title: High sensitivity of specific genotypic tools for detection of X4 variants in antiretroviral-experienced patients suitable to be treated with CCR5 antagonists.
abstract: OBJECTIVE
  Evaluation of the reliability of several V3-based genotypic predictors to infer viral tropism in patients infected with B and non-B strains of HIV-1.
  
  
  METHODS
  Several genotypic tropism predictors were evaluated in plasma (RNA) samples from 198 HIV-1-infected patients, taking as gold standard the results of the phenotypic recombinant virus assay Phenoscript((R)). In addition, for 37 B subtype HIV-1 patients the phenotypic results from plasma samples were also compared with tropism predictions based on V3 amplification from paired peripheral blood mononuclear cells (PBMCs).
  
  
  RESULTS
  A total of 150 paired genotypic/phenotypic results were obtained from plasma specimens. Concordance values ranged from 63% to 85%, depending on the genotypic algorithm used. The best predictors in terms of sensitivity/specificity to detect X4 variants were WebPSSM(X4/R5) (77%/87%), Geno2pheno(FPR) (=) (5%) (80%/77%) and an algorithm combining the '11/25' and 'Net charge' rules, termed Garrido's rule (80%/79%). The performance of genotypic predictors was better testing B than non-B clades. The overall sensitivity ranged from 28% to 94%, reaching 100% in subtype B antiretroviral-experienced patients using WebPSSM(SI/NSI), Geno2pheno(FPR) (> or =) (5%) and Garrido's rule. Conversely, the sensitivity when testing non-B subtypes was poorer, ranging from 17% to 67%. Interestingly, the correlation between genotypic and phenotypic results was better when testing PBMCs than plasma using all genotypic predictors.
  
  
  CONCLUSIONS
  Genotypic tools based on V3 sequences may provide reliable information on HIV-1 tropism when testing clade B viruses, especially in antiretroviral-experienced patients. The sensitivity to detect X4 variants using genotypic tools may improve by testing proviral DNA instead of plasma RNA.
authors.affiliation: Infectious Diseases Department, Hospital Carlos III, Sinesio Delgado 10, 28029 Madrid, Spain.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Seclén
authors.forename: Carolina
authors.initials: C
authors.lastname: Garrido
authors.forename: María del Mar
authors.initials: Mdel M
authors.lastname: González
authors.forename: Juan
authors.initials: J
authors.lastname: González-Lahoz
authors.forename: Carmen
authors.initials: C
authors.lastname: de Mendoza
authors.forename: Vincent
authors.initials: V
authors.lastname: Soriano
authors.forename: Eva
authors.initials: E
authors.lastname: Poveda
mesh_terms: D004279:DNA, Viral; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008826:Microbial Sensitivity Tests / Q000379:methods; D008969:Molecular Sequence Data; D010949:Plasma / Q000821:virology; D012367:RNA, Viral / Q000235:genetics; D015728:Receptors, HIV / Q000032:analysis*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D056189:Viral Tropism; D053585:Virus Attachment
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral; D015728:Receptors, HIV