How Much HIV is Alive? The Challenge of Measuring Replication Competent HIV for HIV Cure Research

A critical knowledge gap in the field of HIV cure research is how best to measure the persistence of replication-competent HIV in the form of intact but latent proviruses. One approach to curing HIV is to eradicate all replication-competent HIV from an individual. It is unlikely that any method, now or in the future, will be able to declare with certainty that all intact proviruses have been eliminated from an individual's body. The difficulty in declaring that all intact proviruses have been eradicated is best illustrated by the two Boston patientswhounderwent allogeneic, hematopoietic stem cell transplantation for uncontrolled malignancy. After successful transplantation and several years of suppressive antiretroviral therapy (ART), HIV DNA or RNA could not be detected in large volumes of blood cells assayed many times from either patient, yet viremia rebound occurred 7–32 weeks after cessation of ART (Henrich et al., 2014). Similarly, it has been difficult to conclude that all HIV has been eliminated even from the Berlin patient who was transplantedwithHIV-resistant cells and inwhomHIV has not been detected in blood for the past decade off of ART (Yukl et al., 2013). As such, laboratory assays to exclude the persistence of intact proviruses in a person are no more likely to be found than is a therapy that eradicates all HIV from a person. The more realistic goal of HIV cure research is to reduce HIV reservoirs and enhance immune control of HIV to undetectable levels in the blood after cessation of ART, also termed, HIV remission. Researchers studying interventions aimed at HIV remission struggle to understand how much their interventions are affecting intact proviruses because of the shortcomings of existing methods to measure them. What matters for the goal of HIV cure is howmuch HIV can replicate. Polymerase chain reaction (PCR)-basedmethods are used to quantify the amount of HIV DNA and HIV RNA in mononuclear cells from blood and lymphoid tissues. Having detectable HIV DNA, however, does not tell us how much HIV could replicate as most of the DNA is defective (Eriksson et al., 2013). Cell-associated HIV RNA has been used as a proxy for “active” reservoirs since RNA is short-lived and its presence implies recent transcription (Pasternak et al., 2013).Measuring low level HIV RNA in blood or other body fluids is another marker for ongoing viral