We and others have shown that there is clonal expansion of HIV infected cells in patients, and that, in some cases, the integrated viral DNA can cause the growth and persistence of infected cells. More recently, we showed that a clonally expanded cell carries an intact provirus and produces infectious HIV in a patient. Because there are limits on the samples that can be obtained from patients, we developed a model using SIV-infected rhesus macaques.
The methods of Maldarelli et al (Science 345: 179, 2014) were used to generate an integration site library from rhesus macaque PBMCs infected in culture with SIV. Six additional libraries were generated from two rhesus macaques (two lymph node and one spleen sample from each animal) that were infected with SIV for four weeks and then treated for approximately one year with a cART regiment that fully suppressed the replication of the virus. Samples were taken during necropsy at the end of the treatment period.
The distribution of the SIV integration sites in the large integration site library (~50,000 independent sites) prepared from rhesus macaque PBMC infected in vitro was quite similar to the distribution of HIV integration sites in human PBMCs. We obtained approximately 380 independent integration sites from the monkey tissue sample and identified 13 clones of expanded cells. Cells from two of the clones were present in both the spleen and lymph node tissue samples.
The presence of expanded clones in two SIV macaques that were treated after 4 weeks of infection shows the cells that are infected early can give rise to expanded clones. Cells from two clones were present in both lymph node and spleen, showing that the distribution of at least some clones was not tissue restricted. Having a large PBMC integration site library makes it possible to look for genes in which the integration of an SIV provirus provides the infected cells with a selective growth advantage in the animal. In this first experiment, there was no evidence for the selection of cells that have integration sites in either BACH2 or MKL2. Our results establish an SIV/macaque model that can be used to study the clonal expansion of infected cells using samples that cannot be obtained from patients.