Supplementary Information. Antibody suppresses viremia in HIV-1-infected individuals

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1 Supplementry Informtion Antiody 0-07 suppresses viremi in HIV--infected individuls Supplementry Figures Supplementry Figure HIV- neutrlizing ctivity of 0-07 Supplementry Figure Suject enrollment nd study design Supplementry Figure Viremi nd 0-07 serum levels in HIV--infected sujects Supplementry Figure Phylogenetic nlysis of plsm env sequences otined efore nd fter 0-07 infusion Supplementry Figure Sttisticl nlysis of virl lod chnges in the sensitive HIV--infected 0 mg/kg dose group Supplementry Figure 6 CD+ nd CD8+ T cell counts Supplementry Figure 7 Nucleotide lignment of N glycn region in study prticipnts Supplementry Figure 8 Reltive frequency of 0-07 escpe muttions in plsm envelope sequences week fter infusion Supplementry Figure 9 SMRT sequencing of sujects HB nd HC Supplementry Tles Supplementry Tle Study prticipnt demogrphics Supplementry Tle Sfety dt Supplementry Tle Clinicl prmeters nd 0-07 serum ctivity Supplementry Tle Phrmcokinetics of 0-07 Supplementry Tle Single Genome Sequence nlysis (positions nd -) Supplementry Tle 6 Pseudovirus neutrliztion dt of sujects plsm envelopes Supplementry Tle 7 Primer-ID deep sequencing of V loop (HXB nt 68-76) Supplementry Tle 8 Comprison of sequencing methods Nture Medicine: doi:0.08/nm.68

2 Pseudotyped viruses Primry culture smples Sutype Tested strins Men IC80 Neutrlized (%) ART Tested smples Men IC80 Neutrlized (%) A off B on C D G _AE 6 n.d _AG _BC _BC AC n.d. 0.0 AD ACD CD All All Geometric men of neutrlized viruses. IC 80 < 0 g/ml. c 00 Pseudotyped viruses 00 Pseudotyped viruses vs. primry cultures Primry cultures 00 Primry cultures from HIV--infected sujects on ART Coverge (%) 7 0 Clde B All cldes 7 0 Pseudoviruses (All cldes) 7 0 off ART IC 80 (μg/ml) IC 80 (μg/ml) IC 80 (μg/ml) Supplementry Figure. HIV- neutrlizing ctivity of 0-07 () Summry of 0-07 neutrlizing in vitro ctivity sed on 06 HIV- pseudotyped viruses comprising sutypes nd recominnt forms. Dt were retrieved from the CATNAP Dtse (Yoon et l., Nucleic Acid Res 0) nd nlyzed using AntiodyDtse y Anthony West (West et l., PNAS 0). Men IC 80 -vlues re color-coded (drk red: < 0. µg/ml; light red: µg/ml, nd ornge: 0. - µg/ml). n.d.: not determined. () 0-07 neutrlizing in vitro ctivity of 79 primry culture smples otined y virl outgrowth ssy from HIV--infected sujects living in the U.S. or Germny. 77 sujects were off nd 0 were on ntiretrovirl therpy (ART; vlues prtilly otined from previous mesurements, Scheid nd Horwitz et l., Nture 06). Neutrlizing ctivity ws determined y the neutrliztion ssy. (c) Illustrtion of the frction (i.e., % coverge; y-xis) of HIV- isoltes/ cultures tht re neutrlized t given IC 80 (μg/ml; x-xis) using the dt sets from () nd (). Nture Medicine: doi:0.08/nm.68

3 87 Sujects screened HIV--infected 9 Enrolled Screen Filure 9 No longer interested 8 Did not meet inclusion criteri 7 Low CD+ T cell count High virl lod 6 Met exclusion criteri Investigtor s discretion for other medicl condition Seizures/Encephlitis Active syphilis Anorml EKG Heptitis B Heptitis C Elevted iliruin Scheduling difficulties 0 Group A mg/kg on ART Group B 0 mg/kg off ART Group C 0 mg/kg off ART Group D 0 mg/kg off ART HIV--negtive Enrolled 0 Screen Filure 6 No longer interested Met exclusion criteri Low hemogloin History of utoimmune disese (pos. ANA) Elevted AST Investigtor s discretion for other medicl condition Uncontrolled hypertension Positive RPR Elevted iliruin Unle to complete lood drw Group A mg/kg Group B 0 mg/kg Group C 0 mg/kg Group D 0 mg/kg Supplementry Figure. Suject enrollment nd study design A totl of 87 HIV--infected nd -uninfected sujects were screened for study prticiption. In oth cohorts, 0-07 ws sequentilly dministered t incresing doses of mg/kg (groups A nd A), 0 mg/kg (groups B nd B), or 0 mg/kg (groups C-D nd C-D) to HIV--infected (groups ) nd HIV--uninfected (groups ) prticipnts. Of totl of 87 sujects screened, 9 HIV--infected nd -uninfected prticipnts were enrolled. Nture Medicine: doi:0.08/nm.68

4 0 mg/kg HIV- RNA (log 0, copies/ml) HB HB HB Dys fter infusion Dys fter infusion Dys fter infusion, conc. (µg/ml) HIV- RNA (log 0, copies/ml) HC HC HC HD HD , conc. (µg/ml) 0 mg/kg HIV- RNA (log 0, copies/ml) HDK HDK HD6K HD7K HD8K Dys fter infusion Dys fter infusion, conc. (µg/ml) HIV- RNA (log 0, copies/ml) HD9K HD0K HDK Dys fter infusion Dys fter infusion Dys fter infusion, conc. (µg/ml) Supplementry Figure. Viremi nd 0-07 serum levels in HIV--infected sujects (, ) HIV- RNA plsm copies (solid red line) nd 0-07 serum concentrtion determined y TZM-l ssy (lue line) fter single intrvenous infusion of 0-07 t dose of 0 mg/kg () or 0 mg/kg (). Arrows nd dshed red lines indicte time of virl reound, defined s n increse of HIV- RNA of t lest 0. log 0 tht is confirmed t the next study visit. Strs indicte initition of ntiretrovirl therpy. Nture Medicine: doi:0.08/nm.68

5 Supplementry Figure (HB) 0 seq c 0-07 PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 7 Dy >0 Dy >0 Dy >0 Dy >0 Dy >0 6 Wk NT >0 > >0 7 Wk SR >0 > >0 8 Wk SG >0 > >0 9 Wk NI >0 > >0 0 Wk SN >0 > >0 0.0 Supplementry Figure. Phylogenetic nlysis of plsm env sequences otined efore nd fter 0-07 infusion () Mximum-likelihood phylogenetic trees of plsm-derived env sequences from sujects smpled efore (/pre-infusion visit) nd t different timepoints (Wk, Wk, Wk, Wk 8, Wk, Wk 6, Wk 0, Wk ) fter 0-07 infusion. Blck sterisks indicte nodes with oostrp support () Amino cid lignment of HxB positions -6 of SGS sequences. Columns one nd two indicte the time point smpled nd numer of sequences, respectively. Yellow oxes denote chnges from dy 0 mjority vrint. Light lue lines indicte intct potentil N-linked glycosyltion motifs t either N or N (when present). (c) Pseudovirus neutrliztion dt of selected sujects plsm envelope sequences. Shown re IC 80 vlues in (µg/ml) of different monoclonl ntiodies tht re currently in or plnned for clinicl testing. IC 80 (µg/ml) > 0.0 Nture Medicine: doi:0.08/nm.68

