| Subject | Child's age | C*03 Gag 296YL9304 | Frequencey | B*42 Nef 71RM979 | Frequency | A*30 Pol 328AY9366 | Frequency | A*30 Env 704IY9712 | Frequency | A*30 Env 794KY9802 | Frequency | B*42 Env 298RI10307 | Frequency | B*42 Env 843IF9851 | Frequency | B*15:10 Rev 52IL960 | Frequency | B*15:10 Vif 78WI987a | Frequency |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| YVDRFFKTL | RPQVPLRPM | AQNPEIVIY | IVNRVRQGY | KYLGSLVQY | RPNNNTRKSI | IPRRIRQGF | IHSISERIL | DWHLGHGVSI | |||||||||||
| yr | |||||||||||||||||||
| 517-M | 0.25 | ········· | 100% | ········· | 100% | ········· | 100% | V·R······ | 68% | ········· | 100% | ·········· | 85% | L········ | 86% | ········· | 100% | ·········· | 100% |
| V·S······ | 22% | ·······R·· | 15% | L···V···· | 13% | ||||||||||||||
| V········ | 4% | ||||||||||||||||||
| I·S······ | 3% | ||||||||||||||||||
| 6 | ········· | 100% | ········· | 100% | ········· | 93% | V·R······ | 97% | ········· | 100% | ·········T | 55% | L········ | 36% | ········· | 100% | ·········· | 100% | |
| ·R······· | 4% | V·RK····· | 2% | ·········V | 29% | L···L···· | 29% | ||||||||||||
| ·K······· | 2% | ··S······V | 13% | L···F···· | 29% | ||||||||||||||
| ··S······I | 1.6% | L···V···· | 5% | ||||||||||||||||
| 517-C | 0.2 | ········· | 100% | ········· | 100% | ········· | 53% | ··K······ | 100% | ····N··L· | 100% | ·TG····R·· | 100% | ········L | 100% | ·RA······ | 94% | ·········· | 40% |
| ········C | 47% | ·RA·····I | 6% | ·······A·· | 36% | ||||||||||||||
| E········· | 18% | ||||||||||||||||||
| ··Q······· | 2% | ||||||||||||||||||
| ··L······· | 2% | ||||||||||||||||||
| ·······I·· | 1.1% | ||||||||||||||||||
| 2.5 | ········· | 98% | ········· | 100% | ········· | 88% | V·R······ | 98.6% | ········· | 91% | ··G····R·· | 51% | L········ | 100% | ·N······· | 76% | E········· | 61% | |
| ······R·· | 2% | ·····L··· | 12% | V·RK····· | 1.2% | ····N···· | 9% | ··G······· | 40% | ·RA······ | 12% | ·······A·· | 30% | ||||||
| ··S······· | 9% | ·H······· | 10% | E······A·· | 5% | ||||||||||||||
| LN······· | 1.3% | ·········· | 4% | ||||||||||||||||
| 5 | ········· | 58% | ········· | 100% | ·····L··· | 82% | V·R······ | 86% | ········· | 91% | ··G····R·· | 82% | L········ | 96% | ·N······· | 59% | E········· | 70% | |
| ·······V· | 39% | ········· | 16% | ··R······ | 13% | ····N···· | 9% | ··G····R·M | 14% | L···V···· | 3% | ·N·L····· | 17% | ·······A·· | 25% | ||||
| ·······A· | 3% | T····L··· | 2% | ··S····R·· | 2% | LN······· | 11% | E······A·· | 5% | ||||||||||
| ·H······· | 7% | ||||||||||||||||||
| ·RA······ | 4% | ||||||||||||||||||
| VN······· | 2% | ||||||||||||||||||
| 8.5 | ·······V· | 75% | ········· | 100% | ·····L··· | 55% | V·R······ | 97% | ········· | 98% | ··G····R·T | 69% | L········ | 49% | LN······· | 71% | E········· | 61% | |
| ········· | 22% | ········· | 41% | V·RK····· | 1.5% | ····N···· | 2% | ··G····R·· | 31% | L·T······ | 21% | ·N·L····· | 21% | E······A·· | 22% | ||||
| ······R·· | 1.6% | T····L··· | 2% | ··R······ | 1.2% | L···L···· | 17% | ·N······· | 7% | ·······A·· | 17% | ||||||||
| ·······A· | 1.5% | L···F···· | 14% | ||||||||||||||||
| HLA association | HLA-C*03 | HLA-B*42 | |||||||||||||||||
| Escape variant | Y303X | R71X | |||||||||||||||||
| q value | 4 × 10-18 |
| 0.25 | 100% | 100% | 100% | 68% | 100% | 85% | 86% | 100% | 100% | ||||||||||
| 22% | 15% | 13% | |||||||||||||||||
| 4% | |||||||||||||||||||
| 3% | |||||||||||||||||||
| 6 | 100% | 100% | 93% | 97% | 100% | 55% | 36% | 100% | 100% | ||||||||||
| 4% | 2% | 29% | 29% | ||||||||||||||||
| 2% | 13% | 29% | |||||||||||||||||
| 1.6% | 5% | ||||||||||||||||||
| 0.2 | 100% | 100% | 53% | 100% | 100% | 100% | 100% | 94% | 40% | ||||||||||
| 47% | 6% | 36% | |||||||||||||||||
| 18% | |||||||||||||||||||
| 2% | |||||||||||||||||||
| 2% | |||||||||||||||||||
| 1.1% | |||||||||||||||||||
| 2.5 | 98% | 100% | 88% | 98.6% | 91% | 51% | 100% | 76% | 61% | ||||||||||
| 2% | 12% | 1.2% | 9% | 40% | 12% | 30% | |||||||||||||
| 9% | 10% | 5% | |||||||||||||||||
| 1.3% | 4% | ||||||||||||||||||
| 5 | 58% | 100% | 82% | 86% | 91% | 82% | 96% | 59% | 70% | ||||||||||
| 39% | 16% | 13% | 9% | 14% | 3% | 17% | 25% | ||||||||||||
| 3% | 2% | 2% | 11% | 5% | |||||||||||||||
| 7% | |||||||||||||||||||
| 4% | |||||||||||||||||||
| 2% | |||||||||||||||||||
| 8.5 | 75% | 100% | 55% | 97% | 98% | 69% | 49% | 71% | 61% | ||||||||||
| 22% | 41% | 1.5% | 2% | 31% | 21% | 21% | 22% | ||||||||||||
| 1.6% | 2% | 1.2% | 17% | 7% | 17% | ||||||||||||||
| 1.5% | 14% | ||||||||||||||||||
| HLA association | HLA-C*03 | HLA-B*42 | |||||||||||||||||
| Escape variant | Y303X | R71X | |||||||||||||||||
| q value | 4 × 10-18 |
Mother 517-M: A*30:02+ B*42+/B*15:10− C*03-ve. Child 517-C: A*30:02+ B*42+/B*15:10+ C*03+. Footprints associated with the HLA class I allele are indicated below the table; known escape variants and q values indicating significance of an HLA-polymorphism association are shown (Carlson et al., 2014). 517-M indicates mother of the child 517-C. Frequency represents percentage at which a particular haplotype is present at the indicated time point.
HLA-B*15:10–restricted Vif epitope is WI9 (WHLGHGVSI, residues 79–87; in bold), but HLA-B*15:10–associated polymorphisms are at the residue 85 (V85A) within the epitope and at the residue 78 (D78E) upstream of the epitope.
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