Table 3 Nef mutations with significant frequency changes across V_E and V_L and their associated epitopes

EC11

V133P

70.7

B49

Nef (136–145)

PLTFGWCYKL

A

F191 V

85.5

B81

Nef (183–192)

WRFDSRLAFH

I

EC42

V10R

99.0

B15

Nef (13–20)

WPAIRERM

A

V10 K

0.0

B15

Nef (13–20)

WPAIRERM

A

G12R

0.0

B15

Nef (13–20)

WPAIRERM

A

M79I

0.0

B51/B15

Nef (72–81)/Nef (75–82)

PQVPLRPMTY/PLRPMTYK

I

N126S

99.2

B51

Nef (120–128)

YFPDWQNYT

I

Y135F

99.2

B15

Nef (137–145)

LTFGWCFKL

A

G140R

0.0

B15

Nef (137–145)

LTFGWCFKL

I

V148I

99.2

B15

Nef (137–145)

LTFGWCFKL

A

EC18

K92R

0.0

B07

Nef (83–91)/Nef (90–97)

AAVDLSHFL/FLKEKGGL

A/I

VC06

V85I

V^a

B15

Nef (84–92)

AVDLSHFLK

I

V85L

V^a

B15

Nef (84–92)

AVDLSHFLK

I

L87I

L^a

B15

Nef (84–92)

AVDLSHFLK

I

R105 K

R^a

B15

Nef (106–114)

RQDILDLWI

A

I114 V

I^a

B15

Nef (106–114)/Nef (116–124)

RQDILDLWI/HTQGYFPDW

I/A

VC10

T15A

59.2

B15

Nef (13–20)

WPTVRERM

I

E182Q

99.9

B15

Nef (183–191)

WRFDSRLAF

A

E182L

0.0

B15

Nef (183–191)

WRFDSRLAF

A

R188G

99.8

B15/B52

Nef (183–191)/Nef (188–196)

WRFDSRLAF/RLAFHHVAR

I

VC14

T71R

94.5

B42

Nef (71–79)

RPQVPLRPM

I

I101 V

5.2

B44

Nef (92–100)

KEKGGLEGL

A

H102Y

4.9

B44

Nef (92–100)/Nef (105–115)

KEKGGLEGL/KRQEILDLWVY

A

H102 N

2.0

B44

Nef (92–100)/Nef (105–115)

KEKGGLEGL/KRQEILDLWVY

A

H116 N

94.5

B44

Nef (105–115)

KRQEILDLWVY

A

P129Q

5.7

B42

Nef (128–137)

TPGPGVRYPL

I

V133I

5.2

B42

Nef (128–137)

TPGPGVRYPL

I

VC15

V85L

66.8

B57

Nef (82–90)

KAAFDLSFF

I

H102Y

68.4

B57

Nef (105–115)

KRQEILDLWVY

A

VC16

Y81F

54.3

B57

Nef (82–90)

KAAFDLSFF

A

H89Y

0.0

B57

Nef (82–90)/Nef (90–97)

KAAFDLSFF/FLKEKGGL

I/A

H102Y

99.9

B14/B57

Nef (105–113)/Nef (105–115)

QRQDILDLW/KRQEILDLWVY

A

H116 N

63.4

B57

Nef (105–115)/Nef (116–124)

KRQEILDLWVY/HTQGYFPDW

A/I

V133T

99.4

B57

Nef (127–135)

YTPGPGIRY

I

V133I

0.0

B57

Nef (127–135)

YTPGPGIRY

I