6 Supplementry Figure continued (HB) seq c Week PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 Week Dy >0 Dy >0 Dy >0 Dy >0 Dy >0 6 Wk SG >0 > >0 7 Wk NS >0 > >0 8 Wk shift >0 > >0 9 Wk SR >0 > >0 0 Wk shift >0 > >0 Wk SR >0 > >0 shift of PNGS from N to N IC 80 (µg/ml) > 0.0 Nture Medicine: doi:0.08/nm.68

7 Supplementry Figure continued (HB) 9 Week Week seq Week Week Week c Week PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 Dy Dy Dy Dy Wk ND >0 > Wk DG >0 > Wk NK >0 > Wk SN >0 > Wk NS >0 > IC 80 (µg/ml) > 0.0 Nture Medicine: doi:0.08/nm.68

8 Supplementry Figure continued (HC) 6 pre-infusion seq c Week PGT BNC7 VRC0 PGDM pre-infusion TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 Dy >0 Dy0 NT > >0 Dy >0 Dy >0 Dy >0 6 Dy0 NT >0 7 Wk NS >0 > >0 8 Wk SN >0 >0.0.6 >0 9 Wk >0 0 Wk NT >0 > >0 Wk >0 Wk DE >0 > >0 IC 80 (µg/ml) > 0.0 Nture Medicine: doi:0.08/nm.68

9 Supplementry Figure continued (HC) seq Week c 0-07 PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 Dy Dy Dy > Dy > Dy Dy Wk SN >0 > Wk SN >0 > Wk NK >0 > Wk NT >0 > Wk NK >0 >0 > Wk SN >0 > IC 80 (µg/ml) > 0.0 Week 0.0 Nture Medicine: doi:0.08/nm.68

10 Supplementry Figure continued (HC) 6 seq Week c PGT BNC7 VRC0 PGDM 00 6 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 Dy Dy Dy Dy Dy Wk SN >0 > Wk NK >0 > Wk NS >0 > Wk SN >0 > Wk NI >0 > Week 0.0 IC 80 (µg/ml) > 0.0 Nture Medicine: doi:0.08/nm.68

11 Supplementry Figure continued (HD) seq Week c 0-07 PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 Week Dy Dy Dy Dy Dy Wk SN >0 > Wk SR >0 > Wk SN >0 > Wk NK >0 > Wk NK >0 > IC 80 (µg/ml) > 0.0 Nture Medicine: doi:0.08/nm.68

12 Supplementry Figure continued (HD) 7 pre-infusion seq c 0-07 PGT BNC7 VRC0 PGDM 00 pre-infusion 78 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 7 pre NT >0 > pre NT >0 > >0 77 pre NT >0 > pre NT >0 > >0 0.0 IC 80 (µg/ml) > 0.0 Nture Medicine: doi:0.08/nm.68

13 Supplementry Figure continued (HDK) seq Week c 0-07 PGT BNC7 VRC0 PGDM TP Muttion IC 80 IC 80 IC 80 IC 80 IC Dy >0 80 Dy >0 8 Dy >0 8 Dy >0 8 Dy >0 8 Wk SR > >0 8 Wk NK > >0 86 Wk ND > >0 87 Wk ND > >0 88 Wk SN > >0 IC 80 (µg/ml) > 0.0 Week Nture Medicine: doi:0.08/nm.68

14 Supplementry Figure continued (HDK) 9 9 seq Week c 0-07 PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC Dy > Dy Dy Dy Dy Wk SR >0 > Wk SN >0 > Wk NS >0 > Wk SG >0 > Wk NK >0 > Wk SN >0 > Week 99 9 IC 80 (µg/ml) > Nture Medicine: doi:0.08/nm.68

15 Supplementry Figure continued (HD6K) c Week 8 Week Week 0 seq PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 Week 8 Week Week Dy Dy >0 0 Dy Dy Wk SA >0 > Wk8 SF >0 > Wk Wk8 SY > IC 80 (µg/ml) > Nture Medicine: doi:0.08/nm.68

16 Supplementry Figure continued (HD8K) seq c 0-07 PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC Dy >0 09 Dy >0 0 Dy >0 Dy >0 Dy >0 Wk NS >0 > >0 Wk SG >0 > >0 Wk NK >0 > >0 6 Wk SN >0 > >0 7 Wk SR >0 > >0 8 Wk SN >0 > >0 0 IC 80 (µg/ml) > Nture Medicine: doi:0.08/nm.68

17 Supplementry Figure continued (HD9K) seq c 0-07 PGT BNC7 VRC0 PGDM 00 TP Muttion IC 80 IC 80 IC 80 IC 80 IC 80 9 Dy0 E >0 > Dy0 E >0 > Dy0 E >0 > IC 80 (µg/ml) > Nture Medicine: doi:0.08/nm.68

18 Supplementry Figure continued (HD0K) seq 6 6 Week 8 Week 7 Week 8 Week 0.0 Nture Medicine: doi:0.08/nm.68

19 Supplementry Figure continued (HDK) seq Nture Medicine: doi:0.08/nm.68

20 0. log 0 (copies/ml) Dys fter infusion Supplementry Figure. Sttisticl nlysis of virl lod chnges in the 0-07-sensitive HIV--infected 0 mg/kg dose group The significnce of virl lod chnges fter 0-07 infusion ws nlyzed using simultneous confidence nds. Ech lue dot represents virl lod mesurement of responder tht received the 0 mg/kg dose. Simultneous confidence nds were computed with the R pckge locfit (version.-9.) using the Gussin fmily for the locl likelihood function. The solid line represents the regression fit nd the dshed lines show the simultneous confidence nds t 9% certinty level. The simultneous confidence nds exclude zero from out dys fter infusion to out 7 dys fter infusion, demonstrting tht there is significnt effect on virl lod reduction during tht time period. Nture Medicine: doi:0.08/nm.68

21 ,00 p=0.09 n.s. n.s. 80 n.s. CD+ /µl, % CD Weeks fter infusion Weeks fter infusion,00 p=0.006 p=0.08 n.s. 80 n.s. CD8+ /µl,000,00, % CD Weeks fter infusion Weeks fter infusion c.0 n.s. CD / CD8 rtio Weeks fter infusion Supplementry Figure 6. CD+ nd CD8+ T cell counts (-) Asolute counts (left pnels) nd reltive frequencies (right pnels) of CD+ () nd CD8+ T cells () efore, nd nd 8 weeks fter 0-07 infusion. (c) CD/CD8 rtio efore, nd nd 8 weeks fter 0-07 infusion. Men is indicted y the red line nd rs represent stndrd devition. Differences etween time points were tested y repeted mesures one-wy ANOVA. If significnt, Dunnett s test ws performed post hoc to compre week nd week 8 to seline, respectively. Nture Medicine: doi:0.08/nm.68

