tailieunhanh - Báo cáo y học: "Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học 'Respiratory Research cung cấp cho các bạn kiến thức về ngành y đề tài: Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping. | Prosperi et al. Retrovirology 2010 7 56 http content 7 1 56 gtr RETROVIROLOGY RESEARCH Open Access Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile gp120 V3-loop RNA and DNA genotyping Mattia CF Prosperi 1 Laura Bracciale1 Massimiliano Fabbiani1 Simona Di Giambenedetto1 Francesca Razzolini2 Genny Meini2 Manuela Colafigli1 Angela Marzocchetti1 Roberto Cauda1 Maurizio Zazzi2 and Andrea De Luca1 3 Abstract Background Trofile is the prospectively validated HIV-1 tropism assay. Its use is limited by high costs long turnaround 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 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 sensitivity 90 specificity 75 . The rate of agreement between DNA- and RNA-based clinical G2P was fair kappa p and DNA-based clinical G2P accurately predicted the plasma ESTA AUROC . 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