Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine

Abstract

Background: The RTS,S/AS01 vaccine targets the circumsporozoite protein of Plasmodium falciparum and has partial protective efficacy against clinical and severe malaria disease in infants and children. We investigated whether the vaccine efficacy was specific to certain parasite genotypes at the circumsporozoite protein locus.

Methods: We used polymerase chain reaction-based next-generation sequencing of DNA extracted from samples from 4985 participants to survey circumsporozoite protein polymorphisms. We evaluated the effect that polymorphic positions and haplotypic regions within the circumsporozoite protein had on vaccine efficacy against first episodes of clinical malaria within 1 year after vaccination.

Results: In the per-protocol group of 4577 RTS,S/AS01-vaccinated participants and 2335 control-vaccinated participants who were 5 to 17 months of age, the 1-year cumulative vaccine efficacy was 50.3% (95% confidence interval [CI], 34.6 to 62.3) against clinical malaria in which parasites matched the vaccine in the entire circumsporozoite protein C-terminal (139 infections), as compared with 33.4% (95% CI, 29.3 to 37.2) against mismatched malaria (1951 infections) (P=0.04 for differential vaccine efficacy). The vaccine efficacy based on the hazard ratio was 62.7% (95% CI, 51.6 to 71.3) against matched infections versus 54.2% (95% CI, 49.9 to 58.1) against mismatched infections (P=0.06). In the group of infants 6 to 12 weeks of age, there was no evidence of differential allele-specific vaccine efficacy.

Conclusions: These results suggest that among children 5 to 17 months of age, the RTS,S vaccine has greater activity against malaria parasites with the matched circumsporozoite protein allele than against mismatched malaria. The overall vaccine efficacy in this age category will depend on the proportion of matched alleles in the local parasite population; in this trial, less than 10% of parasites had matched alleles. (Funded by the National Institutes of Health and others.).

Figures

Figure 1

Study Sites and Genomic Units.

Figure 2. Data Generation and Sample and Data Filtration for the End Point of Primary Clinical Malaria among Children 5 to 17 Months of Age

Vaccine recipients were considered to be out of interval for the dose regimen if they did not receive booster vaccinations according to the schedule specified by the trial protocol. The sample cards used were Whatman FTA cards. PCR denotes polymerase chain reaction.

Figure 3. Complexity of Infection and Frequencies of 3D7-Matched Malaria among Children 5 to 17 Months of Age with the Primary Clinical Malaria End Point

The denominator for the frequencies in Panels B through D is the number of samples representing the primary clinical malaria end point that had sequence data available. Ag denotes Agogo, Ba Bagamoyo, Kil Kilifi, Kin Kintampo, Kom Kombewa, Kor Korogwe, La Lambaréné, Li Lilongwe, Na Nanoro, and Si Siaya.

Figure 4. Cumulative Incidences and Vaccine Efficacy against the Primary Clinical Malaria End Point among Children 5 to 17 Months of Age

Shown is the cumulative incidence of 3D7-matched malaria (Panel A) and 3D7-mismatched malaria (Panel B) among RTS,S/AS01-vaccine recipients and control-vaccine recipients during 12 months of post-vaccination follow-up, the cumulative vaccine efficacy (one minus the ratio [RTS,S/AS01 vs. control] of cumulative incidences of the first or only episode of clinical malaria with a specific haplotype) against 3D7-matched and 3D7-mismatched malaria over the entire post-vaccination follow-up period (Panel C), and the cumulative vaccine efficacy and hazard-ratio vaccine efficacy (one minus the ratio [RTS,S/AS01 vs. control] of instantaneous incidences of the end point under the assumption that incidences are proportional over time) against 3D7-matched and 3D7-mismatched malaria at 12 months after vaccination, with tests for differential haplotype-specific vaccine efficacy (Panel D). The I bars in Panel D indicate 95% confidence intervals.

Figure 5. Vaccine Efficacy against the Primary Clinical Malaria End Point among Children 5 to 17 Months of Age

Shown are the cumulative vaccine efficacy (Panel A) and hazard-ratio vaccine efficacy (Panel B) for the prevention of clinical malaria in which parasites were matches or mismatches with the RTS,S/AS01 vaccine strain (3D7) at each haplotype locus. Estimates were stratified according to study site. For each haplotype locus, the calculation of haplotype-matched vaccine efficacy included only clinical malaria end-point events with samples in which parasites matched 3D7 at the given locus; the calculation of haplotype-mismatched vaccine efficacy included only clinical malaria end-point events with samples in which parasites mismatched 3D7 at the given locus. Asterisks indicate that the difference in efficacy was significant (Q value ≤0.2 for all 28 multiply compared haplotype loci and unadjusted P≤0.05 for the full circumsporozoite protein C-terminal amplicon). FWER denotes family-wise error rate.