TABLE 2.
Infant CTL escape variants in the targeted Gag and Nef epitopesa
| ID | HLA | HXB2 position | Epitope sequence isolated from infant and/or mother | Mutation frequency in infant | Time point in months (infant) | Mutation frequency in mother | Time point in months (mother) | ELISPOT wild-type peptide stimulation results (infant) |
|---|---|---|---|---|---|---|---|---|
| Gag | ||||||||
| 18–26 | KIRLRPGGK | |||||||
| 258 + M | A3 | R-------- | 16/20, 11/22, 1/24 | 1,6,12 | 10/22,2/21 | Del, pn1 | (−) 3,6,12 | |
| 20–29 | RLRPGGKKKY | |||||||
| 411 + M | B15 | --------Q- | 21/22, 21/22, 12/21 | 3,6,9 | 18/21 | Del | NA | |
| 76–86 | RSLYNTVATLY | |||||||
| 135 + M | A68 | K--F-A--V-- | 20/20, 24/24, 10/10 | 6,9,12 | 3/21 | pn1 | NA | |
| 170 | A30 | K---------- | 19/19, 14/22, 5/24 | 6,9,12 | – | (−) 3,6,9,12 | ||
| 211 | A30 | K-------V-- | 21/21,11/22, 23/23, 19/19, 23/23 | 3,6,9,12,15 | – | (−) 3,6,9,12 | ||
| 411 + M | A30 | K--F-A--V-F | 22/22, 22/22, 21/21 | 3,6,9 | 21/21 | Del | (−)1,3,6,9,12 | |
| 145–155 | QAISPRTLNAW | |||||||
| 334 + M | C6 | --M-------- | 0/21, 0/18, 21/21, 23/23 | 1,3,6,9 | Not observed | Del | NA | |
| 167–175 | EVIPMFSAL | |||||||
| 334 + M | A26 | ------T-- | 21/21, 18/18, 21/21, 23/23 | 1,3,6,9 | 19/19 | Del | NA | |
| 180–188 | TPQDLNTML | |||||||
| 211 | B42 | --G------ | 21/21, 22/22, 23/23, 3/19 | 3,6,9,12 | – | NA | (−) 3,6 | |
| 211 | B42 | --A------ | 14/19 | 12 | – | NA | (+) 12 | |
| 211 | B42 | --T------ | 2/19, 23/23 | 12,15 | – | NA | (+) 12 | |
| 272–285 | YSPTSILDI | |||||||
| 135 + M | C12 | ---V----- | 20/20, 24/24, 10/10 | 6,9,12 | 21/21 | pn1 | NA | |
| 294–304 | DYVDRFYKT | |||||||
| 334 + M | A26 | ------F-I | 21/21, 18/18, 21/21, 23/23 | 1,3,6,9 | 19/19 | Del | (−) 3,6,9 | |
| 385–393 | GPKRIVKCF | |||||||
| 211 | B42 | 4/21, 11/22, 17/23, 12/19, 7/23 | 3,6,9,12,15 | – | NA | NA | ||
| 211 | B42 | -TR--I--- | 2/21, 3/19 | 6,12 | – | NA | ||
| 211 | B42 | --R------ | 7/21, 7/22, 2/23, 8/23 | 3,6,9,15 | – | NA | NA | |
| 211 | B42 | --L--I--- | 4/21 | 3 | – | NA | NA | |
| 211 | B42 | --R-M---- | 8/23 | 15 | – | NA | NA | |
| 211 | B42 | --L--I--- | 5/21 | 3 | – | NA | NA | |
| 429–437 | RQANFLGKI | |||||||
| 334 | B13 | --------L | 21/21, 18/18, 2/21, 20/23 | 1,3,6,9 | Not observed | Del | NA | |
| Nef | ||||||||
| 77–85 | RPMTFKGAF | |||||||
| 170 | A30 | S---Y-A-I | 12/24, 24/24l, 10/22, 7/12 | 3,6,9,12 | – | NA | NA | |
| 170 | A30 | S---Y-A-V | 12/24, 3/22, 3/12 | 3,9,12 | – | NA | NA | |
| 170 | A30 | S---Y-A-M | 5/22, 2/12 | 9,12 | – | NA | NA | |
| 211 | B42 | 3/20, 23/23 | 9,15 | – | NA | NA | ||
| 211 | B42 | ----Y-A-F | 23/23, 17/22 | 6,12 | – | NA | NA | |
| 211 | B42 | ---NY-A-V | 17/20, 5/22 | 9,12 | – | NA | NA | |
| 83–91 | AAVDLSHFL | |||||||
| 424 | A6802 | G-L------ | 22/22, 24/24, 12/24 | 1,3,6 | – | NA | NA | |
| 120–128 | YFPDWQNYT | |||||||
| 334 + M | B13 | -----H--- | 24/24, 10/21 | 1,3 | 24/24 | P32 | NA | |
| 334 | B13 | -----O--- | 11/21, 20/20, 23/23 | 3,6,9 | Not observed | P32 | NA |
HXB2 position, gene-specific positions, i.e., Gag and Nef separately; epitope sequences, HBX2 epitope sequences and the alignment of patient sequences in the respective epitope positions; ID, patient IDs and + M indicate the same mutation was observed in the mother sequences, if available; mutation frequency in infant, the number of infant sequences where the mutation was present for each time point in months separated by comma; frequency in mother, the number of mother sequences where the mutation was present for each time point (P32, pregnant at 32 weeks; Del, delivery; pn1, 1 month after delivery; NA, no mother sequences available), separated by comma; ELISPOT, (NA, ELISPOT assay not done; (−) negative ELISPOT observed at different months separated by comma; (+) positive ELISPOT observed at different months separated by comma).