Population Parameters Underlying an Ongoing Soft Sweep in Southeast Asian Malaria Parasites

Abstract

Multiple kelch13 alleles conferring artemisinin resistance (ART-R) are currently spreading through Southeast Asian malaria parasite populations, providing a unique opportunity to observe an ongoing soft selective sweep, investigate why resistance alleles have evolved multiple times and determine fundamental population genetic parameters for Plasmodium. We sequenced kelch13 (n = 1,876), genotyped 75 flanking SNPs, and measured clearance rate (n = 3,552) in parasite infections from Western Thailand (2001–2014). We describe 32 independent coding mutations including common mutations outside the kelch13 propeller associated with significant reductions in clearance rate. Mutations were first observed in 2003 and rose to 90% by 2014, consistent with a selection coefficient of ∼0.079. ART-R allele diversity rose until 2012 and then dropped as one allele (C580Y) spread to high frequency. The frequency with which adaptive alleles arise is determined by the rate of mutation and the population size. Two factors drive this soft sweep: (1) multiple kelch13 amino-acid mutations confer resistance providing a large mutational target—we estimate the target is 87–163 bp. (2) The population mutation parameter (Θ = 2Neμ) can be estimated from the frequency distribution of ART-R alleles and is ∼5.69, suggesting that short term effective population size is 88 thousand to 1.2 million. This is 52–705 times greater than Ne estimated from fluctuation in allele frequencies, suggesting that we have previously underestimated the capacity for adaptive evolution in Plasmodium. Our central conclusions are that retrospective studies may underestimate the complexity of selective events and the Ne relevant for adaptation for malaria is considerably higher than previously estimated.

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance

“…Although other kelch13 mutations exhibit a higher frequency before 2011, C580Y overtakes those in the 2011–2012 sample. Two independent origins of the C580Y mutation were inferred by the observation of shared haplotypes in the vicinity of that mutation (Additional file 1: Figure S4), consistent with previous SNP genotyping analyses of parasites from the Thai–Myanmar border [33] and other SE Asian locations [12].

Fig.

…”

Antimalarial drug resistance: linking Plasmodium falciparum parasite biology to the clinic

“…ART resistance (as manifested by delayed parasite clearance following treatment with an artesunate monotherapy or with an ACT) was first reported in 2008 (ref. 10) but was already present several years earlier in western Cambodia 23 . Treatment failure owing to resistance to one or both components of an ACT has been documented first for ASMQ and, more recently, for DHA-PPQ 36,39,40,47,158 .…”

“…Recent studies show that the initial ‘soft sweeps’ of multiple mutant K13 variants, which emerged and spread on several genetic backgrounds in the Greater Mekong subregion, have transitioned into a ‘hard sweep’ across the region of a small number of parasite genotypes that predominantly harbor the K13 C580Y mutation 19,23,24 . In a recent in vitro study, Asian parasites genetically engineered to express the K13 C580Y mutation outproliferated their isogenic counterparts expressing K13 R539T or I543T 30 .…”

Malaria Epidemiology at the Clone Level

“…Research to understand the underlying genetic background that facilitates emergence of drug resistance is ongoing, thus hoping to identify geographic regions were the risk of de-novo artemisinin resistance development is highest [82, 86]. In parallel, in Southeast Asia the frequency of the Kelch13-C580Y SNP is increasing, showing the selective advantage and spread of artemisinin-resistant clones [87]. …”