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Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

Abstract

We describe an analysis of genome variation in 825 P. falciparum samples from Asia and Africa that identifies an unusual pattern of parasite population structure at the epicenter of artemisinin resistance in western Cambodia. Within this relatively small geographic area, we have discovered several distinct but apparently sympatric parasite subpopulations with extremely high levels of genetic differentiation. Of particular interest are three subpopulations, all associated with clinical resistance to artemisinin, which have skewed allele frequency spectra and high levels of haplotype homozygosity, indicative of founder effects and recent population expansion. We provide a catalog of SNPs that show high levels of differentiation in the artemisinin-resistant subpopulations, including codon variants in transporter proteins and DNA mismatch repair proteins. These data provide a population-level genetic framework for investigating the biological origins of artemisinin resistance and for defining molecular markers to assist in its elimination.

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Figure 1: Population structure in the sample set analyzed.
Figure 2: Chromosome painting.
Figure 3: Genetic and phenotypic differentiation between Cambodian subpopulations.
Figure 4: Evidence for multiple founder effects in Cambodian subpopulations.

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Acknowledgements

We would like to thank V. Cornelius and R. Giacomantonio for their support in producing and reviewing this manuscript; S. Uk and E.S. Phelps for their contributions in the Cambodian studies; and T. Anderson for helpful review comments. The sequencing, genotyping and analysis components of this study were supported by the Wellcome Trust through core funding of the Wellcome Trust Sanger Institute (098051), core funding of the Wellcome Trust Centre for Human Genetics (090532/Z/09/Z) and a Strategic Award (090770/Z/09/Z) and the MRC through the MRC Centre for Genomics and Global Health (G0600718) and an MRC Professorship to D.P.K. (G19/9). Other parts of this study were partly supported by the Wellcome Trust; the MRC; the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, US National Institutes of Health; and a Howard Hughes Medical Institute International Scholarship (55005502) to A.A.D. P.R. is a staff member of the World Health Organization; he alone is responsible for the views expressed in this publication, and they do not necessarily represent the decisions, policy or views of the World Health Organization.

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Authors and Affiliations

Authors

Contributions

S.C., C.A., P.L., S. Suon, S. Sreng, J.M.A., S.D., C.N., C.M.C., D.S., Y.S., C.L., M.M.F., L.A.-E., A.V.O.H., V.A., M.I., F.N., X.S., P.R., F.A., C.D., T.T.H., M.F.B., C.Q.T., A.A.-N., D.J.C., A.A.D., O.K.D., I.Z., J.-B.O., S.A., N.P.D., N.J.W., D.B., A.M.D., C.V.P. and R.M.F. carried out field and laboratory studies to obtain P. falciparum samples for sequencing. C.A., P.L., S. Suon, S. Sreng, J.M.A., S.D., C.N., C.M.C., D.S., Y.S., C.L., M.M.F., F.N., X.S., P.R., F.A., N.J.W., D.B., A.M.D., C.V.P. and R.M.F. carried out clinical studies to obtain ART phenotype data. S.C., D.A., E.D., M.S., S.A., O.K., S.O.O., B.M., C.I.N. and M.B. developed and implemented methods for sample processing and sequencing library preparation. O.M., J.A.-G., M.M., G. Maslen, V.R.-R., D.J. and A.M. developed software for data management and visualization. K.A.R., C.H., D.A. and M.M. carried out validation experiments. C.V.P., S.T.-H., G. McVean and R.M.F. contributed to development of the project. B.M., M.B., C.I.N. and J.C.R. provided project management and oversight. O.M., J.A.-G., M.M., J.O., C.G. and C.C.A.S. carried out data analyses. D.P.K., O.M. and J.A.-G. wrote the manuscript. All authors reviewed the manuscript.

Corresponding author

Correspondence to Dominic P Kwiatkowski.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9, Supplementary Tables 1–6 and 8–14, Supplementary Note (PDF 1595 kb)

Supplementary Table 7

Lists of SNPs that are highly differentiated in the Cambodian outlier subpopulations, compared to KH1. (XLSX 137 kb)

Supplementary Table 8

Lists of SNP that are highly differentiated between the Cambodian subpopulations. (XLSX 210 kb)

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Miotto, O., Almagro-Garcia, J., Manske, M. et al. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat Genet 45, 648–655 (2013). https://doi.org/10.1038/ng.2624

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