Abstract

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.

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Acknowledgements

We thank the patients and communities that provided samples for this study, and our many colleagues who supported this work in the field. Sequencing, data analysis and project coordination were funded by the Wellcome Trust (098051, 090770/Z/09/Z), the Medical Research Council (G0600718) and the UK Department for International Development (M006212). A.B. and I.M. acknowledge the Victorian State Government Operational Infrastructure Support and Australian Government National Health and Medical Research Council Independent Medical Research Institutes Infrastructure Support Scheme (NHMRC IRIISS). S.A. and R.N.P. are funded by the Wellcome Trust (Senior Fellowship in Clinical Science awarded to R.N.P., 091625). This study was supported in part by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health.

Author information

Author notes

    • Roberto Amato
    •  & Sarah Auburn

    These authors contributed equally to this work.

Affiliations

  1. Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    • Richard D Pearson
    • , Roberto Amato
    • , Olivo Miotto
    • , Eleanor Drury
    • , Daniel Mead
    • , Mihir Kekre
    • , Susana Campino
    • , Magnus Manske
    • , Victoria J Cornelius
    • , Bronwyn MacInnis
    • , Kirk A Rockett
    • , Alistair Miles
    • , Julian C Rayner
    •  & Dominic P Kwiatkowski
  2. MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford, UK.

    • Richard D Pearson
    • , Roberto Amato
    • , Olivo Miotto
    • , Jacob Almagro-Garcia
    • , Christina Hubbart
    • , Lee Hart
    • , Ben Jeffery
    • , Victoria J Cornelius
    • , Kirk A Rockett
    • , Alistair Miles
    •  & Dominic P Kwiatkowski
  3. Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories, Australia.

    • Sarah Auburn
    • , Jutta Marfurt
    • , Nicholas M Anstey
    •  & Ric N Price
  4. Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.

    • Olivo Miotto
    •  & Nicholas J White
  5. National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA.

    • Chanaki Amaratunga
    •  & Rick M Fairhurst
  6. National Centre for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia.

    • Seila Suon
  7. Sampov Meas Referral Hospital, Pursat, Cambodia.

    • Sivanna Mao
  8. Eijkman Institute for Molecular Biology, Jakarta, Indonesia.

    • Rintis Noviyanti
    •  & Hidayat Trimarsanto
  9. Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit and Queen Elizabeth Hospital Clinical Research Centre, Kota Kinabalu, Sabah, Malaysia.

    • Timothy William
  10. Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.

    • Maciej F Boni
    • , Christiane Dolecek
    •  & Hien Tinh Tran
  11. Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea.

    • Pascal Michon
    • , Peter Siba
    •  & Livingstone Tavul
  12. Faculty of Medicine and Health Sciences, Divine Word University, Madang, Papua New Guinea.

    • Pascal Michon
  13. Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia.

    • Gabrielle Harrison
    • , Alyssa Barry
    •  & Ivo Mueller
  14. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.

    • Gabrielle Harrison
    • , Alyssa Barry
    •  & Ivo Mueller
  15. Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.

    • Marcelo U Ferreira
  16. Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.

    • Nadira Karunaweera
  17. Institut Pasteur de Madagascar, Antananarivo, Madagascar.

    • Milijaona Randrianarivelojosia
  18. Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu, China.

    • Qi Gao
  19. Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.

    • Francois Nosten
  20. Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

    • Francois Nosten
    •  & Ric N Price

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Contributions

C.A., S.S., S.M., R.N., H.T., J.M., N.M.A., T.W., M.F.B., C.D., H.T.T., N.J.W., P.M., P.S., L.T., G.H., A.B., I.M., M.U.F., N.K., M.R. and Q.G. carried out field and laboratory work to obtain P. vivax samples for sequencing. C.H., E.D., D.M., M.K., S.C., B.M. and K.A.R. developed and implemented methods for sample processing and sequencing library preparation. R.D.P., L.H., B.J. and M.M. managed data production pipelines. S.A., O.M., V.J.C., B.M., K.A.R., A.M., J.C.R., R.M.F., F.N., R.N.P. and D.P.K. contributed to study design and management. R.D.P., R.A., S.A., O.M., J.A.-G. and D.P.K. performed data analyses. R.D.P., R.A., S.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.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–9, Supplementary Tables 1–8 and Supplementary Note.

Excel files

  1. 1.

    Supplementary Data 1

    Gene-level summaries of variation data. The first sheets give aggregate metrics across all 148 samples used for population genetic analyses, and the other three sheets show metrics for WTH, WKH and ID respectively. Summaries are given for both high-quality SNPs (pass) and all discovered SNPs (all). We do not record SNPs or metrics for genes outside the core genome. N/S, nonsynonymous/synonymous ratio; π, nucleotide diversity per base; D, Tajima's D.

  2. 2.

    Supplementary Data 2

    CNV calls. Start and end coordinates, and copy number for all CNV calls longer than 3 kb.

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DOI

https://doi.org/10.1038/ng.3599

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