Fig 1. Sizes of the largest clones of infected and uninfected clones of CD4+ T cells in the three donors.

The sizes of the largest clones of infected cells were determined using the integration site data (available on the HIV DRP RID). The actual sizes of the individual clones were calculated based on the counts of CD4+ T cells for each of the donors, the fraction of the CD4+ T cells that were infected, and the fraction of the infected cells in each clone. Similarly, the sizes of the uninfected clones were calculated based on the number of CD4+ T cells, and the fraction of the total recovered TCR sequences that were obtained for each clone (see Methods). The clone sizes shown in the figures were determined by combining, for each of the donors, the data obtained from all the time points.