Table 1.
Viral sequence analysis.
| Acute phase | |||
|---|---|---|---|
| Group 1 animals | Vif RL8 | Vif RL9 | Nef RL10 |
| rh2349 (wk 6) | nd | nd | nd |
| rh2355 (wk 6) | 100% | 100% | 100% |
| rh2350 (wk 6) | 99% | 27% | nd |
| rh2352 (wk 6) | 97% | 47% | nd |
| rh2357 (wk 6) | 87% | 75% | 97% |
| rh2361 (wk 6) | 100% | 100% | 100% |
| rh2364 (wk 6) | 59% | 37% | 92% |
| rh2365 (wk 6) | nd | nd | nd |
| Group 2 animals | Vif RL8 | Vif RL9 | Nef RL10 |
|---|---|---|---|
| rh2351 (wk 6) | 22% | 33% | 97% |
| rh2353 (wk 6) | 38% | 40% | 95% |
| rh2354 (wk 6) | 92% | 92% | 100% |
| rh2358 (wk 6) | 100% | 100% | 99% |
| rh2360 (wk 6) | 50% | 64% | 99% |
| rh2363 (wk 6) | 94% | 99% | 95% |
| rh2366 (wk 6) | 100% | 69% | 99% |
| rh2367 (wk 6) | 97% | 78% | 100% |
| Chronic phase | |||
|---|---|---|---|
| Group 1 animals | Vif RL8 | Vif RL9 | Nef RL10 |
| rh2349 (wk 35) | 4% | 4% | 7% |
| rh2355 (wk 37) | 0% | 0% | 0% |
| rh2350 (wk 48) | nd | nd | 91% |
| rh2352 (wk 48) | 97% | 17% | 69% |
| rh2357 (wk 45) | nd | nd | 99% |
| rh2361 (wk 48) | 99% | 68% | 99% |
| rh2364 (wk 45) | nd | nd | nd |
| rh2365 (wk 48) | nd | nd | nd |
454 sequencing of the three Mamu-B*08-restricted Vif RL8, Vif RL9, and Nef RL10 CD8+ T-cell epitopes. Vif and Nef were amplified independently and PCR amplicons sequenced by 454. Sequence analysis was carried out using RC454 and V-phaser as previously described21,22. Percentages indicate frequencies of wild type epitope sequence reads for both the acute and chronic phases of infection. Breakthrough animals in Group 1 are identified in yellow. nd = not determined.