Supplementary Table 3. Brazilian Sample Vs. 1000 Genomes Populations Comparison

Supplementary Material

Supplementary Table 1. Allelic and genotypes frequencies of TRIM5 SNPs in HIV-1+ patients and healthy controls from Northeast Brazil stratified according to CCR5 genotypes.
SNPs / Healthy Controls
n (%) / HIV-1 Patients
n (%) / Fisher’s Exact Test
OR (95%CI), p-value
rs16934386 (5’UTR)
CCR5/CCR5 / A / 418 (97.2) / 389 (97.7) / Reference
G / 12 (2.8) / 9 (2.3) / 0.81 (0.30-2.11), 0.665
AA / 203 (94.4) / 190 (95.5) / Reference
AG / 12 (5.6) / 9 (4.5) / 0.80 (0.29-2.13), 0.660
CCR5/CCR5∆32 / A / 36 (94.7) / 27 (96.4) / Reference
G / 2 (5.3) / 1 (3.6) / 0.67 (0.01-13.51), 1.000
AA / 17 (89.5) / 13 (92.9) / Reference
AG / 2 (10.5) / 1 (7.1) / 0.66 (0.01-14.04), 1.000
rs3740996 (H43Y)
CCR5/CCR5 / H / 402 (93.5) / 359 (90.2) / Reference
Y / 28 (6.5) / 39 (9.8) / 1.56 (0.91-2.69), 0.097
HH / 187 (87.0) / 162 (81.4) / Reference
HY / 28 (13.0) / 35 (17.6) / 1.44 (0.81-2.58), 0.217
YY / 0 (0.0) / 2 (1.0) / nc
CCR5/CCR5∆32 / H / 31 (81.6) / 24 (85.7) / Reference
Y / 7 (18.4) / 4 (14.3) / 0.74 (0.14-3.33), 0.747
HH / 12 (63.2) / 10 (71.4) / Reference
HY / 7 (36.8) / 4 (28.6) / 0.69 (0.11-3.75), 0.719
rs10838525 (R136Q)
CCR5/CCR5 / R / 274 (63.7) / 304 (75.2) / Reference
Q / 156 (36.3) / 100 (24.8) / 0.58 (0.42-0.79), 0.0003*
RR / 89 (41.1) / 112 (55.4) / Reference
RQ / 96 (44.7) / 80 (39.6) / 0.66 (0.43-1.01), 0.050
QQ / 30 (14.0) / 10 (5.0) / 0.27 (0.11-0.60), 0.0004*
CCR5/CCR5∆32 / R / 25 (65.8) / 19 (86.4) / Reference
Q / 13 (34.2) / 3 (13.6) / 0.31 (0.05-1.35), 0.130
RR / 7 (36.8) / 8 (72.7) / Reference
RQ / 11 (57.9) / 3 (27.3) / 0.60 (0.08-3.77), 0.694
QQ / 1 (5.3) / 0 (0.0) / nc
*Significant p-value after Bonferroni correction (p<0.017); nc=not calculated
Supplementary Table 2. Adjusted for sex and age logistic regression model of TRIM5 genotypes influence over HIV-1 infection susceptibility
Variable / OR / 95% CI / p-value
Sex / 1.07 / 0.69-1.67 / 0.750
Age / 1.06 / 1.04-1.08 / <0.001*
rs10838525 – RQ / 0.72 / 0.48-1.09 / 0.120
rs10838525 - QQ / 0.33 / 0.14-0.78 / 0.011*
rs3740996 - HY / 0.88 / 0.52-1.47 / 0.620
rs3740996 - YY / 1.83 / 0.14-23.81 / 0.650
rs16934386 -AG / 0.65 / 0.25-1.7 / 0.380
* Significant p-value