22 Sensitive sujects TP seqs HB seqs HB seqs HB seqs HC seqs HC seqs HC seqs HD TP seqs HDK seqs HDK seqs HD6K seqs HD8K seqs HD0K seqs HDK Resistnt sujects seqs HD seqs 0 HD9K Supplementry Figure 7. Nucleotide lignment of N glycn region in study prticipnts Depicted re the different nucleotide motifs encoding the N glycn region (positions -) in ech suject t (d0, pre-infusion for HD) nd four weeks fter infusion of 0-07 (wk nd wk8 for HD6K, HD0K). To the left of ech motif is the numer of sequences mtching prticulr motif. Trnsltion of the 9-nt spn is shown elow ech nucleotide sequence. Yellow oxes highlight nucleotide chnges wy from the mjority vrint. Red oxes highlight mino cid chnges tht disrupt the potentil N-linked glycosyltion site (PNGS) t position, while tourquoise oxes highlight non-synonymous chnges tht do not disrupt the PNGS. Sujects tht hrored 0-07-sensitive viruses on dy 0 re shown on top, sujects tht hrored resistnt viruses t the ottom. Nture Medicine: doi:0.08/nm.68

23 HB HB 6 6 HC HC Viruses with escpe muttion (%) Dys to reound R = HD HDK 9 0 HDK Position Muttion N S D/N D H I K S T Y A F G I N R Y E G K Supplementry Figure 8. Reltive frequency of 0-07 escpe muttions in plsm envelope sequences week fter infusion () Pie chrts illustrte the reltive undnce of prticulr mino cid muttions t envelope residues,, nd s nlyzed y SGS. Type of escpe muttion indicted y color code. () Correltion of time to virl reound (x-xis) nd the percentge of viruses mutted t, or (y-xis). Colors of dots indicte dose groups (0 mg/kg, lck; 0 mg/kg, red). Nture Medicine: doi:0.08/nm.68

24 seq of totl % 7.76% 6 0.% c HB d % % % 7 6. % 6.66 % %.67 %.8 % 9. % 7. % 6.7 %. % 9.06 % 7. %.8 %. % 0.07 % 8.06 %.0 %.0 % % % % % 6 0. % 0.0 % E seq of totl % HC % 99.6 % 9.0 % 99.6 % 0. % 0.00 Supplementry Figure 9. SMRT sequencing of sujects HB nd HC Mximum-likelihood phylogenetic trees of full-length plsm envelope single molecule rel time sequencing of sujects HB () nd HC (c) otined on nd fter 0-07 infusion. Brnches show high-qulity consensus reds (HQCSs) with their respective copy numer visulized y the size of the circle. Tles in () nd (d) summrize otined numer of filtered reds ( seq) for sequence vrints in envelope region - nd the reltive frequency of ech vrint (of totl) for the two sujects, respectively. Arrow in () highlights minor vrint crrying NIN muttion. Nture Medicine: doi:0.08/nm.68

25 Supplementry Tle. Study prticipnt demogrphics Demogrphics of HIV--infected prticipnts enrolled in groups A-D Study ID 0-07 dose Age (yers) Gender Rce Yers since HIV- dignosis HIV- clde ART regimen t enrollment HIV--RNA t dy 0 (copies/ml) CD+ T cell count t dy 0 (cells/ l) HA mg/kg 7 Mle Blck 6 ND RPV/TDF/FTC <0D 70 HA mg/kg 6 Mle Blck/Hispnic ND EVG/coi/TDF/FTC <0D 7 HA mg/kg 9 Femle White/Hispnic 0 ND EFV/TDF/FTC <0 8 HB 0 mg/kg Mle Blck B -,90 9 HB 0 mg/kg 6 Mle Blck B - 6,80 0 HB 0 mg/kg Femle Blck 9 B -,80 66 HC 0 mg/kg Mle Blck B -,60 89 HC 0 mg/kg Mle Blck B - 77, HC 0 mg/kg Mle Blck 6 B - 0,0 HD 0 mg/kg Mle Blck B -,770 0 HD 0 mg/kg Femle White 6 B HDK 0 mg/kg 6 Mle White 6 B - 60,00 0 HDK 0 mg/kg Mle White B - 7,70 60 HD6K 0 mg/kg 8 Mle White B - 0, HD7K 0 mg/kg Mle White 7 B - 9,0 860 HD8K 0 mg/kg Mle White B -, HD9K 0 mg/kg 7 Mle White B - 6, HD0K 0 mg/kg Mle White B - 0, HDK 0 mg/kg Mle White B - 6,00 60 Asolute CD+ T cell count ws cells/ l t screening. RPV - rilpivirine, TDF - tenofovir disoproxil, FTC - emtricitine, EVG - elvitegrvir, coi - coicistt, EFV - efvirenz. <0D - HIV--RNA detected ut elow limit of quntifiction (0 copies/ml). <0 - No HIV- RNA detected. ND: Not determined. Demogrphics of HIV--negtive prticipnts enrolled in groups A-D Study ID 0-07 dose Age (yers) Gender Rce HA mg/kg Mle Blck HA mg/kg 8 Mle Blck HA mg/kg Femle White HB 0 mg/kg 60 Mle Unknown HB 0 mg/kg Mle White HB 0 mg/kg Mle Blck HC 0 mg/kg 9 Mle White HC 0 mg/kg 8 Femle Blck HC 0 mg/kg Mle White HD 0 mg/kg 8 Femle Blck HD 0 mg/kg Mle Multiple HD 0 mg/kg 9 Mle Blck HD 0 mg/kg 7 Mle White/Hispnic HD 0 mg/kg 7 Femle White Nture Medicine: doi:0.08/nm.68

26 Supplementry Tle. Sfety dt Adverse Events Reported AEs % of AEs % of Possily prticipnts relted Mild Moderte Severe mg/kg (n=) 0 mg/kg (n=) 0 mg/kg (n=8) mg/kg (n=) 0 mg/kg (n=) Upper respirtory infection Hedche Skin infection (folliculitis, furunculosis, tine corporis) Surgicl nd medicl procedures (mmmoplsty, hysterectomy, tooth extrction) Uninfected no. of dverse events HIV--infected no. of dverse events Arthrlgi Dyspepsi Gstroenteritis Loclized musculoskeletl pin Rsh Vomiting / Nuse Adominl pin Diplopi Dizziness Depressive episode Dry eyes Elevted totl iliruin Epistxis Hed injury due to fll Herpes zoster Incresed lood pressure Mlise/Ftigue Menorrhgi Pruritus Soft tissue hemtom Toothche Trumtic er injury Urinry trct infection mg/kg (n=) Adverse events reported during weeks of follow-up fter 0-07 infusion y / HIV--negtive nd 6/9 HIV--infected individuls (HA-HD8K), nd during (HDK) nd 0 (HD9K, HD0K) weeks of follow up y the remining HIV- infected individuls. Nture Medicine: doi:0.08/nm.68

