31 subjects with sufficient viable cells studied for T cell and MAIT cell phenotype * One subject was excluded from CD38+HLA-DR+ T cell analysis 30 subjects.

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31 subjects with sufficient viable cells studied for T cell and MAIT cell phenotype * One subject was excluded from CD38+HLA-DR+ T cell analysis 30 subjects (26 matched) with sufficient viable cells studied for T cell and MAIT cell phenotype * One subject was excluded from CD38+HLA-DR+ T cell analysis 27 subjects with sufficient viable cells studied for T cell and MAIT cell phenotype 37 HIV infected subjects of the Core 01/Phaedra cohort recruited from Sydney and Melbourne 30 laboratory workers recruited as controls Early HIV cohort: Frozen PBMC samples from all 37 HIV infected subjects; (77% of subjects within 6 months of seroconversion) Chronic HIV cohort: Frozen PBMC samples from 32 matched HIV infected subjects: (PBMC collected approx. 21 months after Early sample) (HIV negative or control cohort): Frozen PBMC from 30 HIV- untested laboratory donors A second sample from 10 subjects was analysed phenotypically using MR1tetramers An aliquot of the above was activated with MR1 ligands * One sample was excluded due to poor viability after activation A second sample from 10 subjects was analysed phenotypically using MR1tetramers An aliquot of the above was activated with MR1 ligands Supplementary FIG 1. Sample selection for HIV infected and HIV uninfected subjects. Subjects enrolled in the Core 01/Phaedra cohort were antiretroviral therapy naïve subjects who were recruited between the years of PBMC samples were stored frozen in liquid nitrogen. PBMC from subjects who served as HIV negative controls were stored frozen in liquid nitrogen for at least one week prior to thawing and phenotype staining. Samples with high proportions of dead cells in flow cytometry analysis were excluded from further study. Each sample was subjected to phenotypic and functional studies. * On average, subjects had 2.7 x 10 5 doublet excluded, live cells within the lymphocyte gate. Subjects with fewer than 65,000 live cells within the lymphocyte gate were excluded from further analysis.

a b ControlsEarly HIV Chronic HIV p=ns (0.121) p=0.001 p<0.001 p=0.024 p=0.001 ControlsEarly HIV Chronic HIV ControlsEarly HIV Chronic HIV Early HIV p=ns (0.059) p=0.024 p=ns (0.247) Chronic HIV Early HIV Chronic HIV Early HIV Chronic HIV Supplementary FIG 2. Reduction in MAIT cell numbers throughout HIV infection. MAIT cell numbers were calculated by multiplying the proportion of MAIT cells (in Fig 2 within manuscript) by the number of lymphocytes present by full blood examination (in the HIV-infected samples) or by the average lymphocyte count in blood in the controls. a. shows numbers of CD4, CD8 and DN Va7.2 + CD161 + T cell numbers across the 3 cohorts and b. shows a paired analysis of the HIV-infected subjects followed from early to chronic infection.

r= –0.305 p= r= –0.106 p= r= –0.350 p= r= –0.234 p= r= –0.044 p= r= p= r= –0.193 p= r= –0.038 p= a b c d e f g h Supplementary FIG 3. Relationship between MAIT cells and HIV disease progression markers. Correlation plots of total MAIT cells (V  CD161 + T cells) and plasma viral load in the (a) Early HIV cohort and (d) Chronic HIV cohort. Correlations between plasma viral load of the Early HIV cohort and (b) CD8 + MAIT cells or (c) DN MAIT cells (expressed as percentages of total T cells). Correlations between total MAIT cells and total CD4 + T cell counts for the (e) Early HIV cohort or (f) Chronic HIV cohort. Correlations between total MAIT cells and total activated T cells for the (g) Early HIV cohort or (h) Chronic HIV cohort.

MR1:5-OP-RUtet CD161 ControlsChronic HIVControlsChronic HIV Backgated IFN  or TNF expression from MR1tet + CD161 dim cells among lymphocytes Chronic HIVHealthy control Gated on MR1tet + CD161 dim lymphocytes ab p=0.007 p=0.009 Supplementary FIG 4. Activated MAIT cells partially downregulate CD161 and the TCR. (a) Intracellular cytokine expression from MR1:5-OP-RUtet + CD161 dim cells back-gated onto total lymphocytes. (b) IFN  or TNF expression from Healthy controls or Chronic HIV cohorts expressed as proportions or cell counts. (c) Gating of total T cells double positive for MR1:5-OP-RUtet and CD161 (high). (d) Intracellular IFN  or TNF expression from gated cells in Healthy controls and Chronic HIV cohort. Bars represent medians. Healthy controls or Chronic HIV cohorts expressed as proportions or cell counts. A Mann-Whitney test was applied to each data set. (e) Intracellular expression from MR1:5-OP-RUtet + CD161 + lymphocytes of one subject from each of the Healthy controls or Chronic HIV cohorts, backgated onto total lymphocytes to demonstrate that the most cytokine expressing cells are CD3–. Bars represent medians. A Mann-Whitney test was applied to each data set. Chronic HIVHealthy control MR1:5-OP-RUtet Gated on lymphocytesGated on T cells c Gated on lymphocytesGated on T cells CD3 CD161 MR1:5-OP-RUtetCD3 CD161 93% 73% 0.08%0.38% p=0.041 p=0.011 d(i) ControlsChronic HIVControlsChronic HIV CD3 Backgated IFN  or TNF expression from MR1tet + CD161 +(high) cells within lymphocytes Chronic HIVHealthy control e MR1:5-OP-RUtet p=0.010 ControlsChronic HIV ControlsChronic HIV p=0.008 p=ns ControlsChronic HIVControlsChronic HIV p=ns d(ii)