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1 Supporting Information Honegger et al. /pnas.0 HCV proteins Core E E P NS NS NSA NSB NSA NSB HCV peptide pools 9 Fig. S. HCV proteins represented in the nine peptide pool arrays used for the IFN-γ ELISpot assay. Proportion of subjects with IFN- ELISpot peptide pool response 0 SFU/0 PBMCs * * * * * * n= n= n= n= * ** n= n= n= ** * * ** n= * * n= n= month months months - months VL decline log 0 VL decline < log Core/E E P/NS NS NSA/B NSA NSB Fig. S. Distribution of HCV-specific T-cell responses across the viral polyprotein in women with (gray bars, upward y axis) and without (white bars, downward y axis) viral load decline of log 0 by -mo (Fisher s exact test). *P < ; **P <. of9

2 ns A ALT (U/L) nd - (n) B ALT (U/L) nd ns ns ns - VL decline < log 0 VL decline log 0 pregnancy months pregnancy months Fig. S. Postpartum ALT elevation and relation to viral control. (A) Matched pairs analysis of ALT levels among HCV monoinfected women versus third values (Wilcoxon signed-rank test). (B) Longitudinal ALT differences of women with (gray shaded) and without (white) a viral load decline of log 0 or more by -mo (Mann Whitney U test). P value summary: ns, P ; *P < ; ***P < 0; ****P < 00. of9

3 A Viremia (log 0 IU/ml) - months CT/TT CC B # ELISpot peptide pools with 0 SFU/0 PBMCs months C IFN- SFU/0 PBMCs months Fig. S. Influence of IFNL rs990 polymorphism on viral load (A) and breadth (B) and magnitude (C) of longitudinal HCV-specific T-cell responses as measured by IFN-γ ELISpot in genotype infected subjects (Mann Whitney U test). P value summary: ns, P ; *P < ; ****P < 00. of9

4 A Viremia (log 0 IU/ml) P = months M00 M00 M0 M00 M00 M0 B Viremia (log 0 IU/ml) Trimester months Viremia (log 0 IU/ml) Prepregnancy Prepregnancy Prepregnancy Trimester months Fig. S. (A) Comparison of HCV viremia before pregnancy and mo after delivery among the six subjects who had prepregnancy samples available (Wilcoxon signed-rank test). (B) HCV viremia before, during, and -mo after pregnancy for the same six women, divided by whether (Left) or not (Right) they achieved a log 0 viral load decline. of9

5 Table S. Subject ID Individual viral genotypes, IFNL/ genotypes, and demographic characteristics of HCV-infected mothers Age at delivery (y) Estimated duration of HCV infection* (y) Presumed route of infection HCV genotype IFNL rs990 IFNL rs Gravida Pregnancy gestation at delivery (wk) Mode of delivery Breast-feeding duration (wk) M00 First. IDU b CC TT/TT 9. Cesarean 0 Second Cesarean 0 M00 First 0. Needle stick a CC TT/TT.0 Vaginal Second.9.0 Vaginal M00. IDU a CC TT/TT.9 Vaginal 0 M00. IDU a CT ΔG/TT. Vaginal 0 M00. Vertical a CT ΔG/TT.0 Vaginal M009. IDU a CT ΔG/TT. Vaginal 0 M00. IDU a CT ΔG/TT. Vaginal M0 0.9 Unknown a CC TT/TT.9 Vaginal 0 M0 First. IDU a CC TT/TT. Cesarean 0 Second.0. Cesarean 0 M0 Unknown Unknown b CC TT/TT 9.0 Cesarean M09 9 Unknown Unknown a CT ΔG/TT. Cesarean M0. IDU b CT ΔG/TT Vaginal 0 M IDU CT ΔG/TT 9.0 Cesarean 0 M0 First. Vertical a CT ΔG/TT. Cesarean Second Vaginal M0. IDU a CT ΔG/TT 0. Vaginal 0 M0. IDU a CC TT/TT. Vaginal 9 M0. IDU a CC TT/TT. Vaginal 0 M0 9.9 IDU CT ΔG/TT 9. Vaginal 0 M00.9 Unknown a CT ΔG/TT. Vaginal 0 M0 0. IDU a or c CT ΔG/TT.0 Vaginal 0 M0 0. IDU a CC TT/TT 9. Vaginal 0 M0. IDU b CC TT/TT 9. Vaginal M0. IDU b CC TT/TT 9.9 Vaginal M0 Unknown Unknown a or b CT ΔG/TT.9 Vaginal 0 M0 0. IDU a TT ΔG/ΔG 9.9 Vaginal 0 M09 0. IDU b CT ΔG/TT Cesarean 0 M00 First. IDU a CC TT/TT 9. Cesarean 0 Second. 9. Cesarean M0 0. IDU a TT ΔG/ΔG 9.0 Vaginal 0 M0. IDU a TT ΔG/ΔG 9. Vaginal M0. IDU a CT ΔG/TT 9. Vaginal 0 M0. IDU a CC TT/TT.9 Vaginal 9 M0. IDU a CC TT/TT 9. Vaginal 0 M0. IDU a CT ΔG/TT 9. Cesarean M0.0 IDU b TT ΔG/ΔG 9 Cesarean 0 IDU, injection drug use. *Assumed HCV infection acquired mo after initiation of IDU or at end of reported period of IDU if duration less than mo. For mothers followed through two consecutive pregnancies (M00, M00, M0, M0, and M00), the second pregnancy was used for statistical analyses. of9

