title: Quantifying integrated SIV-DNA by repetitive-sampling Alu-gag PCR.
abstract: OBJECTIVE
  Although antiretroviral therapy (ART) effectively suppresses HIV-1 replication, it does not eradicate the virus and ART interruption consistently results in rebound of viraemia, demonstrating the persistence of a long-lived viral reservoir. Several approaches aimed at reducing virus persistence are being developed, and accurate measurements of the latent reservoir (LR) are necessary to assess the effectiveness of anti-latency interventions. We sought to measure the LR in SIV/SHIV-infected rhesus macaques (RMs) by quantifying integrated SIV-DNA.
  
  
  METHODS
  We optimised a repetitive samplingAlu-gagPCR to quantify integrated SIV-DNAex vivoin ART-naïve and ART-experienced SIV/SHIV-infected RMs.
  
  
  RESULTS
  In ART-naïve RMs, we found the median level of integrated SIV-DNA to be 1660 copies and 866 copies per million PBMC during untreated acute and chronic SHIV infection, respectively. Integrated and total SIV-DNA levels were positively correlated with one another. In ART-treated RMs, integrated SIV-DNA was readily detected in lymph nodes and spleen and levels of total (3319 copies/million cells) and integrated (3160 copies/million cells) SIV-DNA were similar after a median of 404 days of ART. In peripheral blood CD4+ T cells from ART-treated RMs, levels of total (3319 copies/million cells) and integrated (2742 copies/million cells) SIV-DNA were not significantly different and were positively correlated.
  
  
  CONCLUSIONS
  The assay described here is validated and can be used in interventional studies testing HIV/SIV cure strategies in RMs. Measurement of integrated SIV-DNA in ART-treated RMs, along with other reservoir analyses, gives an estimate of the size of the LR.
authors: Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
authors: Maud
authors: M
authors: Mavigner
authors: Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
authors: S Thera
authors: ST
authors: Lee
authors: Department of Pediatrics , Emory University School of Medicine , Atlanta , GA , USA.
authors: Jakob
authors: J
authors: Habib
authors: Yerkes National Primate Research Center , Emory University , Atlanta , GA , USA.
authors: Cameron
authors: C
authors: Robinson
authors: Yerkes National Primate Research Center , Emory University , Atlanta , GA , USA.
authors: Guido
authors: G
authors: Silvestri
authors: Department of Pathology and Laboratory Medicine , University of Pennsylvania , Philadelphia , PA , USA.
authors: Una
authors: U
authors: O'Doherty
authors: Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
authors: Ann
authors: A
authors: Chahroudi
keywords: SIV; integration; latency; reservoir; rhesus macaques