Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for sequence-based analysis of diverse human immunodeficiency virus type 1 strains.

Content Provider	Semantic Scholar
Author	Eshleman, Susan H. Hackett, John Swanson, Priscilla A. Cunningham, Shawn P. Drews, Birgit Mammen Zekeng, Léopold Kaptue, Lazare Noche Marlowe, Natalia M.
Copyright Year	2004
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.
File Format	PDF HTM / HTML
Alternate Webpage(s)	http://jcm.asm.org/content/42/6/2711.full.pdf
PubMed reference number	15184457v1
Volume Number	42
Issue Number	6
Journal	Journal of clinical microbiology
Language	English
Access Restriction	Open
Subject Keyword	Amino Acids Biopolymer Sequencing Copy (object) Endopeptidases Genotype determination HIV Infections HIV-1 Immunologic Deficiency Syndromes Laboratory Mutation Ninety Nine RNA-Directed DNA Polymerase Recombinants Subtype (attribute) non-T, non-B childhood acute lymphoblastic leukemia
Content Type	Text
Resource Type	Article