title: Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2.
abstract: High-resolution HIV-1 genotyping of large sample sets is crucial to define the evolving and dynamic epidemics in Asia. Here we present MHAbce v.2, a multi-region hybridization assay that individually discriminates subtypes B, C, CRF01_AE, and virtually all of their described recombinants, based on real-time PCR using subtype-specific TaqMan probes in 8 regions throughout the viral genome. In a validation panel (n=70), the assay performed with a sensitivity of 95.7% and specificity of 99.8%. The assay was field-tested on samples from a retrospective MTCT cohort (n=180; Lampang Province, Northern Thailand; 1996-1998). 177/180 of the samples were typeable, and 94.4% were typed as CRF01_AE. The remaining strains represented even proportions of subtype B and B/CRF01_AE recombinants and were confirmed by sequencing, revealing early links between the heterosexual and IDU HIV-1 epidemics in Thailand. MHAbce v.2, with an area of application including China, India, Southeast Asia, and the Pacific Rim, can be used to develop a comprehensive and detailed picture of this important component of the HIV/AIDS pandemic.
authors.affiliation: Henry M. Jackson Foundation for the Advancement of Military Medicine/US Military HIV Research Program, Rockville, MD 20850, USA. gkijak@hivresearch.org <gkijak@hivresearch.org>
authors.forename: Gustavo H
authors.initials: GH
authors.lastname: Kijak
authors.forename: Sodsai
authors.initials: S
authors.lastname: Tovanabutra
authors.forename: Eric
authors.initials: E
authors.lastname: Sanders-Buell
authors.forename: Veerachai
authors.initials: V
authors.lastname: Watanaveeradej
authors.forename: Mark S
authors.initials: MS
authors.lastname: de Souza
authors.forename: Kenrad E
authors.initials: KE
authors.lastname: Nelson
authors.forename: Vidhaya
authors.initials: V
authors.lastname: Ketsararat
authors.forename: Vilawan
authors.initials: V
authors.lastname: Gulgolgarn
authors.forename: Manu
authors.initials: M
authors.lastname: Wera-arpachai
authors.forename: Somchai
authors.initials: S
authors.lastname: Sriplienchan
authors.forename: Chirasak
authors.initials: C
authors.lastname: Khamboonrueng
authors.forename: Deborah L
authors.initials: DL
authors.lastname: Birx
authors.forename: Merlin L
authors.initials: ML
authors.lastname: Robb
authors.forename: Francine E
authors.initials: FE
authors.lastname: McCutchan
mesh_terms: D000328:Adult; D001208:Asia / Q000453:epidemiology; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods*; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D011247:Pregnancy; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral