1. Supplementary Table 1 Table S1. Population frequency of HLA -A, -B and -C alleles. Rare alleles (frequency < 0.5%) are highlighted by a grey background and alleles not listed in the Alleles Frequency Net Database (www.allelefrequency.com) in any South American population are indicated by *. KIR gene population frequencies are also included. KIR framework genes are highlighted by bold type red letters while genes determining group A haplotype are highlighted by bolded black letters.www.allelefrequency.com

2. Supplementary Table 2 Table S2. KIR genes associated with differences in median viral loads or CD4 counts. Only those genes showing statistical significant differences are shown (p<0.05, Mann-Whitney test). Only KIR2DS4f shows statistically significant association with viral load differences without being limited by low number of negative individuals. IQR: interquartile range, CI: confidence interval.

3. C*01:02 HIV+ (%) HIV- (%) 0 2 4 6 8 10 B*40:02 B*35:43A*23:01 B*57:03 HLA Allotype Population Frequency (%) 0 2 4 6 8 10 B*48:01 C*03:04 A*24:02 B*40:02 A*31:01 C*15:02 A*02:22 B*35:09 B*35:43 HLA 2-locus Haplotypes 0 5 10 15 20 25 30 2DL3 B*50:01 2DL1 B*50:01 2DP1 B*50:01 2DS3 A*02:01 2DS2 A*02:01 2DS4 C*16:01 HLA Alelle - KIR gene combination Population Frequency (%) HIV+<HIV-HIV+>HIV- HIV+<HIV-HIV+>HIV- HIV+<HIV-HIV+>HIV- p=0.029 p=0.020 p=0.012 p=0.031 p=0.005 p=0.008 p=0.024 p=0.050 p=0.012 p=0.029p=0.031p=0.032 p=0.003 p=0.038 p=0.042 Figure S1. HLA alleles and KIR genes association with HIV infection. Cohort frequencies (%) of individual HLA alleles, 2 HLA allele haplotypes and HLA-KIR combinations showing statistically significant differences between HIV infected (HIV+) or HIV uninfected (HIV-) individuals (p-values <0.05, Fisher’s exact test).

4. 3006009001200 A*30:02-B*57:03 A*30:02-C*07:01 B*57:03-C*07:01 A*30:02-B*52:01 A*02:11-B*39:14 A*02:11-C*08:01 A*11:01-B*51:01 A*11:01-C*08:01 A*31:01-C*03:04 A*30:02-C*03:04 A*03:01-C*06:02 A*24:02-C*16:01 A*03:01-C*01:02 B*39:14-C*07:02 A*02:22-B*35:43 A*02:22-C*01:02 A*02:11-B*40:04 A*02:11-C*03:04 B*39:03-C*07:02 A*30:02-C*07:02 B*15:16-C*14:02 B*39:13-C*07:02 B*40:04-C*03:04 B*39:05-C*07:02 A*31:01-C*07:02 A*24:02-B*40:04 B*48:01-C*04:01 A*02:01-B*39:05 A*02:11-B*39:09 B*35:05-C*04:01 A*02:01-C*07:01 A*02:01-C*04:01 B*35:01-C*04:01 A*02:01-B*35:01 A*30:02-C*04:01 B*35:09-C*04:01 A*02:01-B*35:09 B*08:01-C*07:01 B*40:02-C*04:01 A*31:01-B*39:14 B*35:01-C*07:02 CD4 Counts 2-locus Haplotype 123456 log10 Viral Load 0510152025 Population Frequency (%) Mann-Whitney p=0.0044 *** ** A*30:02-B*57:03 A*30:02-C*07:01 B*57:03-C*07:01 A*30:02-B*52:01 A*02:11-B*39:14 A*02:11-C*08:01 A*11:01-B*51:01 A*11:01-C*08:01 A*31:01-C*03:04 A*30:02-C*03:04 A*03:01-C*06:02 A*24:02-C*16:01 A*03:01-C*01:02 B*39:14-C*07:02 A*02:22-B*35:43 A*02:22-C*01:02 A*02:11-B*40:04 A*02:11-C*03:04 B*39:03-C*07:02 A*30:02-C*07:02 B*15:16-C*14:02 B*39:13-C*07:02 B*40:04-C*03:04 B*39:05-C*07:02 A*31:01-C*07:02 A*24:02-B*40:04 B*48:01-C*04:01 A*02:01-B*39:05 A*02:11-B*39:09 B*35:05-C*04:01 A*02:01-C*07:01 A*02:01-C*04:01 B*35:01-C*04:01 A*02:01-B*35:01 A*30:02-C*04:01 B*35:09-C*04:01 A*02:01-B*35:09 B*08:01-C*07:01 B*40:02-C*04:01 A*31:01-B*39:14 B*35:01-C*07:02 Figure S2. Viral load and CD4 counts association with HLA haplotypes. Viral load and CD4 counts were compared between HIV positive (HIV+) subjects expressing a particular 2-locus HLA haplotype (2HLA). Only 2HLA combinations showing significant differences (p<0.05 in the Mann-Whitney test) in viral loads or CD4 counts are shown. For each 2HLA, the distribution of CD4 counts is shown in the left panel, viral load in the middle panel and cohort frequency (%) in the right hand panel. 2HLA are ordered by median viral load in individuals carrying both alleles. Alleles with statistically significant (p<0.05) differences are highlighted by red box-plot if they are associated with higher viral loads or lower CD4 counts and with green box-plots if they were associated with either lower viral load or higher CD4 counts. Boxes indicate the median 25 th and 75 th quartile and whiskers the upper and lower range limits. 2HLA with p-values below 0.01 are indicated by ** and with p-values below 0.001 by ***. HIV+ individuals under treatment (N=11) were excluded from the analysis. The CD4 counts and median viral loads of the entire HIV+ cohort are indicated by the vertical dashed lines in the left and middle panels. Median population frequencies were compared among 2HLA showing higher or lower median viral loads or CD4 counts.