Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2.
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.
Kijak
Gustavo H
GH
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>
Tovanabutra
Sodsai
S
Sanders-Buell
Eric
E
Watanaveeradej
Veerachai
V
de Souza
Mark S
MS
Nelson
Kenrad E
KE
Ketsararat
Vidhaya
V
Gulgolgarn
Vilawan
V
Wera-arpachai
Manu
M
Sriplienchan
Somchai
S
Khamboonrueng
Chirasak
C
Birx
Deborah L
DL
Robb
Merlin L
ML
McCutchan
Francine E
FE
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
D012367:RNA, Viral