Satish was part of a multidisciplinary team that wanted to know more about the effectiveness of drug cocktails. Do these medications completely prevent HIV from replicating and infecting new cells, or is HIV still able to replicate in the presence of these drugs, but at such a low rate that we can’t detect it? Since the virus rebounds immediately when a patient stops antiretroviral therapy — even after having been on the drugs for many years — you might think that the virus must be slowly replicating the whole time. Alternatively, latently infected cells could be a refuge that gives the virus a second lease on life. Under this alternative explanation, the infection might be shut down completely during treatment, yet still rebound years later when latently infected cells are reactivated and begin churning out copies of HIV. So which is it — low replication or no replication during antiretroviral therapy?

Satish points out that this issue can be translated directly into evolutionary terms: “if you have ongoing replication, you should have ongoing evolution.” Low level replication isn’t possible to detect with our current arsenal of technology — but low level evolution can be detected using current sequencing technologies and phylogenetic methods. So the primary question became whether HIV is slowly accruing mutations and evolving during drug therapy, or whether it is “frozen in time.”

To help settle the matter, the team took advantage of data from another medical trial. The original study investigated the idea that a series of breaks from drug treatments would prime patients’ immune systems to handle HIV better — and it had been an utter failure. The repeated pauses in treatment only made peoples’ infections worse and encouraged the evolution of drug resistant viral strains. However, the data collected during the study turned out to be exactly what Satish and his colleagues needed: samples of patients’ HIV populations before treatment and then during a series of “rebound phases” when patients were taking breaks from their drug therapy.