27 Supplementry Tle. Clinicl prmeters nd 0-07 serum ctivity mg/kg HA CD+ Active 0-07 in serum (0.v.c0) HA CD+ Active 0-07 in serum (0.v.c0) Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Screen 76 < Screen 68 <0D Screen 70 < Pre - <0D Pre - <0D Pre - < Bse 70 <0D - <0 <0. <0 Bse 7 <0D - <0 <0. <0 Bse 8 <0 - <0 <0. <0 End - - -,9. <0 End - - -,9 6. <0 End - - -, <0 Dy - <0D -,.6 <0 Dy - <0D -,98.9 <0 Dy - <0 -,7 8. <0 Dy - <0 -,6 0. <0 Dy - <0D -,9. <0 Dy - <0D -,09 6. <0 Dy - <0D - NA NA Dy - <0 -,6. <0 Dy - <0D -, 8.9 <0 Dy ,9 9. <0 Dy 7 (+),0 <0D <0 Dy 7 <0 -,9. <0 Dy (-) 87 < <0 Dy (+) 86 < <0 Dy 0 < <0 Dy - < <0 Dy (+) - <0D <0 Dy - <0D <0 Dy <0D <0 Dy 8 (+) 968 <0D <0 Dy 8 (-) 9 <0 -. <0 Dy - <0-97. <0 Dy (+) - <0 -. <0 Dy - <0-9.9 <0 Dy <0D <0 Dy 6 (+) 88 <0D <0 Dy 6 0 <0 -.6 <0 Dy 8 - <0D <0 Dy 8 (+) - < <0 Dy 8 - < <0 Dy 80 <0 - NA NA Dy (-6) 86 <0-0. <0 Dy 7 <0D - NA NA 0 Dy 0 (+) - <0 - NA NA Dy 0 (-6) - <0 - <0 <0.6 <0 Dy 0 (+8) - <0D - <0 <0.6 <0 Dy 68 7 <0D - 0. <0 Dy 68 (-), <0 - <0 <0.6 <0 Dy 68 (+) <0 <0.6 <0 HA CD+ Active 0-07 in serum (0.v.c0) 0 mg/kg HB CD+ Active 0-07 in serum (0.v.c0) HB CD+ Active 0-07 in serum (0.v.c0) Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Screen 9, Screen 7 8, Screen 87, Pre -, Pre - 7, Pre - 8, Bse 9,90 - <0 <0.6 <0 Bse 0 6,80 - <0 <0.6 <0 Bse 66,80 - <0 <0.6 9 End , <0 End - - -, <0 End - - -, <0 Dy -, ,87. <0 Dy -, , <0 Dy - 0, ,6 60. <0 Dy - 9,0-0., <0 Dy - 6, , <0 Dy -, ,00 0. <0 Dy -,60-0.7, <0 Dy (-) -,090-0.,89 0. <0 Dy (-) -,660-0.,76 0. <0 Dy 7 (+) ,08. <0 Dy 7 (+) ,7 7.7 <0 Dy 7,990 -., <0 Dy (+) 8, <0 Dy (+) ,067. <0 Dy,90-0.,6.6 <0 Dy - 7,0-0.. <0 Dy (-) <0 Dy - 8, <0 Dy 8 7, <0 Dy 8 (+) 79 8, <0 Dy , <0 Dy (+) - 8, <0 Dy (+) -, <0 Dy (-) -, <0 Dy 6 7 9, <0 Dy 6 (+) <0 Dy 6 6, <0 Dy 8 (+) -,90-0. <0 <0. <0 Dy <0 Dy 8 (+) - 6, <0 <0. <0 Dy 7, <0 <0. <0 Dy (-) 78 <0D - <0 <0.6 <0 Dy (+7) 00 7, <0 <0. ND Dy 0 (+) - 7,0 0. <0 <0. <0 Dy 0 (+) - <0 - NA NA 8 Dy 0 (+9) <0 <0.6 <0 Dy 68 (+) 0 6, <0 <0. <0 Dy 68 (+7) 7 <0 - NA NA Dy 68 66,0 - <0 <0.6 <0 HB CD+ Active 0-07 in serum (0.v.c0) 0 mg/kg HC CD+ HC CD+ Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Screen, Screen 7, Screen, Pre -, Pre - 8, Pre -, Bse 89,60 - <0 <0.6 <0 Bse ,60 - <0 <0.6 <0 Bse 0,0 - <0 <0.6 <0 End , <0 End ,76,069.9 <0 End , 96. <0 Dy -,00 0., <0 Dy -, ,79. <0 Dy - 9, ,9 9.6 <0 Dy -, ,98 8. <0 Dy - 7, , 70. <0 Dy - 6,000-0.,8 6.9 <0 Dy ,8 6. <0 Dy (-) - 9, , 8. <0 Dy -,0 -. 8,97.6 <0 Dy , <0 Dy 7 708,00 -.7,9 99. <0 Dy ,7 7.9 <0 Dy ,0 7. <0 Dy 68, , <0 Dy 6 0,670-0.,7 6. <0 Dy ,9.0 <0 Dy -,0-0.8, <0 Dy -,90-0., <0 Dy 8 00,80 0., <0 Dy 8 8 9,80-0., <0 Dy , ,0 0.7 <0 Dy -, <0 Dy - 0,80-0.,66. <0 Dy -, <0 Dy <0 Dy 6 (-) <0 Dy 6 6 7, <0 Dy 8 -, <0 Dy 8 - <0-0.7 <0 Dy 8 (-) -, <0 Dy (+), <0 <0. <0 Dy 66 <0D - <0 <0.6 <0 Dy (+) 78 <0 - <0 <0.6 <0 Dy 0 (-) -, <0 <0. <0 Dy 0 (+) - <0 - <0 <0.6 <0 Dy 0 (+) - <0 - <0 <0.6 <0 Dy 68 89, <0 <0. <0 Dy 68 (-),09 <0D - <0 <0.6 <0 Dy <0 - <0 <0.6 <0 HD CD+ Active 0-07 in serum (0.v.c0) Active 0-07 in serum (0.v.c0) HD CD+ Active 0-07 in serum (0.v.c0) Active 0-07 in serum (0.v.c0) HC CD+ HDK CD+ Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Screen 0 6, Screen Screen 80 6, Pre - 7, Pre -, Pre -, Bse 0,770 - <0 <0.6 <0 Bse <0 <0.6 <0 Bse 0 60,00 - <0 <0.6 - End ,0,6. <0 End ,,.7 <0 End , <0 Dy -, , <0 Dy -, ,89,. <0 Dy -, , <0 Dy - 7, , 78. <0 Dy ,87,00.7 <0 Dy -, ,8.6 <0 Dy -,70 -.,08 7. <0 Dy (+) ,78,08. <0 Dy (-) - 8, , 00. <0 Dy 7 66, , <0 Dy , <0 Dy 7 0,0 -. 6,6. <0 Dy 9 60, ,6 7. <0 Dy (-) ,. <0 Dy 0 8, ,76.6 <0 Dy - 8,960 0.,7 7. <0 Dy (+) ,96. <0 Dy - 6,0 -.0,0 88. <0 Dy 8 0 6,70-0., <0 Dy 8 (+) 0, <0 Dy , ,.7 <0 Dy (-) -, <0 Dy (-) <0 Dy -,00-0.,6 0. <0 Dy 6 (-7) 6, <0 Dy 6 (+6) <0 Dy , <0 Dy 8 -, <0 Dy 8 (-) <0 <0. <0 Dy 8 0 7, <0 Dy 97,00-0. <0 <0. <0 Dy (-7) <0 <0. <0 Dy <0 Dy 0 (+) - 9, <0 <0. <0 Dy 0 (-7) <0 <0. <0 Dy 0 (+7) 70 <0D <0 Dy ,0 0. <0 <0. <0 Dy 68(-7) <0 <0. <0 Dy 68 (+6) 60 <0D - <0 <0. <0 Active 0-07 in serum (0.v.c0) Active 0-07 in serum (0.v.c0) Nture Medicine: doi:0.08/nm.68

