An effective tool for identifying HIV-1 subtypes B, C, CRF01_AE, their recombinant forms, and dual infections in Southeast Asia by the multi-region subtype specific PCR (MSSP) assay

Supachai Sakkhachornphop, Gustavo H. Kijak, Christopher Beyrer, Myat Htoo Razak, Eric Sanders-Buell, Jaroon Jittiwutikarn, Vinai Suriyanon, Merlin L. Robb, Jerome H. Kim, David D Celentano, Francine E. McCutchan, Sodsai Tovanabutra

Research output: Contribution to journalArticle

Abstract

The RV144 Thai vaccine trial has been the only vaccine study to show efficacy in preventing HIV infection. Ongoing molecular surveillance of HIV-1 in Southeast Asia is vital for vaccine development and evaluation. In this study a novel tool, the multi-region subtype specific PCR (MSSP) assay, that was able to identify subtypes B, C, CRF01_AE for Thailand, other Southeast Asian countries, India and China is described. The MSSP assay is based on a nested PCR strategy and amplifies eight short regions distributed along the HIV-1 genome using subtype-specific primers. A panel of 41 clinical DNA samples obtained primarily from opiate users in northern Thailand was used to test the assay performance. The MSSP assay provided 73-100% sensitivity and 100% specificity for the three subtypes in each genome region. The assay was then field-tested on 337 sera from HIV infected northern Thai drug users collected between 1999 and 2002. Subtype distribution was CRF01_AE 77.4% (n=261), subtype B 3.3% (n=11), CRF01_AE/B recombinant 12.2% (n=41), CRF01_AE/C recombinant 0.6% (n=2), and non-typeable 6.5% (n=22). The MSSP assay is a simple, cost-effective, and accurate genotyping tool for laboratory settings with limited resources and is sensitive enough to capture the recombinant genomes and dual infections.

Original languageEnglish (US)
Pages (from-to)70-78
Number of pages9
JournalJournal of Virological Methods
Volume217
DOIs
StatePublished - Jun 1 2015

Fingerprint

Southeastern Asia
HIV-1
Polymerase Chain Reaction
Infection
Vaccines
Genome
Thailand
Opiate Alkaloids
Drug Users
HIV Infections
India
China
HIV
Costs and Cost Analysis
Sensitivity and Specificity
DNA
Serum

Keywords

  • HIV-1
  • MSSP assay
  • Southeast Asia
  • Subtype specific PCR
  • Subtyping

ASJC Scopus subject areas

  • Virology

Cite this

An effective tool for identifying HIV-1 subtypes B, C, CRF01_AE, their recombinant forms, and dual infections in Southeast Asia by the multi-region subtype specific PCR (MSSP) assay. / Sakkhachornphop, Supachai; Kijak, Gustavo H.; Beyrer, Christopher; Razak, Myat Htoo; Sanders-Buell, Eric; Jittiwutikarn, Jaroon; Suriyanon, Vinai; Robb, Merlin L.; Kim, Jerome H.; Celentano, David D; McCutchan, Francine E.; Tovanabutra, Sodsai.

In: Journal of Virological Methods, Vol. 217, 01.06.2015, p. 70-78.

Research output: Contribution to journalArticle

Sakkhachornphop, Supachai ; Kijak, Gustavo H. ; Beyrer, Christopher ; Razak, Myat Htoo ; Sanders-Buell, Eric ; Jittiwutikarn, Jaroon ; Suriyanon, Vinai ; Robb, Merlin L. ; Kim, Jerome H. ; Celentano, David D ; McCutchan, Francine E. ; Tovanabutra, Sodsai. / An effective tool for identifying HIV-1 subtypes B, C, CRF01_AE, their recombinant forms, and dual infections in Southeast Asia by the multi-region subtype specific PCR (MSSP) assay. In: Journal of Virological Methods. 2015 ; Vol. 217. pp. 70-78.
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abstract = "The RV144 Thai vaccine trial has been the only vaccine study to show efficacy in preventing HIV infection. Ongoing molecular surveillance of HIV-1 in Southeast Asia is vital for vaccine development and evaluation. In this study a novel tool, the multi-region subtype specific PCR (MSSP) assay, that was able to identify subtypes B, C, CRF01_AE for Thailand, other Southeast Asian countries, India and China is described. The MSSP assay is based on a nested PCR strategy and amplifies eight short regions distributed along the HIV-1 genome using subtype-specific primers. A panel of 41 clinical DNA samples obtained primarily from opiate users in northern Thailand was used to test the assay performance. The MSSP assay provided 73-100{\%} sensitivity and 100{\%} specificity for the three subtypes in each genome region. The assay was then field-tested on 337 sera from HIV infected northern Thai drug users collected between 1999 and 2002. Subtype distribution was CRF01_AE 77.4{\%} (n=261), subtype B 3.3{\%} (n=11), CRF01_AE/B recombinant 12.2{\%} (n=41), CRF01_AE/C recombinant 0.6{\%} (n=2), and non-typeable 6.5{\%} (n=22). The MSSP assay is a simple, cost-effective, and accurate genotyping tool for laboratory settings with limited resources and is sensitive enough to capture the recombinant genomes and dual infections.",
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AU - Beyrer, Christopher

AU - Razak, Myat Htoo

AU - Sanders-Buell, Eric

AU - Jittiwutikarn, Jaroon

AU - Suriyanon, Vinai

AU - Robb, Merlin L.

AU - Kim, Jerome H.

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AB - The RV144 Thai vaccine trial has been the only vaccine study to show efficacy in preventing HIV infection. Ongoing molecular surveillance of HIV-1 in Southeast Asia is vital for vaccine development and evaluation. In this study a novel tool, the multi-region subtype specific PCR (MSSP) assay, that was able to identify subtypes B, C, CRF01_AE for Thailand, other Southeast Asian countries, India and China is described. The MSSP assay is based on a nested PCR strategy and amplifies eight short regions distributed along the HIV-1 genome using subtype-specific primers. A panel of 41 clinical DNA samples obtained primarily from opiate users in northern Thailand was used to test the assay performance. The MSSP assay provided 73-100% sensitivity and 100% specificity for the three subtypes in each genome region. The assay was then field-tested on 337 sera from HIV infected northern Thai drug users collected between 1999 and 2002. Subtype distribution was CRF01_AE 77.4% (n=261), subtype B 3.3% (n=11), CRF01_AE/B recombinant 12.2% (n=41), CRF01_AE/C recombinant 0.6% (n=2), and non-typeable 6.5% (n=22). The MSSP assay is a simple, cost-effective, and accurate genotyping tool for laboratory settings with limited resources and is sensitive enough to capture the recombinant genomes and dual infections.

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