Detecting HIV-1 integration by repetitive-sampling Alu-gag PCR

Methods. 2009 Apr;47(4):254-60. doi: 10.1016/j.ymeth.2009.01.002. Epub 2009 Feb 3.


In this review, we compare four assays that are currently used to measure HIV integration and discuss their strengths and weaknesses. We then outline advances that have been made toward development of a more robust, more sensitive, quantitative HIV integration assay suitable for clinical use. The assay that we have developed uses repetitive-sampling Alu-gag PCR. The detailed protocol describes our assay step-by-step, the creation of an integration standard cell line and accompanying standard curve, as well as the quantitation of integration and calculation of associated error estimates. Finally, we speculate on fundamental, unresolved issues in HIV latency that can be addressed by measuring HIV integration.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Alu Elements / genetics*
  • Animals
  • DNA, Viral / genetics
  • HIV Integrase / genetics
  • HIV-1 / genetics*
  • HIV-1 / physiology
  • Humans
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Virus Integration / genetics*
  • gag Gene Products, Human Immunodeficiency Virus / genetics*


  • DNA, Viral
  • gag Gene Products, Human Immunodeficiency Virus
  • HIV Integrase
  • p31 integrase protein, Human immunodeficiency virus 1