The frequency of reactivation from latency has reached about half of its maximum in animals treated 4 days post-infection, whereas the level of SIV DNA continues to increase around 100-fold between day 4 and day 10 post-infection. We use a modelling approach to explore the dynamics of early infection and consider the possibility that there are different subsets of infected cells. For example, if we had a subset of cells which is both highly susceptible to infection, and has a high frequency of reactivation from latency, then these cells would both be infected first (orange curve in panel a), and would also make an out-sized contribution to the overall frequency of reactivation from latency. The less susceptible and quiescent pool (green curve in panel a) continues to ‘fill’ over time, but this has relatively little impact on later reactivation rates The frequency of reactivation and SIV DNA levels include contributions from both subsets. However, the small subset of highly active cells can make a major contribution to the frequency of reactivation, while having little effect on total DNA levels. For example, panel b shows experimental data (dots) and along with panel a illustrates that a theoretical subset of only 0.4% of cells that is 100-fold more susceptible to infection, and 500-fold more prone to reactivation, could explain the data on SIV DNA and SIV reactivation frequency.