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Next-generation sequencing to assess HIV tropism

Swenson, Luke C.a; Däumer, Martinb; Paredes, Rogerc

Current Opinion in HIV and AIDS: September 2012 - Volume 7 - Issue 5 - p 478–485
doi: 10.1097/COH.0b013e328356e9da
VIRAL TROPISM: Edited by Annemarie M.J. Wensing and Rolf Kaiser

Purpose of review Deep sequencing of the V3 region of the HIV envelope gene can detect minority non-R5 variants in patients with high sensitivity and specificity. As next-generation sequencing approaches have matured, the clinical utility of deep sequencing for HIV tropism has entered the clinic. Accurate and sensitive tropism testing is essential for successful treatment with the CCR5 antagonist class of antiretrovirals.

Recent findings This review will focus on five aspects of next-generation sequencing for assessing HIV tropism: some background on the necessity of deep sequencing versus other tropism methods; the methodological process of 454 sequencing and analysis; other next-generation sequencing technologies; the diagnostic performance of deep sequencing relative to other tropism assays; and the use of deep sequencing in clinical practice.

Summary This method has emerged quickly as both a research and clinical tool because of its high concordance with commonly used phenotypic tropism assays and its ability to predict virological response to CCR5 antagonist-containing regimens.

aBritish Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada

bInstitute of Immunology and Genetics, Kaiserslautern, Germany

cIrsiCaixa AIDS Research Institute and HIV Unit, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain

Correspondence to Luke C. Swenson, BC Centre for Excellence in HIV/AIDS, 603 – 1081 Burrard Street, Vancouver, BC, Canada V6Z 1Y6. E-mail:

© 2012 Lippincott Williams & Wilkins, Inc.