Dynamics of polymorphism in a malaria vaccine antigen at a vaccine-testing site in Mali

Abstract

Background: Malaria vaccines based on the 19-kDa region of merozoite surface protein 1 (MSP-1(19)) derived from the 3D7 strain of Plasmodium falciparum are being tested in clinical trials in Africa. Knowledge of the distribution and natural dynamics of vaccine antigen polymorphisms in populations in which malaria vaccines will be tested will guide vaccine design and permit distinction between natural fluctuations in genetic diversity and vaccine-induced selection.

Methods and findings: Using pyrosequencing, six single-nucleotide polymorphisms in the nucleotide sequence encoding MSP-1(19) were genotyped from 1,363 malaria infections experienced by 100 children who participated in a prospective cohort study in Mali from 1999 to 2001. The frequencies of 14 MSP-1(19) haplotypes were compared over the course of the malaria transmission season for all three years, in three age groups, and in consecutive infections within individuals. While the frequency of individual MSP-1(19) haplotypes fluctuated, haplotypes corresponding to FVO and FUP strains of P. falciparum (MSP-1(19) haplotypes QKSNGL and EKSNGL, respectively) were most prevalent during three consecutive years and in all age groups with overall prevalences of 46% (95% confidence interval [CI] 44%-49%) and 36% (95% CI 34%-39%), respectively. The 3D7 haplotype had a lower overall prevalence of 16% (95% CI 14%-18%). Multiplicity of infection based on MSP-1(19) was higher at the beginning of the transmission season and in the oldest individuals (aged > or =11 y). Three MSP-1(19) haplotypes had a reduced frequency in symptomatic infections compared to asymptomatic infections. Analyses of the dynamics of MSP-1(19) polymorphisms in consecutive infections implicate three polymorphisms (at positions 1691, 1700, and 1701) as being particularly important in determining allele specificity of anti-MSP-1(19) immunity.

Conclusions: Parasites with MSP-1(19) haplotypes different from that of the leading vaccine strain were consistently the most prevalent at a vaccine trial site. If immunity elicited by an MSP-1-based vaccine is allele-specific, a vaccine based on either the FVO or FUP strain might have better initial efficacy at this site. This study, to our knowledge the largest of its kind to date, provides molecular information needed to interpret population responses to MSP-1-based vaccines and suggests that certain MSP-1(19) polymorphisms may be relevant to cross-protective immunity.

Figure 1. Prevalences of 14 MSP-1₁₉ Haplotypes in a Cohort from Bandiagara, Mali

Infections could have multiple haplotypes, thus haplotype prevalences do not sum to one. Haplotypes corresponding to the FVO, FUP, and 3D7 strains are indicated. Bars indicate 95% CIs.

Figure 2. Prevalence of MSP-1₁₉ Haplotypes over Time in Three Age Groups

Haplotype prevalences from July to January by age group during the three years of the malaria incidence study in Bandiagara, Mali.

Figure 3. MOI by Age

Average MOI over time in three age groups.

Figure 4. Frequency of Symptomatic and Asymptomatic Infections during the Malaria Transmission Season in Three Age Groups

(A) Incidence of symptomatic infection over the course of the transmission season. (B) Prevalence of parasitemia among asymptomatic monthly surveys. Values in the figure represent the average for all three years of the study, since patterns were similar in all years. Bars indicate 95% CIs.

Figure 5. Prevalence of MSP-1₁₉ Haplotypes among Symptomatic and Asymptomatic Infections

Bars indicate 95% CIs. *Chi-square p-value = 0.08 (ETSSRL [3D7]), p < 0.001 (QKNNGL), and p = 0.006 (EKSNGF).

Figure 6. Cumulative Hazard of a Subsequent Clinical Infection according to Change in Predominant Amino Acid

Cumulative hazard functions generated from Cox proportional hazards models of time to next clinical episode as a function of change in predominant amino acid at each polymorphic residue in MSP-1₁₉, year, and age. The cumulative hazard is shown along the y-axis with days on the x-axis. Dashed lines indicate a change in predominant amino acid and solid lines indicate no change at positions 1644, 1691, 1699, 1700, 1701, and 1716. The hazard of a subsequent clinical episode was significantly greater when a change in predominant amino acid occurred at positions 1691, 1700 and 1701.

Figure 7. Association between Change in Predominant Haplotype or Amino Acid and Development of Clinical Symptoms

ORs comparing the odds of a change in predominant haplotype or amino acid during intervals between two consecutive infections during which clinical symptoms developed, to the odds of a change during intervals between consecutive infections during which no symptoms developed, adjusting for year, age, and time between infections. Diamonds indicate point estimates and bars indicate 95% CIs. The dashed line designates an OR of 1, or no effect.