Table S1. - PLOS

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Env. o o doo o do. NA. 31. NA. 32. SVINRVRQGYSPLSF Env-SF15. PVVSTQLLLNGSLAE Env-PE15. QYNLLRAIEAQQHLL. Env-QL15. FVVLSIVNRVRQGYS ...
Table S1: Peptide sequences and percentages of responses Peptide No Gag 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Pol 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 Env 31 32 33 34

Peptide sequence

Peptide abbrevation

ELISPOT Pool

% of individuals with CD4+ response

Number of individuals Median frequency§ & IQR Number of predicted with CD4+ responses of CD4+ responses HLA restrictions

RWIILGLNKIVRMYS GLNKIVRMYSPVSIL GLNKIVRMYSPTSIL ILGLNKIVRMYSPVS PSHKARVLAEAMSQA VDRFYKTLRAEQASQ IVRMYSPVSILDIKQ NWMTDILLVQNANPD FSPEVIPMFSALSEG WIILGLNKIVRMYSP DVYKRWIILGLNKIV EVKNWMTDTLLVQNA YMIKHIVWASRELER IYKRWIILGLNKIVR ESFRDYVDRFYKTLR

Gag-RS15 Gag-GL15 Gag-GL15_T12 Gag-IS15 Gag-PA15 Gag-VQ15 Gag-IQ15 Gag-ND15 Gag-FG15 Gag-WP15 Gag-DV15 Gag-EA15 Gag-YA15 Gag-IR15 Gag-ER15

E F F F F G G G G H H H H I I

13.2 15.8 26.3 21.1 15.8 50 21.1 13.2 23.7 10.5 15.8 5.3 10.5 13.2 7.9

5 6 10 8 6 19 8 5 9 4 6 2 4 5 3

0.034 (0.026-0.11) 0.067 (0.044-0.20) 0.048 (0.034-0.11) 0.027 (0.024-0.084) 0.048 (0.029-0.094) 0.032 (0.020-0.043) 0.035 (0.028-0.040) 0.034 (0.019-0.043) 0.042 (0.030-0.049) 0.056 (0.037-0.09) 0.039 (0.019-0.13) 0.065 (0.047-0.083) 0.033 (0.014-0.057) 0.029 (0.017-0.032) 0.040 (0.011-0.058)

11 15 22 16 8 40 26 6 13 8 11 2 9 10 4

IPEWEFVNTPPLVKL SWTVNDIQKLVGKLV HLKTAVQMAVYIHNF KWEFVNTPPLVKLWY QYALGIIQAQPDRSE ISKFRVYYRDSRDPI NFPISPIETVPVKLR PSGLKKKKSVTVLDM VTSGYIEAEVIPAET IWQLDCTHLEGKVIL QGWKGSPAIFQSSMT EWEFVNTPPLVKLWY VHDIQKLVGKLNWAS KSVTVLDVGDAYFSV HTAGLKKKKSVTVLD

Pol-IL15 Pol-SV15 Pol-HF15 Pol-KY15 Pol-QE15 Pol-II15 Pol-NR15 Pol-PM15 Pol-VT15 Pol-IL15(2) Pol-QT15 Pol-EY15 Pol-VS15 Pol-KV15 Pol-HD15

I I J J J J K K K K L L L L M

7.9 2.6 7.9 2.6 0 2.6 2.6 2.6 2.6 0 0 5.3 2.6 0 0

3 1 3 1 0 1 1 1 1 0 0 2 1 0 0

0.038 (0.020-0.047) 0.091 (0.091-0.091) 0.050 (0.030-0.065) 0.034 (0.034-0.034) 0 (0-0) 0.10 (0.10-0.10) 0.089 (0.089-0.089) 0.032 (0.032-0.032) 0.11 (0.11-0.11) 0 (0-0) 0 (0-0) 0.11 (0.044-0.18) 0.068 (0.068-0.068) 0 (0-0) 0 (0-0)