28 Supplementry Tle. Clinicl prmeters nd 0-07 serum ctivity - continued HDK CD+ Active 0-07 in serum (0.v.c0) HD6K CD+ Active 0-07 in serum (0.v.c0) HD7K CD+ Active 0-07 in serum (0.v.c0) Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Screen 0 97, Screen 90 8, Screen 80, Pre - 9, Pre -, Pre -, Bse 60 7,70 - <0 <0.6 - Bse 700 0,00 - <0 <0.6 - Bse 860 9,0 - <0 <0.6 - End ,9 79. <0 End - - -, <0 End - - -,07 6. <0 Dy - 7, ,.0 <0 Dy - 9, , <0 Dy - 9, ,7 7.9 <0 Dy -, ,8 7. <0 Dy - 8,90-0., <0 Dy - 8, , 9. <0 Dy -, ,0 7.9 <0 Dy -, ,7. <0 Dy (-) -, , 7. <0 Dy ,6 6. <0 Dy 7 (+) , 97. <0 Dy 7 990, ,66 8. <0 Dy (+) , <0 Dy (+) , <0 Dy 880,0-0.9, 66. <0 Dy (-) ,779. <0 Dy (+) ,7 6. <0 Dy -,80-0.7,0.0 <0 Dy 8 60,960-0., <0 Dy 8 (+) ,78 7. <0 Dy 8 960, <0 Dy - 9, ,0.9 <0 Dy <0 Dy - 7, <0 Dy 6 60,000., 9.6 <0 Dy 6 (+), <0 Dy , <0 Dy <0D - NA NA 7 Dy 8-0, <0 Dy 8-9, <0 <0.6 <0 Dy 680 <0 - NA NA Dy,00, <0 <0.6 <0 Dy 80,00 0. <0 <0.6 <0 Dy <0 - NA NA 6 Dy 0 (+9) -, <0 <0.6 <0 Dy 0-0, <0 <0.6 <0 Dy <0-96. <0 Dy ,0-0. <0 <0. <0 Dy 68 (+) 90 0, <0 <0. <0 0 mg/kg HD8K CD+ Active 0-07 in serum (0.v.c0) HD9K CD+ Active 0-07 in serum (0.v.c0) HD0K CD+ Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Screen 780 9, Screen Screen 60 7, Pre - 0, Pre -, Pre - 7, Bse 880,000 - <0 <0.6 - Bse 80 6,960 - <0 <0.6 <0 Bse 760 0,00 - <0 <0.6 <0 End - - -, <0 End , <0 End ,68. <0 Dy - 6, ,9 79. <0 Dy - 6, , <0 Dy -, ,9 60. <0 Dy - 7,0-0., <0 Dy - 6, ,0 69. <0 Dy - 8, , <0 Dy -, ,0 7. <0 Dy -, ,8 8. <0 Dy -,00 -.0, <0 Dy 7, ,0.8 <0 Dy ,0 0.,. <0 Dy ,7 6.6 <0 Dy (-) ,8 0. <0 Dy 60 8,0 0., 89.7 <0 Dy ,78.0 <0 Dy (+) ,90.7 <0 Dy -,00 0.,6 8. <0 Dy <0 Dy 8 80, , <0 Dy , <0 Dy <0 Dy - 7,70-0.,9 0. <0 Dy -, <0 Dy -, <0 Dy 6 90 <0 -,76 6. <0 Dy 6 (+) 70 6, <0 Dy 6 70, <0 Dy 8 (+7) 90 <0 - NA NA 9 Dy 8 (-) - 9, <0 Dy 8 -, <0 Dy - <0-6. <0 Dy (-7) 660,80-0. <0 <0. <0 Dy 70,0-0.6 <0 <0. <0 Dy 0 (-) - <0-96. <0 Dy 0 (-) - 8, <0 <0. <0 Dy 0 -, <0 <0. <0 Dy <0-9. <0 Dy Dy Active 0-07 in serum (0.v.c0) HDK CD+ Active 0-07 in serum (0.v.c0) Timepoint cells/ l cp/ml log 0 ID0 µg/ml ID0 Screen 80 88, Pre - 99, Bse 60 6,00 - <0 <0.80 <0 End , <0 Dy -, ,70. <0 Dy -,00-0.,8 60. <0 Dy (-) - 6,70 -.0,96. <0 Dy , <0 Dy 70 0, , <0 Dy - 79,00 0.,0 6. <0 Dy ,00-0.,9. <0 Dy - 8,00 0.,07 8. <0 Dy , <0 Dy 8 -, Dy Dy Dy <0D: NA: Grey shding: Blue shding: HIV- RNA detected elow limit of quntifiction (0 copies/ml). Not ssessed ecuse of unspecific serum ctivity ginst MuLV-pseudotyped virus. Suject on ntiretrovirl therpy. Use of ART-resistnt pseudovirus ckone. Nture Medicine: doi:0.08/nm.68

