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Background  Partial protective efficacy lasting up to 43 months after vaccination with the RTS,S malaria vaccine has been reported in one cohort (C1) of a Phase IIb trial in Mozambique, but waning efficacy was observed in a smaller contemporaneous cohort (C2). We hypothesized that low dose exposure to asexual stage parasites resulting from partial pre-erythrocytic protection afforded by RTS,S may contribute to long-term vaccine efficacy to clinical disease, which was not observed in C2 due to intense active detection of infection and treatment.    Methodology/Principal Findings  Serum collected 6 months post-vaccination was screened for antibodies to asexual blood stage antigens AMA-1, MSP-1 42 , EBA-175, DBL-α and variant surface antigens of the R29 laboratory strain (VSA R29 ). Effect of IgG on the prospective hazard of clinical malaria was estimated. No difference was observed in antibody levels between RTS,S and control vaccine when all children aged 1–4 years at enrollment in both C1 and C2 were analyzed together, and no effects were observed between cohort and vaccine group. RTS,S-vaccinated children <2 years of age at enrollment had lower levels of IgG for AMA-1 and MSP-1 42  (p<0.01, all antigens), while no differences were observed in children ≥2 years. Lower risk of clinical malaria was associated with high IgG to EBA-175 and VSA R29  in C2 only (Hazard Ratio [HR]: 0.76, 95% CI 0.66–0.88; HR: 0.75, 95% CI 0.62–0.92, respectively).    Conclusions  Vaccination with RTS,S modestly reduces anti-AMA-1 and anti-MSP-1 antibodies in very young children. However, for antigens associated with lower risk of clinical malaria, there were no vaccine group or cohort-specific effects, and age did not influence antibody levels between treatment groups for these antigens. The antigens tested do not explain the difference in protective efficacy in C1 and C2. Other less-characterized antigens or VSA may be important to protection.    Trial Registration  ClinicalTrials.gov  NCT00197041

Impact of the RTS,S Malaria Vaccine Candidate on Naturally Acquired Antibody Responses to Multiple Asexual Blood Stage Antigens