title: Evaluation of the Roche Cobas TaqMan and Abbott RealTime extraction-quantification systems for HIV-1 subtypes.
abstract: OBJECTIVE
  We conducted a comparison of the Abbott Molecular RealTime (Rungis, France) and Roche Diagnostics Cobas Taqman (Meylan, France) automated nucleic acid extraction and real-time polymerase chain reaction (PCR) amplification systems for their capacity to quantify HIV RNA of various subtypes. The systems were tested on culture supernatants belonging to HIV-1 group M (n = 29), HIV-1 group O (n = 8), and HIV-2 (n = 7). We also tested 88 plasma samples from patients infected with HIV-1 group M (B-D [n = 7], A-CRF01 [n = 16], CRF02 [n = 49], and other strains [n = 16]).
  
  
  RESULTS
  The Abbott RealTime system quantified all 29 HIV-1 group M supernatants. One of these samples was not detected by the Roche Cobas TaqMan system. The Abbott RealTime system quantified 7 HIV-1 group O strains. Neither technique cross-reacted with HIV-2. The 79% intraclass correlation coefficient for the 88 plasma samples was barely acceptable, but 4 plasma samples were underestimated by more than 1 log by the Roche Cobas TaqMan system. Similar values were obtained for subtype B and D strains with the tests, indicating that the primers and probes are suitable for these strains. In contrast, the large differences observed with other subtypes, particularly CRF02, show the importance of primer and probe selection.
  
  
  CONCLUSIONS
  The limitation of real-time PCR to span the entire diversity of HIV must be taken into account during treatment monitoring, resistance studies, and clinical trials.
authors.affiliation: Laboratoire de Virologie, Equipe d'accueil 2656, Centre Hospitalier Universitaire Charles Nicolle, 1 rue de Germont, 76031 Rouen, France. marie.gueudin@chu-rouen.fr
authors.forename: Marie
authors.initials: M
authors.lastname: Gueudin
authors.forename: Jean Christophe
authors.initials: JC
authors.lastname: Plantier
authors.forename: Véronique
authors.initials: V
authors.lastname: Lemée
authors.forename: Marie Paule
authors.initials: MP
authors.lastname: Schmitt
authors.forename: Loic
authors.initials: L
authors.lastname: Chartier
authors.forename: Thomas
authors.initials: T
authors.lastname: Bourlet
authors.forename: Annick
authors.initials: A
authors.lastname: Ruffault
authors.forename: Florence
authors.initials: F
authors.lastname: Damond
authors.forename: Muriel
authors.initials: M
authors.lastname: Vray
authors.forename: François
authors.initials: F
authors.lastname: Simon
mesh_terms: D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D015498:HIV-2 / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods*; D014766:Viremia / Q000821:virology