29 Supplementry Tle. Clinicl prmeters nd 0-07 serum ctivity - continued mg/kg HA HA HA Active 0-07 in serum Active 0-07 in serum Active 0-07 in serum (Du.) (Du.) (Du.) Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Screen Screen Screen Pre Pre Pre Bse <0 <.6 <0 Bse <0 <.9 <0 Bse <0 <.9 <0 End, 6. <0 End,67 0. <0 End, <0 Dy 9. <0 Dy <0 Dy,0 80. <0 Dy 6.7 <0 Dy <0 Dy 7 8. <0 Dy (+) 67.9 <0 Dy <0 Dy (+) 9. <0 Dy 7 9. <0 Dy 7 7. <0 Dy 7 8. <0 Dy <0 Dy <0 Dy 89.0 <0 Dy 00.9 <0 Dy 9. <0 Dy 6.0 <0 Dy <0 Dy <0 Dy 8 (+). <0 Dy 8.9 <0 Dy <0 Dy 9.6 <0 Dy <0 Dy <0 Dy <0 Dy <0 Dy 8 (+) <0 <.9 <0 Dy 8 (-).0 <0 Dy (+7).7 <0 Dy (+) <0 <.9 <0 Dy (+) <0 <.9 <0 Dy 0 (+).7 <0 Dy 0 <0 <.9 <0 Dy 0 (-) <0 <.9 <0 Dy 68 <0 <.9 <0 Dy 68 <0 <.9 <0 Dy 68 (+) <0 <.9 <0 0 mg/kg HB HB HB Active 0-07 in serum Active 0-07 in serum Active 0-07 in serum (Du.) (Du.) (Du.) Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Screen Screen Screen Pre Pre Pre Bse <0 <.6 <0 Bse <0 <.9 <0 Bse <0 <.9 <0 End 6,78 8. <0 End, <0 End,6.0 <0 Dy,68.7 <0 Dy,0 9. <0 Dy,96.7 <0 Dy,0 9. <0 Dy,8 76. <0 Dy,9 06. <0 Dy, <0 Dy (-), <0 Dy (-),0 6.0 <0 Dy 7,9 8.0 <0 Dy 7,66. <0 Dy 7, 97. <0 Dy, <0 Dy,.6 <0 Dy <0 Dy <0 Dy <0 Dy <0 Dy <0 Dy <0 Dy <0 Dy 6.6 <0 Dy (+) <0 Dy (-) 8. <0 Dy 6 (+) 68. <0 Dy 6 (+) 06. <0 Dy 6 (+) 78. <0 Dy 8 (+) <0 Dy 8 (+) 9.8 <0 Dy 8 (-) 0 8. <0 Dy.9 <0 Dy (+) <0 Dy 6.7 <0 Dy 0 (-).7 <0 Dy <0 Dy 0 (-7).8 <0 Dy 68 (+) <0 <.9 <0 Dy <0 Dy 68 <0 <.9 <0 0 mg/kg HC HC HC Active 0-07 in serum Active 0-07 in serum Active 0-07 in serum Active 0-07 in serum (Du.) (Du.) (Du.) (Du.) Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Screen Screen Screen Screen Pre Pre Pre Pre Bse <0 <.6 <0 Bse <0 <.9 <0 Bse <0 <.9 <0 Bse <0 <.6 <0 End,99,09. <0 End,9,76.6 <0 End,0,990. <0 End,78,8. <0 Dy, <0 Dy,,060.7 <0 Dy 7,79,.0 <0 Dy, <0 Dy (+),0 7. <0 Dy, 90.7 <0 Dy,88,. <0 Dy 8, <0 Dy 6, <0 Dy 9, <0 Dy,9,.6 <0 Dy 9, <0 Dy 7 (+) 6,08.8 <0 Dy 7 6,67. <0 Dy 7, 9.7 <0 Dy 7 6, <0 Dy,7 6.7 <0 Dy, 79.9 <0 Dy,0 8.0 <0 Dy (+),08 0. <0 Dy,8.6 <0 Dy,7.8 <0 Dy, <0 Dy,99. <0 Dy 8 (+6),7 0.0 <0 Dy 8 (+), <0 Dy 8 (+), 97. <0 Dy 8 (+),6 08. <0 Dy (+) <0 Dy (+),907. <0 Dy (-),6 6. <0 Dy (+) <0 Dy 6 (+) 07. <0 Dy 6 (+9) <0 Dy 6 (+) 9.9 <0 Dy 6. <0 Dy 8 (+) 0 0. <0 Dy 8 (+) 0.7 <0 Dy 8 (+) 8.7 <0 Dy 8 (+) 6. <0 Dy. <0 Dy (+) 7.6 <0 Dy (+) 6. <0 Dy (+) 8.9 <0 Dy 0.7 <0 Dy 0 (+). <0 Dy 0 (-) 6.7 <0 Dy 0 (+) 6. <0 Dy 68 <0 <.9 <0 Dy 68 (+8) 7.7 <0 Dy 68 (+) <0 <.9 <0 Dy 68 (+) <0 <.6 <0 HD HD HD Active 0-07 in serum Active 0-07 in serum Active 0-07 in serum Active 0-07 in serum (Du.) (Du.) (Du.) (Du.) Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Timepoint ID0 µg/ml ID0 Screen Screen Screen Screen Pre Pre Pre Pre Bse <0 <.9 <0 Bse <0 <.9 <0 Bse <0 <.9 - Bse <0 <.9 <0 End 9,87,79.8 <0 End 7,6,0. <0 End, <0 End 8, <0 Dy,00,88.6 <0 Dy,8,0.7 <0 Dy 8, <0 Dy,98 7. <0 Dy 8, <0 Dy,7,0. <0 Dy 7, 99.7 <0 Dy,8 6.9 <0 Dy 7, <0 Dy, 7. <0 Dy (-) 9,7 7.8 <0 Dy,8 8.6 <0 Dy 7 (+), <0 Dy 7,76.0 <0 Dy 7 (+),67 6. <0 Dy 7,00.7 <0 Dy,6 7. <0 Dy, <0 Dy (+), 77.7 <0 Dy,96. <0 Dy (+),0.8 <0 Dy (+),99. <0 Dy (+),787. <0 Dy (+), <0 Dy 8,89 6. <0 Dy 8 (+), 97.9 <0 Dy 8 (+),6 97. <0 Dy 8 (+),9 0.9 <0 Dy <0 Dy (+) <0 Dy (+), <0 Dy (+) <0 Dy <0 Dy <0 Dy 6 (+) 7. <0 Dy 6 (+) <0 Dy <0 Dy 8 (+) 7.7 <0 Dy 8 (+) <0 Dy <0 Dy. <0 Dy (+) <0 <.9 <0 Dy (+) 0.7 <0 Dy (+) 8 0. <0 Dy 0 (-) 68. <0 Dy 0 (+) <0 <.9 <0 Dy <0 Dy 0 (+) <0 Dy <0 Dy 68 (+) <0 <.06 <0 Dy 68 (+) 6.8 <0 Dy 68 (+) HD HD Nture Medicine: doi:0.08/nm.68

30 Supplementry Tle. Phrmcokinetics of 0-07 Phrmcokinetics y study suject ID HIV dose Method (strin) C mx ( g/ml) Adjusted Estimted t / R (dys) Lmd (lower, dys) Lmd (upper, dys) AUC (INF_pred) T lst (dys) C lst ( g/ml) AUC_% Extrp_pred HA Negtive mg/kg HA Negtive mg/kg HA Negtive mg/kg HA Positive mg/kg HA Positive mg/kg HA Positive mg/kg HB Negtive 0 mg/kg HB Negtive 0 mg/kg HB Negtive 0 mg/kg HB Positive 0 mg/kg HB Positive 0 mg/kg HB Positive 0 mg/kg HC Negtive 0 mg/kg HC Negtive 0 mg/kg HC Negtive 0 mg/kg HD Negtive 0 mg/kg HD Negtive 0 mg/kg HD Negtive 0 mg/kg HD Negtive 0 mg/kg HD Negtive 0 mg/kg HC Positive 0 mg/kg HC Positive 0 mg/kg HC Positive 0 mg/kg HD Positive 0 mg/kg HD Positive 0 mg/kg HDK Positive 0 mg/kg HDK Positive 0 mg/kg HD6K Positive 0 mg/kg HD7K Positive 0 mg/kg HD8K Positive 0 mg/kg HD9K Positive 0 mg/kg HD0K Positive 0 mg/kg HDK Positive 0 mg/kg (Du.) (Du.) (Du.) (0.v.c0) (0.v.c0) (0.v.c0) (Du.) (Du.) (Du.) (0.v.c0) (0.v.c0) (0.v.c0) (Du.) (Du.) (Du.) (Du.) (Du.) (Du.) (Du.) (Du.) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) (0.v.c0) , , , , , , , , , , , , , , , , ,689..., , , , , , , , , , , , , , , , , , , , , , , , , Nture Medicine: doi:0.08/nm.68

31 Supplementry Tle. Phrmcokinetics of continued Phrmcokinetics y study group 0-07 dose HIV- of sujects C mx ( g/ml) t / (dys) Men SD Rnge Men SD Rnge mg/kg Negtive mg/kg Positive mg/kg Negtive mg/kg Positive mg/kg Negtive 8, , mg/kg Positive, , All Negtive All Positive Nture Medicine: doi:0.08/nm.68

