Skip to main content
Journal cover image

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.

Publication ,  Journal Article
Sakkhachornphop, S; Kijak, GH; Beyrer, C; Razak, MH; Sanders-Buell, E; Jittiwutikarn, J; Suriyanon, V; Robb, ML; Kim, JH; Celentano, DD ...
Published in: J Virol Methods
June 1, 2015

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.

Duke Scholars

Published In

J Virol Methods

DOI

EISSN

1879-0984

Publication Date

June 1, 2015

Volume

217

Start / End Page

70 / 78

Location

Netherlands

Related Subject Headings

  • Virology
  • Sensitivity and Specificity
  • Polymerase Chain Reaction
  • Molecular Diagnostic Techniques
  • HIV-1
  • HIV Infections
  • Genotyping Techniques
  • Asia, Southeastern
  • 3207 Medical microbiology
  • 1108 Medical Microbiology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Sakkhachornphop, S., Kijak, G. H., Beyrer, C., Razak, M. H., Sanders-Buell, E., Jittiwutikarn, J., … Tovanabutra, S. (2015). 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. J Virol Methods, 217, 70–78. https://doi.org/10.1016/j.jviromet.2015.02.015
Sakkhachornphop, Supachai, Gustavo H. Kijak, Chris Beyrer, Myat Htoo Razak, Eric Sanders-Buell, Jaroon Jittiwutikarn, Vinai Suriyanon, et al. “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.J Virol Methods 217 (June 1, 2015): 70–78. https://doi.org/10.1016/j.jviromet.2015.02.015.
Sakkhachornphop S, Kijak GH, Beyrer C, Razak MH, Sanders-Buell E, Jittiwutikarn J, et al. 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. J Virol Methods. 2015 Jun 1;217:70–8.
Sakkhachornphop, Supachai, et al. “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.J Virol Methods, vol. 217, June 2015, pp. 70–78. Pubmed, doi:10.1016/j.jviromet.2015.02.015.
Sakkhachornphop S, Kijak GH, Beyrer C, Razak MH, Sanders-Buell E, Jittiwutikarn J, Suriyanon V, Robb ML, Kim JH, Celentano DD, McCutchan FE, Tovanabutra S. 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. J Virol Methods. 2015 Jun 1;217:70–78.
Journal cover image

Published In

J Virol Methods

DOI

EISSN

1879-0984

Publication Date

June 1, 2015

Volume

217

Start / End Page

70 / 78

Location

Netherlands

Related Subject Headings

  • Virology
  • Sensitivity and Specificity
  • Polymerase Chain Reaction
  • Molecular Diagnostic Techniques
  • HIV-1
  • HIV Infections
  • Genotyping Techniques
  • Asia, Southeastern
  • 3207 Medical microbiology
  • 1108 Medical Microbiology