Subtype C viruses Subtype B virusesConC 6644 RHPA 2435CAP84 32 1997 6535.3 160CAP61 F10 772 CAAN5342 40CAP85 9 682 PVO.4 40Du422.1 680 WITO4160 40ZM249M.PL1 646 QHO692.42 40Du156.12 381 THRO4156 40ZM109F.PB4 337 SC422661 40ZM214M.PL15 322 TRO.11 40CAP239 G3 293 TRJO4551 40Du151.2 243 REJO4541 40CAP206 8 136 2/11 (18%)ZM233M.PB6 106CAP256 7C 70CAP45 G3 40CAP63 A9 40 Subtype A virusesCAP88 B5 40 Q23.17 968CAP228 51 40 Q769.d22 465CAP244 D3 40 Q168.a2 361CAP255 16 40 Q842.d12 40CAP210 E8 40 Q461.e2 40Du172.17 40 3/5 (60%)ZM197M.PB7 40ZM53M.PB12 40CAP8 6F 40

14/25 (56%) Overall breadth 19/41 (46%)

CAP314 neutralization of subtype A, B and C heterologous viruses at 2 years p.i.

Nature Medicine doi:10.1038/nm.2985

Virus ID PGT128 IC50 Titer (ug/ml)

PNG 332 PNG 301

CT349_39_16 <0.001 + +CT533_T23b_36 <0.001 + +CAP174.1.06_F3_1B 0.002 + +CT072_56_7 0.002 + +CAP37.1.18_D2_19 0.004 + +Ce0665_F2 0.005 + +246F C1G 0.005 + -CT977_69_12 0.005 + +Ko756_38_Tb12 0.005 + +CeCAP200_B8a 0.006 + +CT823_B6_1 0.006 + +7030102001E5(Rev-) 0.007 + +So225_H11_12 0.007 + +235080_3G7env2(Rev-) 0.008 + +CT431_G6_6 0.008 + +Ce1176_A3 0.009 + +CT140_140_B6 0.010 + +1394C9G1(Rev-) 0.011 + +TRP343.2.00_21_2 0.011 + +Ce1172_H1 0.013 + +Ce704810053_2B7 0.014 - +19157834_V1 0.019 + +CA146_H3_3 0.020 + +ZM247v1(Rev-) 0.021 + +329NFU2 0.023 + +Ce704809221_1B3 0.026 + +TRP363.2.00_10_3 0.026 + +20258279_V2 0.028 + +703NFU2 0.033 + +TRP307.2.00_24_1 0.034 + +CT885_H3_2 0.036 + +Ce0626_E6 0.037 + +So706_T10b_3 0.041 + +CAP40.2.01_A3_5 0.049 + +3514597 0.050 + +CT966_E1-7 0.053 - +Ce703010217_B6 0.058 + +CAP225.1.06_A2_18 0.063 + +ME067_A10-15 0.092 + +CA392_H2_6 0.111 + +TRP292.2.00_12_4 0.135 + +CAP224.1.18_C7_3 0.141 + +Ce0985_H7(Rev-) 0.201 + +Ko459_T68_4 0.259 + +1143465.14 0.283 + +Ce704010083_B8 0.287 + +21197826_V1 0.291 + +So405_T24_5 0.317 + +20927783 0.630 + +1107356.07 0.784 + +CAP69.1.12_TA3_1 0.793 + +CA457_H1_1 1.840 + +1170887.08 1.945 - +Ce706010018_2E3 5.200 + +249M B10 7.870 + +Ce1086_B2 >10 - +Ce0393_C3 >10 - +Ce2010_F5 >10 - +Ce0682_E4 >10 + +Ce2060_G9 >10 + +Ce2103_E8 >10 - +Ce703010131_1E2 >10 - +Ce703010054_2A2 >10 - -Ce703010228_1C4 >10 - +Ce704010017_B7 >10 - +Ce0089_G2 >10 + +Ce2052_G10 >10 - +Ce704010069_C6 >10 - +Ce703010010_C4 >10 + +CeCAP45_A2 >10 - +CeCAP210_TA5 >10 + +CeCAP221_B14 >10 - +CeCAP188_1_D1_14(Rev-) >10 - +CeCAP177_1A3 >10 - +ZM249M.PL1 >10 + +BF1266.431a >10 - +591NFU2 >10 - +1245045 >10 - +21283649 >10 - +CAP136.1.16_E6_1 >10 + +CAP220.2.00_A8_5B >10 - +CAP269.2.00_F11_1 >10 + +CAP129.1.15_B2_13 >10 + +CAP217.1.07_D3_1 >10 - +CAP237.1.22_B2_2_39 >10 - +CAP258.2.00_X_23 >10 - +CAP260.2.00_TA1_1B >10 - +CAP266.2.00_E9_h6 >10 - +TRP290.2.00_23_6 >10 + +TRP310.2.00_20_2 >10 - +TRP347.2.00_B1_1 >10 + +722_G4_16 >10 + +So431_C1_1 >10 + +So186_H6_5 >10 - +So722_G4_16 >10 + +Ko426_T78_10 >10 + +Ko870_C2_10 >10 - +CA327_D2_2 >10 + +20417927.07 >10 - +20355851.20 >10 + +20358510.01 >10 + +

Supplementary Figure 2. PGT128 neutralization of subtype C transmitted/founder viruses. PGT128 was tested against a panel of 101 transmitted/founder subtype C viruses, with 55 viruses exhibiting neutralization sensitivity. The presence of intact glycosylation motifs at positions 301 and 332 are indicated for each virus. Neutralization is shown as IC50 (μg ml-1). Gray shading indicates the three viruses without the glycan at 332 that exhibit sensitivity to PGT128. Colors indicate neutralization sensitivity of IC50 > 10 μg ml-1

(blue), 1 to 10 μg ml-1 (yellow), 0.1 to 1 μg ml-1 (orange) and IC50 < 0.1 μg ml-1 (red).