32 Supplementry Tle. Single Genome Sequence nlysis (positions nd -) d0 wk wk wk d0 wk wk wk HB (7) site mt (nd) site mt () site mt () site mt (7) site mt (6) site mt (7) site mt (nd) site mt 7 DNIS wt 0 S N 8 S N 7 DNIS wt 9 DNIS wt S N 6 S R 7 S R N S 8 N S N I N S N I S R N T N del N K S G N H S D S N N I S G S R N D N K N S HB d0 wk wk / wk wk 6 d0 nd d- wk wk wk HB (9) site mt (6) site mt (9/8) site mt () site mt (9) site mt (nd) site mt (7) site mt (8) site mt NNIS wt 7 S N 6 / S N S N DNLS wt DNLS wt 7 DNLS wt DNIS wt 6 NNIS wt / N D N I DNIS wt 0 N T 6 DNIS wt DNIS wt / N S N T N T 6 N S N T D/N G 0 / N H DNIS wt DNIS wt N S / N K D/N K S N / S G S R N K 0 / S I N S D/N E / D/N G N K 0 / D/N K NNIS wt / 0 D/N E / 0 N T HC d0 wk wk wk d0 wk wk wk HC () site mt (6) site mt (8) site mt (nd) site mt (9) site mt (0) site mt () site mt (nd) site mt DNIS wt 6 DNIS wt 7 S N 9 DNIS wt S N S N 6 N K S R N S N T N S N I N S N K N K D/N E S G N D DNIS wt S G N I S R N D HC d0 wk wk wk d0 wk wk wk HD () site mt (9) site mt () site mt (0) site mt () site mt (nd) site mt (nd) site mt (nd) site mt NNIS wt 7 D/N K S N 7 NNIS wt N T 6 S N D/N K D/N K NNIS wt N I S N S I S R S R N D N S N S N T HD d0 wk wk wk d0 wk wk wk HDK () site mt (0) site mt () site mt (nd) site mt () site mt () site mt (9) site mt (nd) site mt DNIS wt 7 DNIS wt 7 N D DNIS wt DNIS wt 7 S N N D S N N S N K N K S R S N S R S G N K N Y HDK d0 wk wk / wk 8 wk / wk 0 d0 wk wk wk HD6K () site mt (nd) site mt (/0) site mt (/) site mt (6) site mt (nd) site mt () site mt (nd) site mt DNIS wt / S A 0 / DNIS wt DNIS wt S N / DNIS wt / 0 S Y NNIS wt 6 S R 0 / S F / 0 S F N K 0 / S Y / 0 N K S G / 0 D/N E N S D/N K N T HD8K d0 wk wk wk d0 wk wk / wk 8 wk HD9K (0) site mt (nd) site mt (nd) site mt (nd) site mt (9) site mt (nd) site mt (/0) site mt () site mt 0 D/N E 9 DNIS wt / S N 9 DNIS wt / 8 DNIS wt N T / 0 N T D/N E / S R / N D 0 / N S 0 / D/N E HD0K d0 wk wk wk HDK (6) site mt (nd) site mt () site mt (nd) site mt 6 DNIS wt 0 S N S G D/N E S R N S N T Sequences contining premture stopcodons or lrge internl deletions tht would compromise Env functionlity were excluded from this nd ll other downstrem nlyses. Nture Medicine: doi:0.08/nm.68

33 Supplementry Tle 6. Pseudovirus neutrliztion dt of sujects plsm envelopes HB HB HC HD8K HDK HD 0-07 PGT BNC7 VRC0 PGDM PGT BNC7 VRC0 PGDM00 SGS Sequence ID TP IC 0 IC 80 IC 0 IC 80 IC 0 IC 80 IC 0 IC 80 IC 0 IC 80 SGS Sequence ID TP IC 0 IC 80 IC 0 IC 80 IC 0 IC 80 IC 0 IC 80 IC 0 IC 80 HB-D0-006-B_S Dy >0 >0 HB-D0-0-C_S Dy >0 >0 HB-D0-006-C7_S6 Dy >0 >0 HB-D0-0-C7_S Dy >0 >0 HB-D0-006-F0_S Dy >0 >0 HB-D0-06-B_S Dy >0 >0 HB-D0-06-B_S Dy >0 >0 HB-D0-06-C8_S8 Dy >0 >0 HB-D0-06-G6_S Dy >0 >0 HB-D0-06-E9_S Dy >0 >0 6 HB-W-006-D0_S7 Wk >0 >0 >0 > >0 >0 6 HB-W-00-A_S7 Wk >0 >0 >0 > >0 >0 7 HB-W-006-A6_S Wk >0 >0 >0 > >0 >0 7 HB-W-00-C9_S80 Wk >0 >0 >0 > >0 >0 8 HB-W-006-B_S Wk >0 >0 >0 > >0 >0 8 HB-W-00-D_S8 Wk >0 >0 >0 > >0 >0 9 HB-W-006-D_S8 Wk >0 >0 >0 > >0 >0 9 HB-W-00-D7_S8 Wk >0 >0 >0 > >0 >0 0 HB-W-006-H6_S6 Wk >0 >0 >0 > >0 >0 0 HB-W-00-F_S87 Wk >0 >0 >0 > >0 >0 HB-D0-0-G0_S Dy HB-W-00-F_S88 Wk >0 >0 >0 > >0 >0 HB-D0-09-B_S9 Dy HC-D0-066-A_S68 Dy >0 >0 HB-D0-09-B6_S Dy HC-D0-066-B_S69 Dy0 >0 > >0 >0 HB-D0-09-C7_S6 Dy HC-D0-066-C_S70 Dy >0 >0 6 HB-W-08-F7_S Wk >0 >0 >0 > HC-D G_S Dy >0 >0 7 HB-W-0-C0_Se Wk >0 >0 >0 > HC-D F0_S90 Dy >0 >0 8 HB-W-0-C7_S0e Wk >0 >0 >0 > HC-D F_S9 Dy >0 >0 9 HB-W-0-G_S6 Wk >0 >0 >0 > HC-W-0706-B8_S0 Wk >0 >0 >0 > >0 >0 0 HB-W-0-H_S67 Wk >0 >0 >0 > HC-W-0706Pl-B_S96 Wk >0 >0 >0 > >0 >0 9 HC-W-0706Pl-G_S Wk >0 >0 HC-D0-006-A_S9 Dy HC-W-0706Pl-A_S Wk >0 >0 >0 > >0 >0 HC-D0-006-F_S Dy HC-W-076-D_S66 Wk >0 >0 HC-D0-06-C_S66 Dy >0 > HC-W-076-F7_S69 Wk >0 >0 >0 > >0 >0 6 HC-D0-06-D_S67 Dy > HC-D0-06-F9_S7 Dy HC-D0-006-F7_S Dy HC-D0-06-H0_S8 Dy HC-D0-006-G_S Dy HC-W-006-F6_S8 Wk >0 >0 >0 > < HC-D0-06-B_S0 Dy HC-W-006-H_S9 Wk >0 >0 >0 > < HC-D0-06-E0_S9 Dy HC-W-06-A0_S Wk >0 >0 >0 > HC-D0-06-G_S Dy HC-W-06-A6_S9 Wk >0 >0 >0 > HC-W-006-G_S9 Wk >0 >0 >0 > HC-W-06-E_S9 Wk >0 >0 >0 >0 >0 > < HC-W-006-H_S Wk >0 >0. > HC-W-06-G_S Wk >0 >0 >0 > < HC-W-066-C7_S77 Wk >0 >0 >0 > HC-W-066-F_S8 Wk >0 >0 >0 > HD-D0-006-A_S67 Dy HC-W-066-G_S89 Wk >0 >0 >0 > HD-D0-006-D6_S7 Dy HD-D0-006-H_S8 Dy HDK-D0-066-E_S Dy >0 >0 68 HD-D0-076-B_S Dy HDK-D0-066-F7_S7 Dy >0 >0 69 HD-D0-076-B7_S6 Dy HDK-D0-0666Pl-D_S8 Dy >0 >0 70 HD-W-006-C_S9 Wk >0 >0. > HDK-D0-0666Pl-A_S Dy >0 >0 7 HD-W-006-C_S9 Wk >0 >0 >0 > HDK-D0-0666Pl-C_S7 Dy >0 >0 7 HD-W-066-A6_S9 Wk >0 >0.6 > HDK-W-066Pl-A_S Wk >0 > >0 >0 7 HD-W-066-D9_S6 Wk >0 >0 >0 > HDK-W-066Pl-B_S7 Wk >0 > >0 >0 7 HD-W-066-F9_S Wk >0 >0 >0 > HDK-W-066Pl-B9_S9 Wk >0 > >0 >0 87 HDK-W-066Pl-A_S7 Wk >0 > >0 >0 89 HDK-D C_S Dy > HDK-W-066Pl-A_S Wk >0 > >0 >0 90 HDK-D0-066Pl-F_S7 Dy HDK-D0-066Pl-D_S7 Dy HD6K-D B_S9 Dy HDK-D0-066Pl-D_S8 Dy HD6K-D0-066-F_S0 Dy >0 9 HDK-D F6_S Dy HD6K-D C0_S Dy HDK-W-066-A6_Se Wk >0 >0 >0 > HD6K-D C6_S Dy HDK-W-0666-A_S Wk >0 >0 >0 > HD6K-W-0706-G_S6 Wk >0 > > HDK-W-0666-C_S9 Wk >0 >0 >0 > HD6K-W D6_S6 Wk8 >0 >0.9 > HDK-W-0666-C_S0 Wk >0 >0 >0 > HD6K-W F_S69 Wk HDK-W-066-D0_S9 Wk >0 >0 >0 > HD6K-W G0_S70 Wk8 >0 > HDK-W-0696-A6_S6 Wk >0 >0 >0 > HD8K-D B_S9 Dy >0 >0 09 HD8K-D A_S69 Dy >0 >0 7 HD-preinf-096-A_S6 pre >0 >0 >0 > HD8K-D A9_S7 Dy >0 >0 76 HD-preinf-096-B_S6 pre >0 >0.90 > >0 >0 HD8K-D F6_S90 Dy >0 >0 77 HD-preinf-096-D8_S66 pre >0 >0 >0 > HD8K-D H6_S9 Dy >0 >0 78 HD-preinf-096-H_S7 pre >0 >0.80 > >0 >0 HD8K-W-0706Pl-C6_S6 Wk >0 >0.9 > >0 >0 HD8K-W-0706Pl-G_S77 Wk >0 >0 >0 > >0 >0 9 HD9K-D B_S0 Dy0 >0 >0 >0 > HD8K-W-0706Pl-H8_S80 Wk >0 >0.8 > >0 >0 0 HD9K-D C_S Dy0 >0 >0 >0 > HD8K-W-0706Pl-E_S86 Wk >0 >0 >0 > >0 >0 HD9K-D0-076Pl6-A0_S86 Dy0 >0 >0 >0 > HD8K-W-0706Pl-E9_S87 Wk >0 > > >0 >0 8 HD8K-W-0706Pl-F7_S89 Wk >0 >0 >0 > >0 >0 Responders HD6K HDK HC HC HB HD HD9K Non-responders Pseudoviruses re continully numered y suject ID (from HB-HD9K). Pseudovirus numers correspond to numering in phylogenetic trees of Figure S. Nture Medicine: doi:0.08/nm.68

