Table 2. G-to-A hypermutation signatures in viral genomes after nine days of infection in chimpanzee primary CD4+ T cells are dependent on Vif.
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.
| ΔVif | sabVif | rcmVif | smmVif | cpzVif | |
|---|---|---|---|---|---|
| Sequenced clones | 16 | 9 | 21 | 25 | 21 |
| Total bp sequenced | 9169 | 7688 | 21446 | 27577 | 23891 |
| G>A in GG context a | 51 | 62 | 2 | 1 | 0 |
| G>A in GA context | 8 | 0 | 6 | 1 | 1 |
| Total number of G>A | 60 | 62 | 10 | 2 | 1 |
| G>A mutation rate (%) | 0.65 | 0.81 | 0.05 | 0.01 | 0.00 |
| Intact Vif ORF b | NA | 2/9 | all | all | all |
| Hypermut: Hypermutant clones p<0.05 c | 6/16 | 6/9 | 0/21 | 0/25 | 0/21 |
| Hyperfreq: Hypermutant clones d (strongest pattern) e | 8/16 (7 GG, 1 GR) | 6/9 (6 GG) | 2/21 (2 GA) | 0/25 | 0/21 |
| Other mutations | 5 | 5 | 14 | 13 | 15 |
| Other mutation rate (%) | 0.05 | 0.07 | 0.07 | 0.05 | 0.06 |
a, number of G-to-A mutations in the GG context
b, number of intact Vif open reading frame (ORF), NA, not applicable
c, Number of clones that are significantly considered as hypermutant (p<0.05) using Hypermut 2.0 [30]
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].