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.
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.
Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand.
Supachai
S
Sakkhachornphop
U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA.
Gustavo H
GH
Kijak
Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
Chris
C
Beyrer
Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.
Myat Htoo
MH
Razak
U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA.
Eric
E
Sanders-Buell
Northern Drug Treatment Center, Chiang Mai 50200, Thailand.
Jaroon
J
Jittiwutikarn
Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand.
Vinai
V
Suriyanon
U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA.
Merlin L
ML
Robb
U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
Jerome H
JH
Kim
Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
David D
DD
Celentano
U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA.
Francine E
FE
McCutchan
U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA. Electronic address: stovanabutra@hivresearch.org.
Sodsai
S
Tovanabutra
D001210:Asia, Southeastern; D060005:Genotyping Techniques / Q000379:methods*; D015658:HIV Infections / Q000175:diagnosis* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity
HIV-1; MSSP assay; Southeast Asia; Subtype specific PCR; Subtyping