title: Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for sequence-based analysis of diverse human immunodeficiency virus type 1 strains.
abstract: The Celera Diagnostics ViroSeq HIV-1 Genotyping System is a Food and Drug Administration-cleared, integrated system for sequence-based analysis of drug resistance mutations in subtype B human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for the analysis of diverse HIV-1 strains. Plasma samples were obtained from 126 individuals from Uganda, Cameroon, South Africa, Argentina, Brazil, and Thailand with viral loads ranging from 2.92 to >6.0 log(10) copies/ml. HIV-1 genotyping was performed with the ViroSeq system. HIV-1 subtyping was performed by using phylogenetic methods. PCR products suitable for sequencing were obtained for 125 (99%) of the 126 samples. Genotypes including protease (amino acids 1 to 99) and RT (amino acids 1 to 321) were obtained for 124 (98%) of the samples. Full bidirectional sequence data were obtained for 95 of those samples. The sequences were categorized into the following subtypes: A1/A2 (16 samples), B (12 samples), C (13 samples), D (11 samples), CRF01_AE (9 samples), F/F2 (9 samples), G (7 samples), CRF02_AG (32 samples), H (1 sample), and intersubtype recombinant (14 samples). The performances of the individual sequencing primers were examined. Genotyping of duplicate samples in a second laboratory was successful for 124 of the 126 samples. The identity level for the sequence data from two laboratories ranged from 98 to 100% (median, 99.8%). The ViroSeq system performs well for the analysis of plasma samples with diverse non-B subtypes. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in non-subtype B strains of HIV-1.
authors.affiliation: Department of Pathology, The Johns Hopkins Medical Institutions, Ross Bldg. 646, 720 Rutland Ave., Baltimore, MD 21205, USA. seshlem@jhmi.edu
authors.forename: Susan H
authors.initials: SH
authors.lastname: Eshleman
authors.forename: John
authors.initials: J
authors.lastname: Hackett
authors.forename: Priscilla
authors.initials: P
authors.lastname: Swanson
authors.forename: Shawn P
authors.initials: SP
authors.lastname: Cunningham
authors.forename: Birgit
authors.initials: B
authors.lastname: Drews
authors.forename: Catherine
authors.initials: C
authors.lastname: Brennan
authors.forename: Sushil G
authors.initials: SG
authors.lastname: Devare
authors.forename: Léopold
authors.initials: L
authors.lastname: Zekeng
authors.forename: Lazare
authors.initials: L
authors.lastname: Kaptué
authors.forename: Natalia
authors.initials: N
authors.lastname: Marlowe
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D024882:Drug Resistance, Viral; D005838:Genotype; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D019562:Viral Load
chemical_list: D017931:DNA Primers