Abstract

We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin, the frontline antimalarial drug. Across 15 locations in Southeast Asia, we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains, which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin), arps10 (apicoplast ribosomal protein S10), mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd, arps10, mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population.

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Acknowledgements

We thank the following colleagues for their efforts in support of this work: P. Vauterin, G. Band and Q.S. Le; J. Anderson, D. Dek, S. Duong, R. Gwadz, S. Mao, V. Ou, B. Sam, C. Sopha, V. Try and T. Wellems; the personnel at Phuoc Long Hospital, Bu Gia Map Health Station, Malaria Control Center of Binh Phuoc Province, Vietnam; M. Phommasansack, B. Phimphalat and C. Vilayhong; and A.K. Tshefu. Special thanks are given to V. Cornelius and K. Johnson for their continual support of the analysis group. The sequencing for this study was funded by the Wellcome Trust through core funding of the Wellcome Trust Sanger Institute (098051). The Wellcome Trust also supports the Wellcome Trust Centre for Human Genetics (090532/Z/09/Z), the Resource Centre for Genomic Epidemiology of Malaria (090770/Z/09/Z) and the Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme. The Centre for Genomics and Global Health is supported by the UK Medical Research Council (G0600718). This work was funded in part by the Bill and Melinda Gates Foundation (OPP1040463), the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, US National Institutes of Health and the Department for International Development (PO5408). P.R. is a staff member of the World Health Organization. The views expressed in this publication are those of the authors and do not necessarily reflect the positions, decisions, policies or views of their employers or of the funding organizations.

Author information

Author notes

    • Olivo Miotto
    •  & Roberto Amato

    These authors contributed equally to this work.

Affiliations

  1. Wellcome Trust Sanger Institute, Hinxton, UK.

    • Olivo Miotto
    • , Roberto Amato
    • , Bronwyn MacInnis
    • , Jacob Almagro-Garcia
    • , Daniel Mead
    • , Samuel O Oyola
    • , Magnus Manske
    • , Jim Stalker
    • , Eleanor Drury
    • , Susana Campino
    •  & Dominic P Kwiatkowski
  2. Medical Research Council (MRC) Centre for Genomics and Global Health, University of Oxford, Oxford, UK.

    • Olivo Miotto
    • , Roberto Amato
    • , Bronwyn MacInnis
    • , Jacob Almagro-Garcia
    • , Magnus Manske
    • , Jim Stalker
    • , Susana Campino
    • , Lucas Amenga-Etego
    • , Chris C A Spencer
    • , Gilean McVean
    •  & Dominic P Kwiatkowski
  3. Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.

    • Olivo Miotto
    • , Elizabeth A Ashley
    • , Charles Woodrow
    • , Francois Nosten
    • , Aung Pyae Phyo
    • , Caterina I Fanello
    • , Nicholas P Day
    • , Arjen M Dondorp
    •  & Nicholas J White
  4. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

    • Roberto Amato
    • , Jacob Almagro-Garcia
    • , Chris C A Spencer
    • , Gilean McVean
    •  & Dominic P Kwiatkowski
  5. Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

    • Elizabeth A Ashley
    • , Mehul Dhorda
    • , Charles Woodrow
    • , Hien Tinh Tran
    • , Francois Nosten
    • , Aung Pyae Phyo
    • , Paul N Newton
    • , Mayfong Mayxay
    • , Caterina I Fanello
    • , Marie Onyamboko
    • , Nicholas P Day
    • , Arjen M Dondorp
    •  & Nicholas J White
  6. Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA.

    • Chanaki Amaratunga
    • , Pharath Lim
    •  & Rick M Fairhurst
  7. National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia.

    • Pharath Lim
    • , Char Meng Chuor
    • , Chea Nguon
    • , Seila Suon
    •  & Sokunthea Sreng
  8. Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA.

    • Mehul Dhorda
    • , Christopher G Jacob
    • , Shannon Takala-Harrison
    •  & Christopher V Plowe
  9. WorldWide Antimalarial Resistance Network (WWARN), Asia Regional Centre, Mahidol University, Bangkok, Thailand.

    • Mehul Dhorda
  10. Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.

    • Mallika Imwong
    • , Sasithon Pukrittayakamee
    •  & Kesinee Chotivanich
  11. Navrongo Health Research Centre, Navrongo, Ghana.

    • Lucas Amenga-Etego
  12. Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.

    • Thuy-Nhien Nguyen Thanh
    •  & Hien Tinh Tran
  13. Global Malaria Programme, World Health Organization, Geneva, Switzerland.

    • Pascal Ringwald
  14. Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand.

    • Delia Bethell
  15. Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.

    • Francois Nosten
    •  & Aung Pyae Phyo
  16. Lao Oxford Mahosot Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Laos.

    • Paul N Newton
    •  & Mayfong Mayxay
  17. Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Laos.

    • Mayfong Mayxay
  18. Center of Malariology, Parasitology and Entomology, Ministry of Health, Vientiane, Laos.

    • Maniphone Khanthavong
    •  & Bouasy Hongvanthong
  19. Department of Medical Research, Lower Myanmar, Yangon, Myanmar.

    • Ye Htut
    • , Kay Thwe Han
    •  & Myat Phone Kyaw
  20. Malaria Research Group and Dev Care Foundation, Dhaka, Bangladesh.

    • Md Abul Faiz
  21. Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo.

    • Marie Onyamboko
  22. Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria.

    • Olugbenga A Mokuolu
  23. Howard Hughes Medical Institute, University of Maryland School of Medicine, Baltimore, Maryland, USA.

    • Christopher V Plowe
  24. Department of Statistics, University of Oxford, Oxford, UK.

    • Gilean McVean

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Contributions

C.A., P.L., M.D., M.I., L.A.-E., T.-N.N.T., H.T.T., D.B., F.N., A.P.P., S.P., K.C., C.M.C., C.N., S. Suon, S. Sreng, P.N.N., M. Mayxay, M.K., B.H., Y.H., K.T.H., M.P.K., M.A.F., C.I.F., M.O. and O.A.M. carried out field and laboratory work to obtain P. falciparum samples for sequencing. E.A.A., C.A., P.L., T.-N.N.T., H.T.T., D.B., F.N., A.P.P., S.P., K.C., C.M.C., C.N., P.N.N., M. Mayxay, M.K., B.H., Y.H., K.T.H., M.P.K., M.A.F., C.I.F., M.O. and O.A.M. carried out clinical studies to obtain parasite clearance data. D.M., S.O.O., E.D., S.C. and B.M. developed and implemented methods for sample processing and sequencing library preparation. J.S. and M. Manske managed data production pipelines. E.A.A., C.W., P.R., C.G.J., S.T.-H., C.V.P., N.P.D., A.M.D., R.M.F., N.J.W., O.M., B.M. and D.P.K. contributed to study design and management. O.M., R.A., J.A.-G., C.C.A.S., G.M. and D.P.K. performed data analyses. O.M., R.A., J.A.-G., C.C.A.S., G.M. and D.P.K. performed data analyses. O.M., R.A. and D.P.K. drafted the manuscript, which was reviewed by all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dominic P Kwiatkowski.

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https://doi.org/10.1038/ng.3189

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