Genomic analysis of local variation and recent evolution in Plasmodium vivax

RD Pearson; R Amato; S Auburn; O Miotto; J Almagro-Garcia; C Amaratunga; S Suon; S Mao; R Noviyanti; H Trimarsanto; J Marfurt; NM Anstey; T William; MF Boni; C Dolecek; HT Tran; NJ White; P Michon; P Siba; L Tavul; G Harrison; A Barry; I Mueller; MU Ferreira; N Karunaweera; M Randrianarivelojosia; Q Gao; C Hubbart; L Hart; B Jeffery; E Drury; D Mead; M Kekre; S Campino; M Manske; VJ Cornelius; B MacInnis; KA Rockett; A Miles; JC Rayner; RM Fairhurst; F Nosten; RN Price; DP Kwiatkowski

Journal article

Genomic analysis of local variation and recent evolution in Plasmodium vivax

RD Pearson, R Amato, S Auburn, O Miotto, J Almagro-Garcia, C Amaratunga, S Suon, S Mao, R Noviyanti, H Trimarsanto, J Marfurt, NM Anstey, T William, MF Boni, C Dolecek, HT Tran, NJ White, P Michon, P Siba, L Tavul Show all

Nature Genetics | NATURE PUBLISHING GROUP | Published : 2016

DOI: 10.1038/ng.3599

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..

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University of Melbourne Researchers

Prof Ivo Mueller Author

Grants

Awarded by UK Research and Innovation

Funding 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.