G-to-A hypermutation signatures in viral genomes after nine days of infection in chimpanzee primary CD4+ T cells are dependent on Vif.

a, number of G-to-A mutations in the GG contextb, number of intact Vif open reading frame (ORF), NA, not applicablec, Number of clones that are significantly considered as hypermutant (p30]d, Number of clones that that were considered as positive for hypermutation at the significance level of 0.05 [31]e, Strongest pattern, pattern in which the evidence of hypermutation appeared to be the strongest [31].Primary CD4+ T cells from the chimpanzee donor 1 were infected with replication competent viruses HIV:ΔVif, sabVif, rcmVif, smmVif, or cpzVif. Cells were harvested after nine days of infection and genomic DNA was extracted. Viral fragments and clones were retrieved as described in the methods. Sequences were analyzed for G-to-A (“G>A”) hypermutation significance using Hypermut [30] and Hyperfreq [31], as described in the methods.