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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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.

Author information

Author notes

    • Youry Se

    Deceased.

Affiliations

  1. Medical Research Council (MRC) Centre for Genomics and Global Health, University of Oxford, Oxford, UK.

    • Olivo Miotto
    • , Jacob Almagro-Garcia
    • , Kirk A Rockett
    • , Lucas Amenga-Etego
    • , Oliver Koch
    • , Alistair Miles
    • , Chris I Newbold
    • , Chris C A Spencer
    •  & Dominic P Kwiatkowski
  2. Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.

    • Olivo Miotto
    • , Mallika Imwong
    • , François Nosten
    • , Nicholas P Day
    • , Nicholas J White
    •  & Arjen M Dondorp
  3. Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    • Olivo Miotto
    • , Jacob Almagro-Garcia
    • , Magnus Manske
    • , Bronwyn MacInnis
    • , Susana Campino
    • , Kirk A Rockett
    • , Daniel Alcock
    • , Eleanor Drury
    • , Mandy Sanders
    • , Gareth Maslen
    • , Valentin Ruano-Rubio
    • , Dushyanth Jyothi
    • , Samuel O Oyola
    • , Julian C Rayner
    • , Chris I Newbold
    • , Matthew Berriman
    •  & Dominic P Kwiatkowski
  4. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

    • Jacob Almagro-Garcia
    • , Kirk A Rockett
    • , Christina Hubbart
    • , Valentin Ruano-Rubio
    • , Alistair Miles
    • , John O'Brien
    • , Chris C A Spencer
    • , Gilean McVean
    •  & Dominic P Kwiatkowski
  5. National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA.

    • Chanaki Amaratunga
    • , Pharath Lim
    • , Jennifer M Anderson
    • , Xin-zhuan Su
    •  & Rick M Fairhurst
  6. National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia.

    • Pharath Lim
    • , Seila Suon
    • , Sokunthea Sreng
    • , Socheat Duong
    • , Chea Nguon
    •  & Char Meng Chuor
  7. Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand.

    • David Saunders
    • , Mark M Fukuda
    •  & Delia Bethell
  8. USAMC-AFRIMS, Phnom Penh, Cambodia.

    • Youry Se
    •  & Chantap Lon
  9. Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA.

    • Mark M Fukuda
  10. Navrongo Health Research Centre, Navrongo, Ghana.

    • Lucas Amenga-Etego
    • , Abraham V O Hodgson
    •  & Victor Asoala
  11. Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.

    • Mallika Imwong
  12. Howard Hughes Medical Institute, University of Maryland School of Medicine, Baltimore, Maryland, USA.

    • Shannon Takala-Harrison
    •  & Christopher V Plowe
  13. Shoklo Malaria Research Unit, Mae Sot, Tak, Thailand.

    • François Nosten
  14. Centre for Tropical Medicine, University of Oxford, Oxford, UK.

    • François Nosten
    • , Christiane Dolecek
    • , Tran Tinh Hien
    • , Maciej F Boni
    • , Nicholas P Day
    • , Nicholas J White
    •  & Arjen M Dondorp
  15. Global Malaria Programme, World Health Organization, Geneva, Switzerland.

    • Pascal Ringwald
  16. Unité d'Immunologie Moléculaire des Parasites, Institut Pasteur, Paris, France.

    • Frédéric Ariey
  17. Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.

    • Christiane Dolecek
    • , Tran Tinh Hien
    • , Maciej F Boni
    •  & Cao Quang Thai
  18. MRC Laboratories, Fajara, The Gambia.

    • Alfred Amambua-Ngwa
    •  & David J Conway
  19. London School of Hygiene and Tropical Medicine, London, UK.

    • David J Conway
  20. Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies of Bamako, Bamako, Mali.

    • Abdoulaye A Djimdé
    •  & Ogobara K Doumbo
  21. Institut de Recherche en Sciences de la Santé, Direction Régionale de l'Ouést, Bobo-Dioulasso, Burkina Faso.

    • Issaka Zongo
    •  & Jean-Bosco Ouedraogo
  22. Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

    • Sarah Auburn
  23. Department of Statistics, University of Oxford, Oxford, UK.

    • Chris Gamble
  24. Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.

    • Chris I Newbold

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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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dominic P Kwiatkowski.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–9, Supplementary Tables 1–6 and 8–14, Supplementary Note

Excel files

  1. 1.

    Supplementary Table 7

    Lists of SNPs that are highly differentiated in the Cambodian outlier subpopulations, compared to KH1.

  2. 2.

    Supplementary Table 8

    Lists of SNP that are highly differentiated between the Cambodian subpopulations.

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DOI

https://doi.org/10.1038/ng.2624

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