Table 2 Gag mutations with significant frequency changes across VE and VL and their associated epitopes
Patient | Mutation | Frequency (%) | Epitope | ||||
|---|---|---|---|---|---|---|---|
VE | VL | HLA | Position | Sequence | Location | ||
EC02 | A83S | 0.0 | 22.9 | B52 | Gag (74–82) | ELRSLYNTV | A |
S278C | 0.0 | 22.8 | B52 | Gag (275–282) | RMYSPTSI | I | |
EC11 | K26R | 0.0 | 94.1 | B81 | Gag (19–27) | IRLRPGGKK | I |
EC42 | E40Q | Ea | 17.7 | B51 | Gag (36–44) | WASRELERF | I |
N126S | Sa | 79.9 | B15 | Gag (127–135) | QVSQNYPIV | A | |
N126R | Sa | 21.0 | B15 | Gag (127–135) | QVSQNYPIV | A | |
EC18 | K28Q | 33.9 | 0.0 | B07 | Gag (22–30) | RPGGKKHYM | I |
K28R | 65.9 | 99.6 | B07 | Gag (22–30) | RPGGKKHYM | I | |
I34L | 21.0 | 99.8 | B52 | Gag (34–44) | LVWASRELERF | I | |
R39K | 0.0 | 99.5 | B52 | Gag (34–44) | LVWASRELERF | I | |
R43Q | 17.2 | 0.0 | B52 | Gag (34–44) | LVWASRELERF | I | |
R76K | 20.2 | 0.0 | B07 | Gag (71–79) | GSEELRSLY | I | |
T280A | 79.7 | 0.0 | B07/B52 | Gag (274–282)/Gag (275–282) | VRMYSPVSI/RMYSPTSI | I | |
T280V | 19.9 | 0.0 | B07/B52 | Gag (274–282)/Gag (275–282) | VRMYSPVSI/RMYSPTSI | I | |
T280S | 0.0 | 99.7 | B07/B52 | Gag (274–282)/Gag (275–282) | VRMYSPVSI/RMYSPTSI | I | |
VC10 | N126S | 0.7 | 94.2 | B15 | Gag (127–135) | QVSQNYPIV | A |
N126S | 0.0 | 5.6 | B15 | Gag (127–135) | QVSQNYPIV | A | |
A146P | 39.9 | 37.6 | B15 | Gag (144–152)/Gag (147–155) | HQAISPRTL/ISPRTLNAW | I | |
A146S | 59.3 | 62.4 | B15 | Gag (144–152)/Gag (147–155) | HQAISPRTL/ISPRTLNAW | I | |
S173T | 43.1 | 67.5 | B15 | Gag (168–175) | VIPMFSAL | I | |
I223V | 41.6 | 32.4 | B15 | Gag (226–236) | GQMREPRGSDI | A | |
T280S | 45.3 | 66.7 | B15/B52 | Gag (274–282)/Gag (275–282) | VRMYSPTSI/RMYSPTSI | I | |
T280I | 52.7 | 17.4 | B15/B52 | Gag (274–282)/Gag (275–282) | VRMYSPTSI/RMYSPTSI | I | |
VC14 | V82I | 99.7 | 77.9 | B44 | Gag (78–86) | LYNTVATLY | I |
C87Y | 97.4 | 99.7 | B44 | Gag (78–86) | LYNTVATLY | A | |
I147L | 99.7 | 81.1 | B42 | Gag (144–152) | HQAISPRTL | I | |
S310T | 99.7 | 81.1 | B44 | Gag (306–316) | AEQASQDVKNW | I | |
VC15 | V82I | 43.4 | 84.9 | B57 | Gag (76–86) | RSLYNTVATLY | I |
D121A | 30.6 | 81.8 | B57 | Gag (114–122) | KTQQAAADK | I | |
T122A | 49.2 | 82.1 | B57 | Gag (114–122) | KTQQAAADK | I | |
H124N | 59.7 | 0.0 | B57 | Gag (114–122) | KTQQAAADK | A | |
N271T | 0.0 | 24.7 | B57 | Gag (274–282) | VRMYSPVSI | A | |
T280V | 1.8 | 98.8 | B57 | Gag (274–282) | VRMYSPVSI | I | |
VC16 | I34L | 32.2 | 0.0 | B57 | Gag (34–44) | LVWASRELERF | I |
V35I | 32.6 | 0.0 | B57 | Gag (34–44) | LVWASRELERF | I | |
V46I | 29.3 | 0.0 | B57 | Gag (34–44) | LVWASRELERF | A | |
V82L | 25.9 | 0.0 | B57 | Gag (76–86) | RSLYNTVATLY | I | |
A118P | 24.9 | 0.0 | B57 | Gag (114–122) | KTQQAAADK | I | |
A119T | 24.9 | 0.0 | B57 | Gag (114–122) | KTQQAAADK | I | |
T122A | 4.8 | 71.6 | B57 | Gag (114–122) | KTQQAAADK | I | |
G123K | 24.7 | 0.0 | B57 | Gag (114–122) | KTQQAAADK | A | |
H124N | 99.1 | 64.4 | B57/B14 | Gag (114–122)/Gag (127–135) | KTQQAAADK/QVSQNYPIV | A | |
H124S | 0.7 | 35.3 | B57/B14 | Gag (114–122)/Gag (127–135) | KTQQAAADK/QVSQNYPIV | A | |
S125R | 30.9 | 0.0 | B57/B14 | Gag (114–122)/Gag (127–135) | KTQQAAADK/QVSQNYPIV | A | |
Q127H | 76.7 | 98.3 | B14 | Gag (127–135) | QVSQNYPIV | I | |
I138L | 75.5 | 94.1 | B14 | Gag (127–135) | QVSQNYPIV | A | |
A146P | 74.6 | 99.4 | B57 | Gag (145–155) | QAISPRTLNAW | I | |
A163G | 78.3 | 75.4 | B14/B57 | Gag (160–168)/Gag (162–172) | EEKAFSPEV/KAFSPEVIPMF | I | |
S165N | 77.6 | 75.0 | B14/B57 | Gag (160–168)/Gag (162–172) | EEKAFSPEV/KAFSPEVIPMF | I | |
V168T | 0.0 | 22.8 | B14/B57 | Gag (160–168)/Gag (162–172) | EEKAFSPEV/KAFSPEVIPMF | I | |
S173T | 37.7 | 74.1 | B57 | Gag (162–172) | KAFSPEVIPMF | A | |
V191I | 33.3 | 99.4 | B14 | Gag (183–191) | DLNMMLNIV | I | |
T242N | 78.4 | 99.5 | B57 | Gag (240–249) | TSTLQEQIGW | I | |
D295N | 0.0 | 9.9 | B14 | Gag (298–306) | DRFFKTLRA | A | |
K335R | 49.2 | 58.9 | B14 | Gag (329–337) | DCKTILKAL | I | |
A340G | 70.9 | 96.6 | B14 | Gag (329–337) | DCKTILKAL | A | |