HIV-1 exists within individuals as a complex mixture of variants often referred to as a quasispecies. During the past 10 years, there have been many studies of the distribution and clinical significance of "low-abundance" or "minority" drug-resistance variants present in plasma in proportions below 20% to 30% -- the limit of detection of standard genotypic resistance testing using dideoxy-terminator "Sanger" sequencing. HIV-1 "deep" sequencing using NGS technologies have been widely used in research settings to study the clinical significance of low-abundance drug resistance mutations. In addition, NGS is commercially available for several niche clinical applications such as determining HIV-1 tropism before using a CCR5 inhibitor.

In this webinar, Dr. Shafer will review the scenarios in which low-abundance HIV-1 drug-resistance mutations are most clinically relevant, the most influential studies of NGS for HIV-1 drug resistance testing, and the practical aspects of NGS that have so far slowed its widespread adoption for most routine HIV-1 genotypic resistance testing.

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Speaker: Robert W. Shafer MD

Duration: 1.0 hrs.

Level of Instruction: Basic

Reviewed: March, 2018 

  • The material presented is still relevant.


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Course Information
Course Date:
June 18, 2015
Course Objectives
  • Describe the prevalence and clinical significance of low-abundance HIV-1 drug resistance testing in newly infected antiretroviral naive patients and in patients with a history of antiretroviral treatment failure.
  • Explain the promises and limitations of NGS deep sequencing for HIV-1 drug resistance testing including the published experience with the 454, Ion Torrent, PacBio, and Illumina sequencing platforms.
  • Recognize the practical laboratory and bioinformatic considerations that must be understood before implementing NGS deep sequencing for research or clinical applications.
Next-Generation Sequencing (NGS) Technologies for HIV Drug Resistance Testing
Speaker Information
Robert W. Shafer MD  [ view bio ]
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