Nature Medicine doi:10.1038/nm.2985

0 10 20 30 50 75 100 125 150 17520

200

2,000

20,000

200,000Autologous

CAP239CAP255

Du151.2

Du156

AC10

RHPA

TRO.11

6535.3

Q23.17

ConC

CAAN

160 glycanNo 160 glycan

0 10 20 30 50 75 100 125 150 17520

200

2,000

20,000

200,000

CAP8

CAP61

CAP206CAP210

CAP239CAP228

CAP63

CAP255

CAP84

Du156Du422ZM53MZM109F

ZM197MZM233MWITO6535.3Q461.e2Q23.17Q842.d12Q168.a2

Autologous

CAP45

ConC

Q259.d2

160 glycanNo 160 glycan

Time after infection (weeks)

Neu

tral

izat

ion

titer

(ID50

)

2 weeks15 weeks

6 months

12 months

22 months

40 monthsCAP8 CAP256

4 weeks15 weeks6 months

12 months

21 months

39 months

CAP8

CAP256

Neu

tral

izat

ion

titer

(ID50

)

Time after infection (weeks)

160CAP8

(n) MRNCSFKITTELKDKKQKVYALFY (20)

---------------Q-------- (6) ---------------E-------- (5) ---------------T-------- (2) -------L-------Q-------- (1) ---------------Q-T------ (1) ---------------E---H---- (1) ---------------I-------- (1) ---------------A-------- (1) ----------------K------- (1) -------------------S---- (1) ------N----------------- (1)

------N----------------- (3) ------N------------F---- (2) ------N------------S---- (1) ------N---------R------- (1) ------N-I----------S---- (1) -------------------S---- (2) ----------------K------- (1)

------N----------------- (7) ------N------------F---- (5) -------------------H---- (2)

------N--------------I-- (6) ------N------------H---- (1) ------N---------KN------ (1) ------N---------K----I-- (1) ------N------------F-I-- (1) ------N------------N---- (1) ------N-----------E----- (1) ------N---------K-E--I-- (2) ------N-----R-----E----- (2) R-----N-----R-----E----- (1) R-----N--------------V-- (1) -----------------T------ (1)

------N---------K-E--I-- (9) ------N---------K----I-- (1) ------N--------------T-- (1)

(n) IKNCSFNTITEVRDKQKKEYALFY (4)

-------AT--L---K-------- (6)

------------------------ (5) -----------------R------ (1)

--------T--------------- (6) -------AT--------------- (1) -------AT------I-------- (1) -------ATS-L---E-------- (1) --------T--L---I-------- (1) ------SAT--L---I-------- (1) ------------------------ (4) ------T----------------- (1) -----------------E------ (1) ------D----------------- (1)

--------T--LK--I-------- (9) T------AT---K--I-------- (3) T------AT---K----------- (1) -------AT---K--I-------- (1) -------IT------I-------- (1) -----------------N------ (1)

------------S----N------ (14) -------AT------E-------- (7) -R-----AT------E-------- (1) -R-----ATS-L---E-------- (1)

156 160CAP256

156

ConC

0 50 100 1500

10,000

20,000

30,000

40,000

ConC

0 25 50 75 1000

10,000

20,000

30,000

40,000

a. b.

c.

Nature Medicine doi:10.1038/nm.2985

mAb (IC50 titers) PNG 160 PG9 PG16

CAP8.2 weeks - >10 >10CAP8.12 months + 0.14 >10CAP8.2 weeks K160N + 0.10 >10

CAP256.1 month - >10 >10CAP256.12 months + 1.60 >10CAP256.1 month I162T + 0.64 >10

TRO.11 (control) + 5.33 0.22

Donor subtype A APercentage breadtha 79%b 73%b

aPercentage of a multi-subtype panel of viruses neutralized with IC50 <50 ug/mlbWalker et al, 2009, cWalker et al, 2011

PGT145

>101.583.38

>100.649.58

0.044

A or D78%c

aPercentage of a multi-subtype panel of viruses neutralized with IC50 <50 ug/ml

Nature Medicine doi:10.1038/nm.2985

Acute Chronic Acute 1 year50

60

70

80

90

100

Subtype C

P = 0.1690

(n = 68) (n = 62)

Unmatched

(n = 20) (n = 20)

Matched

P = undefined

PN

G 1

60 fr

eque

ncy

Acute Chronic50

60

70

80

90

100

Subtype B

(n = 88) (n = 86)

Unmatched

P = undefined

PN

G 1

60 fr

eque

ncy

Nature Medicine doi:10.1038/nm.2985

a.

332 glycan 160 glycan

CAP177 N332* -CAP314 N332 -CAP255 N332* +

CAP8 N160* -CAP256 N160* -CAP257 N160** +CAP287 N160** +CAP312 N160** +

*Gray et al, 2011; ** unpublished dataBold text highlights subjects characterized in this study

b.

Acute 1 year

CAP177 88% - +CAP314 46% - +CAP217 23%* - +CAP244 9%* - +CAP45 0%* - +

*Gray et al, 2011Bold text highlights subjects characterized in this study

CAPRISA PTID

Percentage neutralization breadth

332 glycan

The presence of the 332 or 160 glycan in acute viruses from all individuals in the CAPRISA 002 / 004 cohorts developing glycan-dependent BCN antibodies

The evolution of the 332 glycan does not necessarily result in neutralization breadth

CAPRISA PTID

Major BCN specificity at 2-3 years

Acute sequence

Nature Medicine doi:10.1038/nm.2985