Resting CD4+ T cells are a reservoir of latent HIV-1. ART. However in animals with high levels of chronic viral replication turnover was high. SIV DNA half-life within resting CD4 cells correleated with viral load (p?=?0.0052) at the Gag KP9 CTL epitope. At a second CTL epitope in Tat (KVA10) there was a pattern towards an association of SIV DNA half-life in resting CD4 cells and viral load (p?=?0.0971). Further we found that the turnover of resting CD4+ T cell SIV DNA was higher for escape during early contamination than for escape later in contamination (p?=?0.0084). Our results suggest viral DNA within resting CD4 T cells is usually more labile and may be more susceptible to reactivation/eradication treatments when there are higher levels of computer virus replication and during early/acute contamination. Introduction The clinical outcome for HIV-infected individuals has improved dramatically since the development of potent combination antiretroviral therapies (cART) [1] [2]. Upon the cessation of treatment however viral replication is usually quickly re-established due to the presence of latent reservoirs such as the resting CD4+ T cell pool [3]-[6]. Several eradication studies aimed at purging HIV-1 from the latent reservoir are currently in progress [7]-[9]. Preliminary results of clinical studies of purging using current drugs suggests that these may have only a small impact on the total latent reservoir [10]-[14]. It is likely there will need to be a better use of current brokers perhaps in combination with newer brokers to have a clinically useful benefit in reducing the latent reservoir. Understanding the stability and persistence of the latent reservoir has important implications for optimising the effectiveness of these strategies [15]. The majority of studies of HIV DNA turnover and latency have been performed under ART where a very slow turnover TAK-875 of HIV DNA TAK-875 is usually observed [5] [16]-[23]. However little is known about the turnover of HIV DNA during active contamination and whether this may be a better time for interventions to reduce latency. SIV contamination of macques provides a model to study the dynamics of latent HIV contamination where the timing and strain of the contamination is known. Resting CD4 T cells TAK-875 in blood are probably a singificant reservoir of latent HIV and SIV contamination and readily sampled over time. Other blood cells including antigen-presenting cells as well as cells in other tissues are also likely to be singificant reservoirs of latent HIV and SIV although are less well studied. We previously developed a novel approach to measuring SIV DNA turnover in resting CD4+ T cells during active SIV contamination of macaques by studying the rate of change of viral immune escape mutants in serial plasma RNA and in resting CD4+ T cell SIV DNA samples an approach that we termed the ‘escape clock’ for measuring latency turnover [24]. That approach utilized a quasispecies-specific qRT-PCR [25] that was able to measure the frequency of wild type (WT) and escape mutant computer virus (EM) at a Mane-A1*084:01-restricted epitope in Gag that we termed KP9. While the rate of escape from the wildtype KP9 sequence to the escape mutant (K165R-EM) sequence was rapid in plasma the time taken for the K165R-EM mutant to accumulate in the DNA of resting CD4+ T cells was variable. A delay in the appearance of the mutant in the resting CD4 T cell DNA would suggest a slowly turning over reservoir. Using a mathematical TAK-875 modelling approach we showed that this rate of turnover of SIV DNA in resting CD4+ T cells was highly dependent on the viral load of the infected macaques with extremely high Rabbit Polyclonal to ADCK2. rates of SIV DNA turnover seen in animals with high chronic viral loads [15] [24]. The observation of high SIV DNA turnover during active contamination has important implications for strategies aimed at ‘purging’ the SIV reservoir. For example one prediction from the “escape clock” result is usually that the higher levels of viral replication during early SIV or HIV-1 contamination would lead to higher levels of turnover of the latent reservoir during early contamination. This hypothesis is relevant to determining the optimal time to begin treatment with both purging drugs and cART as recent studies have reported lower frequencies of latently infected cells as a consequence of very early cART treatment [26]-[30]. One limitation of the previous approach was the reliance on a quasispecies-specific qRT-PCR.