David Lockhart
The HIV infecting two tissues in the body may represent a single randomly mixing population or may be compartmentalized into reproductively isolated groups. We examine local variation within 3 siteson the cervix relative to the blood of 8 women. Genetic diversity in the two compartments were compared using the pooled means test of Gilbert & Rossini. Compartmentalization was determined using the permutation method of Slatkin & Maddison. Homogeneity of viral sequences from the different cervical sites was examined using randomization tests. We hypothesize that apparent compartmentalization occurs as a result of bursts of monoclonal replication. We defined a burst as 5 or more sequences each within a distance of .01 of each other. Identification of such bursts requires the enumeration of maximal cliques of a graph of their relationships. This enumeration is computationally intensive, but Du et al give an algorithm that works well for sparse graphs.
