Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts

Abstract

Population genetic diversity of Plasmodium falciparum antigenic loci is high despite large bottlenecks in population size during the parasite life cycle. The prevalence of genetically distinct haplotypes at these loci, while well characterized in humans, has not been thoroughly compared between human and mosquito hosts. We assessed parasite haplotype prevalence, diversity, and evenness using human and mosquito P. falciparum infections collected from the same households during a 14-month longitudinal cohort study using amplicon deep sequencing of two antigenic gene fragments (ama1 and csp). To a prior set of infected humans (n = 1,175/2,813; 86.2% sequencing success) and mosquito abdomens (n = 199/1,448; 95.5% sequencing success), we added sequences from infected mosquito heads (n = 134/1,448; 98.5% sequencing success). The overall and sample-level parasite populations were more diverse in mosquitoes than in humans. Additionally, haplotype prevalences were more even in the P. falciparum human population than in the mosquito population, consistent with balancing selection occurring at these loci in humans. In contrast, we observed that infections in humans were more likely to harbor a dominant haplotype than infections in mosquitoes, potentially due to removal of unfit strains by the human immune system. Finally, within a given mosquito, there was little overlap in genetic composition of abdomen and head infections, suggesting that infections may be cleared from the abdomen during a mosquito's lifespan. Taken together, our observations provide evidence for the mosquito vector acting as a reservoir of sequence diversity in malaria parasite populations. IMPORTANCE Plasmodium falciparum is the deadliest human malaria parasite, and infections consisting of concurrent, multiple strains are common in regions of high endemicity. During transitions within and between the parasite's mosquito and human hosts, these strains are subject to population bottlenecks, and distinct parasite strains may have differential fitness in the various environments encountered. These bottlenecks and fitness differences may lead to differences in strain prevalence and diversity between hosts. We investigated differences in genetic diversity and evenness between P. falciparum parasites in human and mosquito hosts collected from the same households during a 14-month longitudinal study in Kenya. Compared to human parasite populations and infections, P. falciparum parasites observed in mosquito populations and infections were more diverse by multiple population genetic metrics. This suggests that the mosquito vector acts as a reservoir of sequence diversity in malaria parasite populations.

Keywords: Plasmodium falciparum; comparative genomics; genetic diversity; malaria; transmission.

FIG 1

Mosquito abdomens and heads do not contain similar infections. (A) P. falciparum infection of mosquito abdomens and heads of mosquitoes for which both compartments were tested using PCR. (B) Multiplicity of infection of infected mosquito abdomen and head samples. Gray lines link MOIs from an individual mosquito. (C) For 89 mosquitoes with infections of both the abdomen and the head, the proportions of the set of haplotypes in the mosquito found in the abdomen only, head only, or both are shown. The mean counts for each of the three groups were used to obtain the proportions. (D) Prevalence of each ama1 and csp haplotype in the mosquito abdomen population compared to the mosquito head population. Each dot represents a unique ama1 or csp haplotype, and bars indicate the 95% bootstrapped confidence intervals.

FIG 2

The mosquito P. falciparum population is more diverse and less even than the human P. falciparum population. (A) Prevalence of each ama1 and csp haplotype in the human population compared to the mosquito population. Each dot represents a unique ama1 or csp haplotype, and bars indicate the 95% bootstrapped confidence intervals. The lower threshold was defined as haplotypes observed in fewer than 5% of combined human and mosquito samples. Haplotype prevalences were considered higher in one compartment if the 95% bootstrapped confidence intervals did not overlap the expected prevalence (i.e., the overall prevalence across all samples). (B) Diversity of P. falciparum populations by host and genetic marker across orders of diversity. Ribbons are bootstrapped 95% confidence intervals. Higher values indicate more diversity. The slope of the line across orders q is a measure of haplotype evenness in the population. (C) Haplotype evenness of human and mosquito samples. Bars are bootstrapped 95% confidence intervals. Higher values indicate more similar prevalence of haplotypes in the population.

FIG 3

Compared to mosquito samples, human samples are more often dominated by a single haplotype. (A) Proportion of samples with monoclonal and polyclonal infections. Numbers are counts for each category. (B) Distributions of within-sample evenness (q = 1) by genetic marker and host. Lower values indicate more dominance by individual haplotypes within the strain mixture.