Supplementary Table 3. Brazilian Sample vs. 1000 Genomes Populations Comparison

SNPs / Brazilian / 1000 genomes database / Chi-squared test with Yates’continuity corretion
X-squared, p-value
HC / HIV / AFR / AMR / EUR / HC vs. AFR / HC vs. AMR / HC vs. EUR / HIV vs. AFR / HIV vs. AMR / HIV vs. EUR
rs16934386
A / 456 (97.4) / 418 (98.1) / 1210
(91.5) / 688
(99.1) / 1006
(100.0) / Reference
G / 12
(2.6) / 8
(1.9) / 112
(8.5) / 6
(0.9) / 0
(0.0) / 17.81,
2.446e-05 * / 4.24,
0.039 * / 22.93,
1.682e-06 * / 15.77,
7.16e-05 * / 1.45,
0.228 / 15.77,
7.16e-05 *
AA / 222 (94.9) / 205 (96.2) / 554
(83.8) / 341
(98.3) / 503
(100.0) / Reference
AG / 12
(5.1) / 8
(3.8) / 102
(10.2) / 6
(1.7) / 0
(0.0) / 15.85,
6.868e-05 * / 4.30,
0.038 * / 23.12,
1.524e-06 * / 19.17,
1.194e-05 * / 1.47,
0.225 / 15.86,
6.831e-05*
GG / 0
(0.0) / 0
(0.0) / 5
(0.8) / 0
(0.0) / 0
(0.0) / 0.840,
0.359 / nc / nc / 0.73,
0.394 / nc / Nc
rs3740996 (H43Y)
H / 424 (90.6) / 381 (89.4) / 1270
(96.1) / 584
(84.1) / 885
(88.0) / Reference
Y / 44
(9.4) / 45 (10.6) / 52
(3.9) / 110
(15.9) / 121
(12.0) / 19.3,
1.12e-05 * / 9.56,
0.002 * / 1.96,
0.162 / 25.77,
3.847e-07 * / 5.75,
0.016 * / 0.49,
0.483
HH / 191 (81.7) / 170 (79.8) / 612
(92.6) / 245
(70.6) / 390
(77.5) / Reference
HY / 42
(17.9) / 41 (19.3) / 46
(7.0) / 94
(27.1) / 105
(20.9) / 22.32,
2.313e-06 * / 6.65,
0.001 * / 0.81,
0.368 / 26.08,
3.272e-07 * / 4.40,
0.036* / 0.19,
0.665
YY / 1
(0.4) / 2
(0.9) / 3
(0.5) / 8
(2.3) / 8
(1.6) / 1.464e-29,
1.000 / 2.62,
0.105 / 1.05,
0.306 / 0.19,
0.658 / 1.02,
0.313 / 0.13,
0.719
rs10838525 (R136Q)
R / 315 (67.3) / 322 (75.6) / 1186
(89.7) / 531
(76.5) / 619
(61.5) / Reference
Q / 153 (32.7) / 104 (24.4) / 136
(10.3) / 163
(23.5) / 387
(38.5) / 126.51,
2.2e-16 * / 11.50,
0.0007 * / 4.35,
0.037 * / 53.09,
3.19e-13 * / 0.08,
0.779 / 25.62,
4.15e-07 *
RR / 105 (44.9) / 118 (55.4) / 533
(80.6) / 207
(59.7) / 193
(38.4) / Reference
RQ / 105 (44.9) / 86 (40.4) / 120
(18.2) / 117
(33.7) / 233
(46.3) / 80.81,
<2.2e-16 * / 9.55,
0.002 * / 1.06,
0.302 / 46.85,
7.678e-12 * / 1.69,
0.194 / 8.18,
0.004 *
QQ / 24
(10.2) / 9
(4.2) / 8
(1.2) / 23
(6.6) / 77
(15.3) / 63.46,
1.636e-15 * / 4.65,
0.031 * / 4.03,
0.045 * / 10.88,
0.001 * / 0.53,
0.466 / 22.13,
2.54e-06 *
*significant p-value
NC = Not calculated.
HC = Healthy controls individuals.
HIV= HIV-1 positive individuals.
AFR = African (African Caribbean in Barbados; African Ancestry in Southwest US, Esan in Nigeria; Gambian in Western Division, The Gambia; Luhya in Webuye, Kenya; Mende in Sierra Leone; Yoruba in Ibadan, Nigeria).
AMR = American (Colombian in Medellin, Colombia; Mexican Ancestry in Los Angeles, California; Peruvian in Lima, Peru; Puerto Rican in Puerto Rico).
EUR = European (Utah residents with Northern and Western European ancestry; Finnish in Finland; British in England and Scotland; Iberian populations in Spain; Toscani in Italy).

