title: Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping.
abstract: BACKGROUND
  Trofile is the prospectively validated HIV-1 tropism assay. Its use is limited by high costs, long turn-around time, and inability to test patients with very low or undetectable viremia. We aimed at assessing the efficiency of population genotypic assays based on gp120 V3-loop sequencing for the determination of tropism in plasma viral RNA and in whole-blood viral DNA. Contemporary and follow-up plasma and whole-blood samples from patients undergoing tropism testing via the enhanced sensitivity Trofile (ESTA) were collected. Clinical and clonal geno2pheno[coreceptor] (G2P) models at 10% and at optimised 5.7% false positive rate cutoff were evaluated using viral DNA and RNA samples, compared against each other and ESTA, using Cohen's kappa, phylogenetic analysis, and area under the receiver operating characteristic (AUROC).
  
  
  RESULTS
  Both clinical and clonal G2P (with different false positive rates) showed good performances in predicting the ESTA outcome (for V3 RNA-based clinical G2P at 10% false positive rate AUROC = 0.83, sensitivity = 90%, specificity = 75%). The rate of agreement between DNA- and RNA-based clinical G2P was fair (kappa = 0.74, p < 0.0001), and DNA-based clinical G2P accurately predicted the plasma ESTA (AUROC = 0.86). Significant differences in the viral populations were detected when comparing inter/intra patient diversity of viral DNA with RNA sequences.
  
  
  CONCLUSIONS
  Plasma HIV RNA or whole-blood HIV DNA V3-loop sequencing interpreted with clinical G2P is cheap and can be a good surrogate for ESTA. Although there may be differences among viral RNA and DNA populations in the same host, DNA-based G2P may be used as an indication of viral tropism in patients with undetectable plasma viremia.
authors.affiliation: Infectious Diseases Clinic, Catholic University of Sacred Heart, Rome, Italy. ahnven@yahoo.it
authors.forename: Mattia C F
authors.initials: MC
authors.lastname: Prosperi
authors.forename: Laura
authors.initials: L
authors.lastname: Bracciale
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Fabbiani
authors.forename: Simona
authors.initials: S
authors.lastname: Di Giambenedetto
authors.forename: Francesca
authors.initials: F
authors.lastname: Razzolini
authors.forename: Genny
authors.initials: G
authors.lastname: Meini
authors.forename: Manuela
authors.initials: M
authors.lastname: Colafigli
authors.forename: Angela
authors.initials: A
authors.lastname: Marzocchetti
authors.forename: Roberto
authors.initials: R
authors.lastname: Cauda
authors.forename: Maurizio
authors.initials: M
authors.lastname: Zazzi
authors.forename: Andrea
authors.initials: A
authors.lastname: De Luca
mesh_terms: D000328:Adult; D004279:DNA, Viral / Q000235:genetics*; D005260:Female; D005838:Genotype; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015497:HIV-1 / Q000145:classification* / Q000502:physiology; D006801:Humans; D008297:Male; D008875:Middle Aged; D011533:Proviruses / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D015728:Receptors, HIV / Q000032:analysis*; D012680:Sensitivity and Specificity; D056189:Viral Tropism; D014773:Virology / Q000379:methods*; D053585:Virus Attachment
chemical_list: D004279:DNA, Viral; D015699:HIV Envelope Protein gp120; D012367:RNA, Viral; D015728:Receptors, HIV; C514793:gp120 protein, Human immunodeficiency virus 1