title: Comparison between rules-based human immunodeficiency virus type 1 genotype interpretations and real or virtual phenotype: concordance analysis and correlation with clinical outcome in heavily treated patients.
abstract: We compared 2 rules-based genotype interpretation systems and real or virtual phenotype through a retrospective analysis of a prospective trial. Genotypes were determined with VircoGEN II (VIRCO) and were interpreted with either RetroGram 1.4 or TRUGENE HIV-1 (guidelines 3.0) or original virtual phenotype (Virtual Phenotype; VIRCO), as available in the year 2000. Among 188 human immunodeficiency virus (HIV) type 1 isolates, overall concordance (kappa agreement) was observed for the 2 rules-based systems, whereas striking discordances were noted between them and real and virtual phenotype interpretations for stavudine, didanosine, zalcitabine, abacavir, and amprenavir (kappa<0.4). Clinical evaluation of a subset of 173 patients showed that both rules-based sensitivity scores were independently associated with HIV RNA loads <400 copies/mL at week 16 of during-treatment analysis (TRUGENE: odds ratio [OR], 2.90; 95% confidence interval [CI], 1.52-5.52; P=.001; RetroGram: OR, 2.34; 95% CI, 1.21-4.55; P=.012), whereas, in contrast to real or virtual phenotype, interpretations according to biological cut-offs were not (OR, 1.91; 95% CI, 0.77-4.76; P=.162).
authors.affiliation: Institute of Infectious and Tropical Diseases, University of Brescia, P. le Spedali Civili 1, 25123 Brescia, Italy. carlotorti@hotmail.com
authors.forename: Carlo
authors.initials: C
authors.lastname: Torti
authors.forename: Eugenia
authors.initials: E
authors.lastname: Quiros-Roldan
authors.forename: Wilco
authors.initials: W
authors.lastname: Keulen
authors.forename: Luigia
authors.initials: L
authors.lastname: Scudeller
authors.forename: Sergio
authors.initials: S
authors.lastname: Lo Caputo
authors.forename: Charles
authors.initials: C
authors.lastname: Boucher
authors.forename: Francesco
authors.initials: F
authors.lastname: Castelli
authors.forename: Francesco
authors.initials: F
authors.lastname: Mazzotta
authors.forename: Piera
authors.initials: P
authors.lastname: Pierotti
authors.forename: Anne Mieke
authors.initials: AM
authors.lastname: Been-Tiktak
authors.forename: Giovanni
authors.initials: G
authors.lastname: Buccoliero
authors.forename: Michele
authors.initials: M
authors.lastname: De Gennaro
authors.forename: Giampiero
authors.initials: G
authors.lastname: Carosi
authors.forename: Carmine
authors.initials: C
authors.lastname: Tinelli
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000494:pharmacology* / Q000627:therapeutic use*; D024882:Drug Resistance, Viral; D005260:Female; D005814:Genes, Viral / Q000235:genetics; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D008297:Male; D016017:Odds Ratio; D010641:Phenotype; D012307:Risk Factors; D016879:Salvage Therapy; D016896:Treatment Outcome
chemical_list: D019380:Anti-HIV Agents