Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2

Gustavo H. Kijak, Sodsai Tovanabutra, Eric Sanders-Buell, Veerachai Watanaveeradej, Mark S. de Souza, Kenrad E. Nelson, Vidhaya Ketsararat, Vilawan Gulgolgarn, Manu Wera-arpachai, Somchai Sriplienchan, Chirasak Khamboonrueng, Deborah L. Birx, Merlin L. Robb, Francine E. McCutchan

Research output: Contribution to journalArticlepeer-review

41 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)178-191
Number of pages14
Issue number1
StatePublished - Feb 5 2007
Externally publishedYes


  • Asia
  • HIV-1
  • Molecular epidemiology
  • Multi-region hybridization assay (MHA)
  • Recombinant forms
  • Thailand

ASJC Scopus subject areas

  • Virology


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