Close kinship within multiple-genotype malaria parasite infections

Malaria infections containing multiple parasite genotypes are ubiquitous in nature, and play a central role in models of recombination, intra-host dynamics, virulence, sex ratio, immunity and drug resistance evolution in Plasmodium. While these multiple infections (MIs) are often assumed to result from superinfection (bites from multiple infected mosquitoes), we know remarkably little about their composition or generation. We isolated 336 parasite clones from eight patients from Malawi (high transmission) and six from Thailand (low transmission) by dilution cloning. These were genotyped using 384 single-nucleotide polymorphisms, revealing 22 independent haplotypes in Malawi (2–6 per MI) and 15 in Thailand (2–5 per MI). Surprisingly, all six patients from Thailand and six of eight from Malawi contained related haplotypes, and haplotypes were more similar within- than between-infections. These results argue against a simple superinfection model. Instead, the observed kinship patterns may be explained by inoculation of multiple related haploid sporozoites from single mosquito bites, by immune suppression of parasite subpopulations within infections, and serial transmission of related parasites between people. That relatedness is maintained in endemic areas in the face of repeated bites from infected mosquitoes has profound implications for understanding malaria transmission, immunity and intra-host dynamics of co-infecting parasite genotypes

Population Structure Shapes Copy Number Variation in Malaria Parasites.

If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen

Parasites bearing a single copy of the multi-drug resistance gene (pfmdr-1) with wild-type SNPs predominate amongst Plasmodium falciparum isolates from Malawi

We genotyped 160 P. falciparum infections from Malawi for pfmdr-1 copy number changes and SNPs associated with in vivo tolerance and poor in vitro sensitivity to the component drugs of Coartem. We also measured in vitro susceptibility of 49 of these isolates to a variety of drugs in clinical use or with a potential for use in Africa. All 160 infections carried a single copy of pfmdr-1 but 34% exhibited sequence variation at 4 of the 5 polymorphic sites in pfmdr-1. Isolates carrying 86-Asn and 184-Tyr pfmdr-1 alleles were significantly less sensitive (p < 0.001) to mefloquine, lumefantrine, artemether and dihydroartemisinin compared with those bearing 86-Tyr and 184-Phe polymorphisms. This study provides baseline measures prior to policy change: continued surveillance for changes in baseline drug susceptibility, pfmdr-1 copy number and SNPs, and other putative Coartem resistance loci will be necessary to provide an early warning of emerging Coartem resistance in this setting. (C) 2009 Elsevier B.V. All rights reserved

Evanescent Wave Reduction Using a Segmented Wavemaker in a Two Dimensional Wave Tank

Evanescent waves are created by the wavemaking process during tank testing. They have long been a nuisance for engineers as they contaminate the wave field in the tank and result in additional inertial force experienced by a wavemaker. Evanescent waves are created by the mismatch between the motion of the wavemaker and the motion of the uid particles in a progressive wave. To avoid contamination of test results, often a considerable distance must be left between the wavemaker and the test area. This space requirement may be costly for small research groups or companies who wish to have a facility to perform some basic proof-of-concept tests in-house, but are restricted for space. The initial aim of this project was to develop a wavemaker which minimised this space requirement over a large range of frequencies. The exploration into the behaviour of evanescent waves from the point of view of the fundamentals of hydrodynamics has been very enlightening. It became clear with the discovery of an interference pattern between the evanescent waves, that this pattern can be optimised to effectively cancel out the evanescent wave fieeld. This interference pattern arises from a phase shift of � radians experienced by some of the evanescent waves, with respect to the others. The significance of this in hydrodynamics is that it explains the existence of negative added mass. The application for this knowledge far out reaches the topic of reducing the distortion in a wave tank. The ability to minimise the added mass of a wavemaker has a great deal of potential in both active absorbing wavemakers and wave energy conversion. For active absorbing wavemakers, the minimisation of added mass may be useful in the absorption of unwanted waves which can be particularly troublesome at high frequencies. The concept of designing the geometry of a wavemaker to simply match the motion of the uid particles has long been proposed; however, the difficulty with designing such a wavemaker is that the ideal geometry is frequency dependent. Hence, a design that eliminates the evanescent waves at one particular frequency will not be able to do so for other frequencies. An investigation into the design of a segmented wavemaker is presented here, as its geometry can easily be adjusted to suit different frequencies. The wavemaker theory for the multi-body problem of the segmented wavemaker is developed, and a new aspect of wavemaker theory that predicts a phase shift of � radians in some of the evanescent waves is presented for the first time. A hypothesis is put forward, and then investigated, proposing that this phase shift can be exploited to create an interference pattern that can effectively cancel out the evanescent waves. The hydrodynamics of the segmented wavemaker were constrained using the Newton-Euler equations of motion with Eliminated Constraints (NE-EC). This approach facilitated a comparison between wavemakers with multiple degrees of freedom and traditional wavemakers with a single degree of freedom. The lengths and strokes of each segment in the wavemaker are optimised to reduce the distortion caused by the evanescent waves using two approaches. Approach one follows the traditional ideas and optimises the lengths and strokes of the segments to best approximate the motion of the uid particles in a progressive wave. Approach two optimises the lengths and strokes of the segments in order to minimise the distance between the wavemaker and the testable area in the tank. Approach two exploits the phase shift in the evanescent waves by finding the optimal interference pattern that effectively cancels out the evanescent waves. A comparison between both approaches shows that effectively eliminating the distortion caused by the evanescent waves is much more achievable by optimising the interference pattern between the evanescent waves, rather than trying to approximate a progressive wave. The results for the segmented wavemakers optimised using approach two predicted that the distortion can be effectively eliminated for a wide range of frequencies using a segment wavemaker consisting of three aps. A sensitivity analysis indicates that the performance of the wavemaker is somewhat effected by errors in the segments strokes, but the overall performance is still better than what has been developed to date

<i>F</i>_<i>ST</i> estimates based on 2001–2014 WGS data plotted with respect to inter-clinic distance.

<p>Annotations refer to site comparisons using abbreviated clinic names (MLA for Maela, 55 parasite samples; WPA for Wang Pha, 103 parasite samples; MKK for Mae Kon Ken, 4 parasite samples; and MKT for Mawker Thai, 16 parasite samples). All parasite samples were single-infection. For clinic pair, A and B say, the <i>F</i>_<i>ST</i> estimate was based on <i>n</i>_A + <i>n</i>_B parasite samples, where <i>n</i> denotes the number of parasite samples per clinic. Error bars represent 95% confidence intervals, based on boostrapping over SNPs.</p