title: A combined screening platform for HIV treatment failure and resistance.
abstract: BACKGROUND
  To develop a low cost method to screen for virologic failure of antiretroviral therapy (ART) and HIV-1 drug resistance, we performed a retrospective evaluation of a screening assay using serial dilutions of HIV-1 RNA-spiked blood plasma and samples from patients receiving >6 months of first-line ART.
  
  
  METHODS
  Serial dilution testing was used to assess sensitivity of a simple PCR-based assay (targeted at ≥1,000 HIV RNA copies/mL). We created blood plasma minipools of five samples, extracted HIV RNA from the pools, PCR amplified the reverse transcriptase (RT) coding region of the HIV-1 pol gene from extracted RNA, sequenced PCR product of positive pools, and used sequences to determine drug resistance. Sensitivity, specificity, and predictive values were determined for different levels of virologic failure based on maximum viral loads of individual samples within a pool.
  
  
  RESULTS
  Of 295 samples analyzed, 43 (15%) had virologic failure at ≥50 copies/mL (range 50-10,500 copies/mL, four at ≥1,000 copies/mL). The assay demonstrated 100% sensitivity to detect virus from these four samples, requiring only one round of PCR, and 56% and 89% sensitivity to detect samples with ≥50 and ≥500 copies/mL using two rounds. Amplified PCR products of all positive pools were successfully sequenced and 30% harbored ≥1 major resistance mutation. This method would have cost 10% of the combined costs of individual viral load and resistance testing.
  
  
  CONCLUSIONS
  We present a novel method that can screen for both virologic failure of first-line ART and drug resistance. The method is much less expensive than current methods, which may offer sustainability in resource-limited settings.
authors.affiliation: Department of Medicine, University of California San Diego, La Jolla, California, United States of America. mtilghman@ucsd.edu
authors.forename: Myres W
authors.initials: MW
authors.lastname: Tilghman
authors.forename: Susanne
authors.initials: S
authors.lastname: May
authors.forename: Josué
authors.initials: J
authors.lastname: Pérez-Santiago
authors.forename: Caroline C
authors.initials: CC
authors.lastname: Ignacio
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Little
authors.forename: Douglas D
authors.initials: DD
authors.lastname: Richman
authors.forename: Davey M
authors.initials: DM
authors.lastname: Smith
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000627:therapeutic use*; D024882:Drug Resistance, Viral; D005260:Female; D015658:HIV Infections / Q000175:diagnosis / Q000188:drug therapy*; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008297:Male; D008875:Middle Aged; D012367:RNA, Viral / Q000097:blood; D012189:Retrospective Studies; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017211:Treatment Failure; D019562:Viral Load; D055815:Young Adult; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D019380:Anti-HIV Agents; D012367:RNA, Viral; D054302:pol Gene Products, Human Immunodeficiency Virus