Replication Rate and Evolution in the Human Immunodeficiency Virus

Population genetic and virological methods yield estimates for the mean replication rate of the Human Immunodeficiency Virus type 1 (HIV-1) that differ by six fold. I present a simple model that can reconcile the estimates obtained from each method by considering the role of intra-host population structure on viral dynamics. The model shows how latently infected cells, which may produce only a small fraction of infective viruses, can nonetheless have an important influence on estimates of mean replication rate. This contribution of latently infected cells is most important when considering the evolution of HIV and the clinical consequences of viral evolution.