TY - JOUR
T1 - 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
AU - Sakkhachornphop, Supachai
AU - Kijak, Gustavo H.
AU - Beyrer, Chris
AU - Razak, Myat Htoo
AU - Sanders-Buell, Eric
AU - Jittiwutikarn, Jaroon
AU - Suriyanon, Vinai
AU - Robb, Merlin L.
AU - Kim, Jerome H.
AU - Celentano, David D.
AU - McCutchan, Francine E.
AU - Tovanabutra, Sodsai
N1 - Funding Information:
We are very grateful to the subjects for their participation in this study. The authors thank staff members at the Henry M. Jackson Foundation for technical advice, the research staffs at Northern Drug Treatment Center and RIHES for Cohort building and specimen collections. We extend our gratitude to Dr. Thira Sirisanthana, Dr. Namtip Srirak, Mr. Kittipong Rungruengthanakit, Mr. Rassamee Keawvichit, Mrs. Kanlaya Wongworapat and Mr. Peter Lange for their advice and supports on conducting the study. We are indebted to Ms. Meera Bose and Mr. Peter Phuc Pham for HIV-1 sequence analysis. This study was supported by the Fogarty AIDS International for Research and Training Program, Johns Hopkins Bloomberg School of Public Health, grants number D43TW000010-25 and a cooperative agreement (W81XWH-11-2-0174) between the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., and the U.S. Department of Defense (DOD). We wish to thank the National Research University Project under Thailand's Office of the Higher Education Commission for partial financial support.
Publisher Copyright:
© 2015 Elsevier B.V.
PY - 2015/6/1
Y1 - 2015/6/1
N2 - 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.
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.
KW - HIV-1
KW - MSSP assay
KW - Southeast Asia
KW - Subtype specific PCR
KW - Subtyping
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U2 - 10.1016/j.jviromet.2015.02.015
DO - 10.1016/j.jviromet.2015.02.015
M3 - Article
C2 - 25725414
AN - SCOPUS:84924691983
SN - 0166-0934
VL - 217
SP - 70
EP - 78
JO - Journal of Virological Methods
JF - Journal of Virological Methods
ER -