Supplementary Table 4. Brazilian Sample vs. HapMap Populations Comparison

SNPs / Brazilian / HapMap database / Chi-squared test with Yates’continuity corretion
X-squared value, p-value
HC / HIV / CEU / CHB / YRI / HC vs.
CEU / HC vs. CHB / HC vs. YRI / HIV vs. CEU / HIV vs.CHB / HIV vs. YRI
rs16934386
A / 456 (97.4) / 418 (98.1) / 158
(100.0) / 82
(100.0) / - / Reference
G / 12
(2.6) / 8
(1.9) / 0
(0.0) / 0
(0.0) / - / 2.88,
0.090 / 1.12,
0.291 / Nc / 1.78,
0.182 / 0.59,
0.443 / nc
AA / 222 (94.9) / 205 (96.2) / 79
(100.0) / 41
(100.0) / - / Reference
AG / 12
(5.1) / 8
(3.8) / 0
(0.0) / 0
(0.0) / - / 2.94,
0.086 / 1.14,
0.285 / Nc / 1.80,
0.179 / 0.58,
0.440 / nc
GG / 0
(0.0) / 0
(0.0) / 0
(0.0) / 0
(0.0) / - / nc / nc / Nc / Nc / nc / nc
rs3740996 (H43Y)
H / 424 (90.6) / 381 (89.4) / 197
(87.2) / 236
(86.1) / 281
(95.8) / Reference
Y / 44
(9.4) / 45 (10.6) / 29
(12.8) / 38
(13.9) / 13
(4.4) / 1.56,
0.212 / 3.07,
0.080 / 5.77,
0.016 * / 0.55,
0.460 / 1.44,
0.230 / 8.05,
0.004 *
HH / 191 (81.7) / 170 (79.8) / 86
(76.1) / 100
(73.0) / 134
(91.2) / Reference
HY / 42
(17.9) / 41 (19.3) / 25
(22.1) / 36
(26.3) / 13
(8.8) / 0.70,
0.401 / 3.18,
0.074 / 5.42,
0.020 * / 0.26,
0.612 / 1.98,
0.159 / 6.78,
0.009 *
YY / 1
(0.4) / 2
(0.9) / 2
(1.8) / 1
(0.7) / 0
(0.0) / 0.48,
0.486 / 1.766e-28,
1.000 / 4.820e-28,
1.000 / 0.02,
0.876 / 8.353e-29,
1.000 / 0.28,
0.591
rs10838525 (R136Q)
R / 315 (67.3) / 322 (75.6) / 143
(63.3) / 262
(96.3) / 260
(89.0) / Reference
Q / 153 (32.7) / 104 (24.4) / 83
(36.7) / 10
(3.7) / 32
(11.0) / 0.93,
0.334 / 82.64,
<2.2e-16 * / 44.94,
2.027e-11 * / 10.35
0.001 * / 50.73,
1.059e-12 * / 19.56,
9.756e-06 *
RR / 105 (44.9) / 118 (55.4) / 43
(38.1) / 126
(92.6) / 117
(80.1) / Reference
RQ / 105 (44.9) / 86 (40.4) / 57
(50.4) / 10
(7.4) / 26
(17.8) / 1.06,
0.302 / 65.75,
5.126e-16 * / 35.55,
2.484e-09 * / 5.35,
0.021 * / 47.08,
6.823e-12 * / 21.02,
4.536e-06 *
QQ / 24
(10.2) / 9
(4.2) / 13
(11.5) / 0
(0.0) / 3
(2.1) / 0.27,
0.603 / 23.74,
1.102e-06 * / 15.05
0.0001 * / 8.09,
0.004 * / 7.31,
0.007 * / 1.90,
0.168
*significant p-value
NC = Not calculated.
HC = Healthy controls individuals.
HIV= HIV-1 positive individuals.
CEU = Utah residents with Northern and Western European ancestry.
CHB = Han Chinese in Beijing, China.
YRI = Yoruba in Ibadan, Nigeria.