title: Evaluation of two commercial kits for the detection of genotypic drug resistance on a panel of HIV type 1 subtypes A through J.
abstract: We compared the two commercially available sequencing kits for HIV-1 drug resistance testing, the ViroSeq Genotyping System (Applied Biosystems, Foster City, CA, U.S.A.) and the TRUGENE HIV-1 Genotyping Kit (Visible Genetics, Inc., Toronto, Ontario, Canada), with our in-house genotyping system. Fifteen viral isolates from African patients (6 treated and 9 untreated) covering a panel of HIV-1 subtypes A through J and 7 plasma samples from Belgian and African patients (2 treated and 5 untreated) were tested. All the samples could be amplified and sequenced by the three systems; however, for all systems, alternative amplification/sequencing primers had to be used for some samples belonging to subtype B as well as to other subtypes. The consensus sequence was partially derived from only one strand for the in-house system and for the ViroSeq Genotyping System. The TRUGENE HIV-1 Genotyping Kit scored the highest number of ambiguities, followed by the ViroSeq Genotyping System and the in-house system. For 11 samples, these differences in reporting mixtures affected 14 resistance-related positions, which altered the interpretation toward protease inhibitors for 2 samples when using version 1.2 RetroGram software (Virology Networks, Utrecht, The Netherlands). All three systems were able to sequence diluted samples with a viral load down to 10 3 or 10 4 RNA copies/ml. Our data therefore suggest that the performance of amplification and sequencing primers must be improved to allow fast and reliable resistance testing for all HIV-1 subtypes.
authors.affiliation: Laboratoire de Rétrovirologie, Centre de Recherche Public-Santé, Luxembourg.
authors.forename: E
authors.initials: E
authors.lastname: Fontaine
authors.forename: C
authors.initials: C
authors.lastname: Riva
authors.forename: M
authors.initials: M
authors.lastname: Peeters
authors.forename: J C
authors.initials: JC
authors.lastname: Schmit
authors.forename: E
authors.initials: E
authors.lastname: Delaporte
authors.forename: K
authors.initials: K
authors.lastname: Van Laethem
authors.forename: K
authors.initials: K
authors.lastname: Van Vaerenbergh
authors.forename: J
authors.initials: J
authors.lastname: Snoeck
authors.forename: E
authors.initials: E
authors.lastname: Van Wijngaerden
authors.forename: E
authors.initials: E
authors.lastname: De Clercq
authors.forename: M
authors.initials: M
authors.lastname: Van Ranst
authors.forename: A M
authors.initials: AM
authors.lastname: Vandamme
mesh_terms: D004345:Drug Industry; D004352:Drug Resistance, Microbial / Q000235:genetics*; D005838:Genotype; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D011933:Reagent Kits, Diagnostic
chemical_list: D011933:Reagent Kits, Diagnostic