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Table 2 Nonsynonymous mutations in Pol CTL epitopes assessed from Sanger consensus sequences

From: Deep sequencing of the HIV-1 polymerase gene for characterisation of cytotoxic T-lymphocyte epitopes during early and chronic disease stages

    

Distribution of mutation by stage of infection

pol protein

Epitope position

Wild type CTL epitope

Escape CTL mutation

Early HIV samples: n = 15 (%)

Chronic HIV samples: n = 34 (%)

p value

PR

PR (11 – 20)

VTIKIGGQLK

I15V

73,3

59.4

0.345

PR (30 – 38)

DTVLEDMNL

M36I/L

98

79

0.702

RT

RT (33 – 41)

ALVEICTEM

V35T/K/M

100

100

N/A

RT (202 – 210)

IEELRQHLL

I202V

10

17.7

1.000

RT (269 – 277)

QIYAGIKVK

A272P/G/S*

80

55

0.345

Not within epitope RT 329

I

I329V/L

20

5.8

0.160

RT (375 – 383)

IAMESIVIW

I375V

20

11.8

0.660

IN

Not within epitope IN 206

T

T206S

20

15

0.687

IN (218 – 227)

TKIQNFRVYY

K219N/Q

10

17.6

1.000

IN (278 – 288)

DDCVASRQDED

S283D/G

100

95

1.000

  1. *Codon had significant dN/dS ratio (p value = 0.001). CTL = cytotoxic T-lymphocyte; N/A = not applicable; PR = protease; RT = reverse transcriptase; IN = integrase; Pol = polymerase