Admixture in Humans of Two Divergent Plasmodium knowlesi Populations Associated with Different Macaque Host Species

Abstract

Human malaria parasite species were originally acquired from other primate hosts and subsequently became endemic, then spread throughout large parts of the world. A major zoonosis is now occurring with Plasmodium knowlesi from macaques in Southeast Asia, with a recent acceleration in numbers of reported cases particularly in Malaysia. To investigate the parasite population genetics, we developed sensitive and species-specific microsatellite genotyping protocols and applied these to analysis of samples from 10 sites covering a range of >1,600 km within which most cases have occurred. Genotypic analyses of 599 P. knowlesi infections (552 in humans and 47 in wild macaques) at 10 highly polymorphic loci provide radical new insights on the emergence. Parasites from sympatric long-tailed macaques (Macaca fascicularis) and pig-tailed macaques (M. nemestrina) were very highly differentiated (FST = 0.22, and K-means clustering confirmed two host-associated subpopulations). Approximately two thirds of human P. knowlesi infections were of the long-tailed macaque type (Cluster 1), and one third were of the pig-tailed-macaque type (Cluster 2), with relative proportions varying across the different sites. Among the samples from humans, there was significant indication of genetic isolation by geographical distance overall and within Cluster 1 alone. Across the different sites, the level of multi-locus linkage disequilibrium correlated with the degree of local admixture of the two different clusters. The widespread occurrence of both types of P. knowlesi in humans enhances the potential for parasite adaptation in this zoonotic system.

Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

“…Generally, there are low levels of complexity per infection in clinical P. knowlesi isolates, most containing one predominant haploid genotype each (Table S3). The estimates of within-infection genomic complexity (1 − F WS ) were similar for cluster 1 and cluster 2 isolates [mean within-infection fixation index (F WS ) values of 0.94 and 0.95 respectively; MannWhitney test; P = 0.40] and correlated highly with indices independently derived by counting the number of distinct alleles in a previously performed 10-locus microsatellite genotypic analysis (Pearson's r 2 = 0.76, P = 6.4 × 10 −10 ) (Table S3) (18). Despite the differences in overall nucleotide diversity in the different clusters, the relative proportions of synonymous, nonsynonymous, intronic, and intergenic SNPs observed were similar in each (respectively 14%, 16%, 13%, and 57% for cluster 1; 14%, 17%, 13%, and 56% for cluster 2; and 13%, 18%, 14%, and 55% for cluster 3).…”

“…S2). The assignment of the clinical isolates into two distinct clusters shown here also was compared with an independent assignment recently performed using a STRUCTURE analysis of 10-locus microsatellite genotype data for 40 of the 48 isolates (18). All isolates had the same cluster assignment by both methods, except for one cluster 1 isolate, which had an intermediate cluster assignment in the microsatellite analysis (Fig.…”

“…Recent multilocus microsatellite analysis has indicated a deep population subdivision in P. knowlesi associated with long-tailed and pig-tailed macaques; both major types infect humans and occur sympatrically at most sites in Malaysia, but the two types show some additional geographical differentiation across sites (18).…”

A Review of Plasmodium knowlesi among Macaques in Malaysia

“…A recent study by Divis et al (2015), high genetic differences were observed among P. knowlesi isolated from macaque in Borneo and Peninsular Malaysia. In a study by Muehlenbein et al (2015), Plasmodium parasites isolated from M. fascicularis and M. nemestrina in Sabah showed significant difference suggesting genetic specificity to different host species.…”

“…P. knowlesi can be fatal in case of severe clinical malaria (Cox-Sing et al, 2008). The increase in number of identified cases is due to the availability of better diagnostic tools and the increase in transmission of P. knowlesi from macaques host to humans via mosquitoes (Divis et al, 2015). Its symptoms among humans may be found similar to other malaria parasites (Moyes et al, 2014).…”