coreceptor usage was predicted based on this dataset using different software-based machine-learning algorithms as well as simple classical rules. All the sophisticated machine-learning methods showed a good concordance of above 85%. Geno2Pheno (false-positive rate cutoff of 5-15%) and CoRSeqV3-C were found to have a high predicting capability in determining both HIV-1 subtype C X4-tropic and R5-tropic strains. The current sophisticated genotypic tropism tools based on V3 loop perform well for tropism prediction in HIV-1 subtype C strains and can be used in clinical settings.
authors.affiliation: Division of Clinical Virology, Department of Microbiology, St. John's Medical College Hospital, Bangalore, India.
authors.forename: Soham
authors.initials: S
authors.lastname: Gupta
authors.forename: Ujjwal
authors.initials: U
authors.lastname: Neogi
authors.forename: Hiresave
authors.initials: H
authors.lastname: Srinivasa
authors.forename: Anita
authors.initials: A
authors.lastname: Shet
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D005838:Genotype; D015699:HIV Envelope Protein gp120 / Q000737:chemistry* / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics / Q000502:physiology*; D010446:Peptide Fragments / Q000737:chemistry* / Q000235:genetics*; D010641:Phenotype; D012680:Sensitivity and Specificity; D012984:Software; D056189:Viral Tropism
chemical_list: D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments