title: Magnetic-silica based nucleic acid extraction for Human Immunodeficiency Virus Type-1 drug-resistance testing in low viremic patients.
abstract: Human Immunodeficiency Virus Type-1 (HIV-1) drug-resistance testing is challenging for viral loads below 1,000 copies/mL, but, according to HIV-1 guidelines, it should be considered for improving patient management and treatment options. High-recovery and high-purity extraction methods can enhance standard performances of HIV-1 genotyping assays based on direct full-population sequencing. Aim of the present study was to evaluate performances of the NucliSENS easyMAG (NeM) (BioMerieux, Marcy l'Etoile, F) semi-automated nucleic acid extraction system combined with the direct full-population sequencing ViroSeq HIV-1 genotyping (Abbott, IL, US), for detecting drug resistance in samples with HIV-1 RNA<1,000 copies/mL (n=62). Data were compared with those from the ViroSeq manual extraction in 86 samples with HIV-1 RNA<1,000 copies/mL and studied on HIV-1 reference standards. HIV-1 genotyping was successful in 98% of samples extracted with NeM (61/62) and in 84% of those extracted with ViroSeq (72/86) (X(2)=8.508, p=0.004). HIV-1 RNA levels in samples successfully processed with NeM were significantly lower than those in manually processed ones (mean+/-SD, respectively, 285+/-222 copies/mL vs. 403+/-269 copies/mL) (p=0.004). For HIV-1 RNA levels <300 and 500 copies/mL, performances of HIV-1 genotyping with NeM were significantly high (97% and 98%, vs. 68% and 78% for manual extraction). As assessed on HIV-1 RNA reference standards, the detection rate at 200 copies/mL for HIV-1 genotyping with NeM extraction was 100%. In conclusion, these data support that HIV-1 direct full-population sequencing combined with NeM is associated with a significantly high success rate, thus improving the management of HIV-1 drug resistance in low viremic patients.
authors.affiliation: Microbiology and Virology Laboratory, Ospedale Amedeo di Savoia, Corso Svizzera 164, 10149 Torino, Italy.
authors.forename: Maria Grazia
authors.initials: MG
authors.lastname: Milia
authors.forename: Tizano
authors.initials: T
authors.lastname: Allice
authors.forename: Gabriella
authors.initials: G
authors.lastname: Gregori
authors.forename: Stefano
authors.initials: S
authors.lastname: Mussino
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Orofino
authors.forename: Stefano
authors.initials: S
authors.lastname: Bonora
authors.forename: Valeria
authors.initials: V
authors.lastname: Ghisetti
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology; D016009:Chi-Square Distribution; D024882:Drug Resistance, Viral; D005838:Genotype; D015658:HIV Infections / Q000097:blood / Q000188:drug therapy / Q000821:virology*; D015497:HIV-1 / Q000737:chemistry / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D008280:Magnetics; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000302:isolation & purification*; D012189:Retrospective Studies; D017423:Sequence Analysis, RNA / Q000379:methods*; D012822:Silicon Dioxide; D019562:Viral Load; D014766:Viremia / Q000097:blood
chemical_list: D019380:Anti-HIV Agents; D012367:RNA, Viral; D012822:Silicon Dioxide