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

doi:10.1016/j.virol.2006.07.055

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

41 Scopus citations

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.

Original language	English
Pages (from-to)	178-191
Number of pages	14
Journal	Virology
Volume	358
Issue number	1
DOIs	https://doi.org/10.1016/j.virol.2006.07.055
State	Published - 5 Feb 2007

Keywords

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

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10.1016/j.virol.2006.07.055

Cite this

Kijak, G. H., Tovanabutra, S., Sanders-Buell, E., Watanaveeradej, V., de Souza, M. S., Nelson, K. E., Ketsararat, V., Gulgolgarn, V., Wera-arpachai, M., Sriplienchan, S., Khamboonrueng, C., Birx, D. L., Robb, M. L., & McCutchan, F. E. (2007). Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2. Virology, 358(1), 178-191. https://doi.org/10.1016/j.virol.2006.07.055

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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.",

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Kijak, GH, Tovanabutra, S, Sanders-Buell, E, Watanaveeradej, V, de Souza, MS, Nelson, KE, Ketsararat, V, Gulgolgarn, V, Wera-arpachai, M, Sriplienchan, S, Khamboonrueng, C, Birx, DL, Robb, ML & McCutchan, FE 2007, 'Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2', Virology, vol. 358, no. 1, pp. 178-191. https://doi.org/10.1016/j.virol.2006.07.055

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T1 - Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2

AU - Kijak, Gustavo H.

AU - Tovanabutra, Sodsai

AU - Sanders-Buell, Eric

AU - Watanaveeradej, Veerachai

AU - de Souza, Mark S.

AU - Nelson, Kenrad E.

AU - Ketsararat, Vidhaya

AU - Gulgolgarn, Vilawan

AU - Wera-arpachai, Manu

AU - Sriplienchan, Somchai

AU - Khamboonrueng, Chirasak

AU - Birx, Deborah L.

AU - Robb, Merlin L.

AU - McCutchan, Francine E.

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N2 - 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.

AB - 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.

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KW - Multi-region hybridization assay (MHA)

KW - Recombinant forms

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