6 Table S. Predictors of log 0 decline in viremia at - or -mo Viral load decline: Third to mo Viral load decline: Third to mo Variable n Median (IQR) n Median (IQR) P n Median (IQR) n Median (IQR) P Maternal age at delivery (y). (., 0). (., 0.) 0.. (, 0.). (., 0) 0. Estimated duration of 9. (.,.). (.,.) (.,.).9 (.,.) HCV infection Gravida (, ) (.,.) 0. (.,.). (., ) 0.9 Pregnancy gestation (wk).9 (., 9.) 9 (., 9.) 0..9 (., 9.9) 9. (., 9.) 0. HCV viral load (log 0 IU/mL) Third. (.,.).0 (.,.0). (.,.). (., ) 0. ALT (U/L) Third 9. (.,.) 0 (,.) 0.. (0.,.) 9. (,.) mo 0 (., ) (., 0) 9 (., ). (., 0) -mo (, ) (, ) (., ) (, 9) 0.9 ELISpot magnitude (EM) Third 0 (0,.) 0 (0, ). (0, 90). (0, ) 0. -mo. (0, 99) 0 (9, 9). (0, ). (., 9) ΔEM mo* 0 (0,.). (0, ) 0.9. (-0, ) 0 (., ) 0. -mo 0 (0, 9.) 00 (0, 0) (0, 0) 9 0 (., 0) ΔEM mo* 0 (0, 0) 9 (-., 0) 0 0. (-, 0). (0, 090) 0 ELISpot breadth (EB) Third (0,.) (0, ) (0,.) (0, ) 0. -mo (0, ) (., ) 0 0. (0, ). (, ) ΔEB mo* 0 (0,.) (0, ) 0 (-0., ) (0, ) 0. -mo 0 (0, ) (, ) (0,.) 9 (0., ) ΔEB mo* 0 (0, 0). (-0., ) 0 0 (-0., 0.) (0,.) 0. New ELISpot responses -mo 0 (0, ) (, ) 0 (0, ). (,.) 0. -mo 0 (0, 0). (0., ) (0, 0.). (0,.) Viral genotype or IFNL rs990 genotype CC 0. 9 CT or TT 9 Mode of delivery Cesarean 0. Vaginal 0 Breastfed ever Yes No Breastfed wk Yes 9 No 9 Boldface entries indicate P <. *Δ indicates difference between third and values (e.g., value mo value third ). Number of HCV peptide pools that had negative ELISpot responses in the third and positive responses at the indicated time point. of9

7 Table S. HLA class I associations with log 0 decline in viremia at - or -mo Viral load decline: Third to -mo Viral load decline: Third to -mo HLA allele (n = ), % (n = ), % P P-adjusted (n = ), % (n = ), % P P-adjusted A*0: A*0: A*0: A*:0 A*: A*: A*:0 0 A*: A*9:0 0 0 A*0: A*: A*:0 A*: A*:0 B*0: B*0:0 B*: B*: B*: B*: B*: B*: B*:0 B*: B*9: B*9:0 B*0: B*0: B*:0 0. B*: B*: B*: B*:0 0 0 B*: C*0: C*0:0 9 C*0: C*0:0 C*0:0 0. C*0: C*0:0 0. C*0: C*0:0 0. C*:0 0 0 C*: C*:0 0 Boldface entries indicate P <. of9

8 Table S. HLA class II associations with log 0 decline in viremia at - or -mo Viral load decline: Third to -mo Viral load decline: Third to -mo HLA Allele (n = ) % (n = ), % P P-adjusted (n = ), % (n = ), % P P-adjusted DRB*0: DRB*0: DRB*0: DRB*0:0 0 DRB*0: DRB*0: DRB*0: DRB*0:0 9 DRB*09: DRB*0: DRB*: DRB*: DRB*:0 0. DRB*:0 0 0 DRB*:0 DRB*: 0 0. DRB*: DRB*: DRB*0: DRB*0: DRB*0:0 0 0 DRB*0: DRB*0:0 0. DRB*0: DRB*0: DQB*0: DQB*0:0 9 DQB*0: DQB*0: DQB*0: DQB*0: DQB*0: DQB*0: DQB*0: DQB*0: DQB*0:0 0 0 DQA*0: DQA*0: DQA*0: DQA*0: DQA*0: DQA*0:0 9 DQA*0: DQA*0: DQA*0: DQA*0: DQA*0: DPB*0:0 9 DPB*0:0 9 DPB*0: DPB*0: DPB*0: DPB*0: DPB*0:0 0. DPB*0: DPB*: DPB*:0 0 DPA*0: of9

9 Table S. Cont. Viral load decline: Third to -mo Viral load decline: Third to -mo HLA Allele (n = ) % (n = ), % P P-adjusted (n = ), % (n = ), % P P-adjusted DPA*0: DPA*0: DPA*0:0 0 DPA*0: Boldface entries indicate P <. 9of9

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