34 Supplementry Tle 7. Primer-ID deep sequencing of V loop (HXB nt 68-76) Suject IDs (totl) Sequence motif IDs of totl IDs (totl) IDs of totl HB HB HC HC HD G(N/D)IR - NxS 00% % N muttion 0 0% 0.99% S muttion 0 0% % D/N muttion 0 0% 0 0% G(N/D)IR - NxS 70 00% % N muttion 0 0% 9.60% S muttion 0 0% 7 6.9% D/N muttion 0 0% 0.% G(N/D)IR - NxS 6 00% 0.0% N muttion 0 0% 0.6% S muttion 0 0% 79.% D/N muttion 0 0% 0.60% G(N/D)IR - NxS 00% % N muttion 0 0% 8.0% S muttion 0 0% % D/N muttion 0 0% 0 0% G(N/D)IR - NxS 66 00% 0.7% N muttion 0 0% 90.% S muttion 0 0% % D/N muttion 0 0% 0 8.6% IDs: Numer of distinct primer IDs (coverge > 0) tht yielded n unmiguous mjority consensus. Nture Medicine: doi:0.08/nm.68

35 Supplementry Tle 8. Comprison of sequencing methods HB dy 0 week site mut SGS PrimerID Deep Seq SMRT site mut SGS PrimerID Deep Seq SMRT % of seqs % of seqs % of seqs % of seqs % of seqs % of seqs NNIS -.7% 9.9%.76%,7 S N 6.%.0% %,877 DNIS - 8.8% 60.8%.90%,88 N D 7.86%.0% 9 8.%,009 S N % 6 N S.9% 9.8%.8%, S G.7% 6.8%.6% Totl of seqs ,66 S I.7%.%.9% N K.7% - -.6% 9 D/N K.7% - -.0% N H.7% % 0 D/N G.7% - -.6% 7 N I - -.%.66% 9 S R - -.8%.% 09 N T - -.0% 9 7.7% 9 D/N H % 0.% 6 DNIS % 67 DNKS % 7 D/N E % KTIS K/T % 66 DKIN K/N % NNIS % Totl of seqs 8,0 HC dy 0 week site mut SGS PrimerID Deep Seq SMRT site mut SGS PrimerID Deep Seq SMRT % of seqs % of seqs % of seqs % of seqs % of seqs % of seqs DNIS % 00.00% %,8 S N 60.7% 7.7% %,79 N K.% 6.8% 7.07% 9 Totl of seqs 6,8 N T 0.7%.0% N S.7%.69% 69.66%,08 D/N E.7% 0.0% - - N I % S R % - - N H % - - N D % - - D/N G % - - DNIS % NNIS % Totl of seqs 8 0 6,77 HD dy 0 week site mut SGS PrimerID Deep Seq SMRT site mut SGS PrimerID Deep Seq SMRT % of seqs % of seqs % of seqs % of seqs % of seqs % of seqs NNIS % 99.9% %,707 S N 6.0%.08% 7.69%, DNIS % 0.6% 68 D/N K 8.% 8.6% %,8 NNLS % - - N S.7% 6.78% 0 6.6% 69 D/N K % S R 8.%.08% 0.% S R % 6 S G - -.%.%, N D.7%.07% 6.0% 69 Totl of seqs 66,8 N I 8.%.0%.6% 7 S I - -.% 9.% 6 N T.7%.6% % 77 NNIS % 0.0% N H %.% N K %.8% 9 N Y % Totl of seqs 90 0,98 Nture Medicine: doi:0.08/nm.68