8 1 5 2 NA 2 1 1 2 NA NA 6 1 NA NA

SVINRVRQGYSPLSF PVVSTQLLLNGSLAE QYNLLRAIEAQQHLL FVVLSIVNRVRQGYS

Env-SF15 Env-PE15 Env-QL15 Env-FS15

M M M N

0 2.6 0 5.3

0 1 0 2

0 (0-0) 0.073 (0.073-0.073) 0 (0-0) 0.065 (0.014-0.12)

NA 2 NA 5

35 36 37 38 39 40 41 42 43 44 45 Nef 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Tat 61 62 63 64

AVERYLKDQQLLGIW RTFIMIVGGLIGLRI WVTVYYGVPVWKEAE AVERYLRDQQLLGIW RVVEREKRAVGLLGA LTEGEIIIRSENLTN TVWGIKQLQARVLAV WVTVYYGVPVWKDAE FYAARKIIGDIRQAH GIKQLQARVLAVERY IVQQQSNLLRAIKAQ

Env-AW15 Env-RI15 Env-WE15 Env-AW15_L7 Env-RA15 Env-LN15 Env-TV15 Env-WE15_D13 Env-FH15 Env-GY15 Env-IQ15

FPVRPQVPLRPMTYR AVDLSHFLKEKGGLM GWPFKLVPVDPREVQ GWFLKEKGGLDGLIY EVLMWKFDSRLAFHH SWFLKEKGGLEGLIY EVLMWKFDSRLALTH KWSKNRIVGWPAVRE QVPLRPMTYKGALDL GKWSKSSIVGWSAVR RWEFDSSLARRHLAR EVLVWRFDSRLAFHH GWCFKLVPVEPEEVE GWCFKLVPVDPDEVE GLDGLIYSKKRQEIL ITKALGISYGRKKRR CFLKKGLGISYGRKK SYHCLVCFQTKGLGI DHQNLISKQPLPRTQ

§ % of total CD4+ T cells

N N N O O O O P P P P

0 2.6 0 0 0 0 0 2.6 0 5.3 0

0 1 0 0 0 0 0 1 0 2 0

0 (0-0) 0.087 (0.087-0.087) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-0) 0.020 (0.020-0.020) 0 (0-0) 0.022 (0.016-0.028) 0 (0-0)

NA 3 NA NA NA NA NA 2 NA 5 NA

Nef-FR15 B Nef-AM15 B Nef-GQ15 B Nef-GY15 B Nef-EH15 C Nef-SY15 C Nef-EH15_L12_T13 C Nef-KE15 C Nef-QL15 D Nef-GR15 D Nef-RR15 D Nef-EH15_V4_R6 D Nef-GE15 E Nef-GE15_D10_D12 E Nef-GL15 E

21.1 13.2 5.3 13.2 28.9 10.5 23.7 2.6 5.3 5.3 2.6 7.9 2.6 7.9 0

8 5 2 5 11 4 9 1 2 2 1 3 1 3 0

0.031 (0.024-0.061) 0.067 (0.043-0.090) 0.022 (0.013-0.031) 0.017 (0.011-0.027) 0.038 (0.029-0.053) 0.060 (0.049-0.068) 0.039 (0.033-0.050) 0.025 (0.025-0.025) 0.049 (0.020-0.079) 0.079 (0.043-0.12) 0.067 (0.067-0.067) 0.026 (0.024-0.056) 0.028 (0.028-0.028) 0.060 (0.036-0.11) 0 (0-0)

5 6 3 4 22 1 22 1 0 4 2 4 NA (donor not typed) 5 NA

Tat-IR15 Tat-CK15 Tat-SI15 Tat-DQ15

2.6 0 7.9 5.3

1 0 3 2

0.086 (0.086-0.086) 0 (0-0) 0.038 (0.016-0.067) 0.035 (0.016-0.053)

3

A A A A

4 3