publication . Other literature type . Article . 2016

Genomic analysis of local variation and recent evolution in Plasmodium vivax

Marcelo Ferreira; Julian C. Rayner; Lee Hart; Nadira Karunaweera; Daniel Mead; Alistair Miles; Alyssa Barry; Francois Nosten; Sarah Auburn; Dominic Kwiatkowski; ...
Open Access
  • Published: 27 Jun 2016
  • Publisher: Springer Science and Business Media LLC
  • Country: United Kingdom
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 ...
Subjects
free text keywords: Article
Funded by
RCUK| MRC Centre for Genomics and Global Health
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: G0600718
  • Funding stream: MRC
,
WT| Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 098051
  • Funding stream: Cellular and Molecular Neuroscience
,
WT| Resource centre for genomic epidemiology of malaria.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 090770
  • Funding stream: Immune System in Health and Disease
56 references, page 1 of 4

Gething, PW. A long neglected world malaria map: Plasmodium vivax endemicity in 2010. PLoS Negl Trop Dis. 2012; 6: e1814 [OpenAIRE] [PubMed]

Miller, LH, Mason, SJ, Clyde, DF, McGinniss, MH. The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-group genotype, FyFy. N Engl J Med. 1976; 295: 302-4 [PubMed]

Ménard, D. Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people. Proc Natl Acad Sci U S A. 2010; 107: 5967-71 [OpenAIRE] [PubMed]

Price, RN. Vivax malaria: neglected and not benign. Am J Trop Med Hyg. 2007; 77: 79-87 [OpenAIRE] [PubMed]

Battle, KE. The global public health significance of Plasmodium vivax. Adv Parasitol. 2012; 80: 1 [PubMed]

White, NJ. Determinants of relapse periodicity in Plasmodium vivax malaria. Malar J. 2011; 10: 297 [OpenAIRE] [PubMed]

Price, RN. Global extent of chloroquine-resistant Plasmodium vivax: a systematic review and meta-analysis. Lancet Infect Dis. 2014; 14: 982-91 [OpenAIRE] [PubMed]

Karunaweera, ND. Extensive microsatellite diversity in the human malaria parasite Plasmodium vivax. Gene. 2008; 410: 105-112 [OpenAIRE] [PubMed]

Barry, AE, Waltmann, A, Koepfli, C, Barnadas, C, Mueller, I. Uncovering the transmission dynamics of Plasmodium vivax using population genetics. Pathog Glob Health. 2015; 109: 142-152 [OpenAIRE] [PubMed]

Koepfli, C. Plasmodium vivax diversity and population structure across four continents. PLoS Negl Trop Dis. 2015; 9: e0003872 [OpenAIRE] [PubMed]

Carlton, JM. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 2008; 455: 757-763 [OpenAIRE] [PubMed]

Dharia, NV. Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes. Proc Natl Acad Sci U S A. 2010; 107: 20045-50 [OpenAIRE] [PubMed]

Hester, J. De novo assembly of a field isolate genome reveals novel Plasmodium vivax erythrocyte invasion genes. PLoS Negl Trop Dis. 2013; 7: e2569 [OpenAIRE] [PubMed]

Chan, ER. Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax. PLoS Negl Trop Dis. 2012; 6: e1811 [OpenAIRE] [PubMed]

Neafsey, DE. The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet. 2012; 44: 1046-1050 [OpenAIRE] [PubMed]

56 references, page 1 of 4
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 ...
Subjects
free text keywords: Article
Funded by
RCUK| MRC Centre for Genomics and Global Health
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: G0600718
  • Funding stream: MRC
,
WT| Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 098051
  • Funding stream: Cellular and Molecular Neuroscience
,
WT| Resource centre for genomic epidemiology of malaria.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 090770
  • Funding stream: Immune System in Health and Disease
56 references, page 1 of 4

Gething, PW. A long neglected world malaria map: Plasmodium vivax endemicity in 2010. PLoS Negl Trop Dis. 2012; 6: e1814 [OpenAIRE] [PubMed]

Miller, LH, Mason, SJ, Clyde, DF, McGinniss, MH. The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-group genotype, FyFy. N Engl J Med. 1976; 295: 302-4 [PubMed]

Ménard, D. Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people. Proc Natl Acad Sci U S A. 2010; 107: 5967-71 [OpenAIRE] [PubMed]

Price, RN. Vivax malaria: neglected and not benign. Am J Trop Med Hyg. 2007; 77: 79-87 [OpenAIRE] [PubMed]

Battle, KE. The global public health significance of Plasmodium vivax. Adv Parasitol. 2012; 80: 1 [PubMed]

White, NJ. Determinants of relapse periodicity in Plasmodium vivax malaria. Malar J. 2011; 10: 297 [OpenAIRE] [PubMed]

Price, RN. Global extent of chloroquine-resistant Plasmodium vivax: a systematic review and meta-analysis. Lancet Infect Dis. 2014; 14: 982-91 [OpenAIRE] [PubMed]

Karunaweera, ND. Extensive microsatellite diversity in the human malaria parasite Plasmodium vivax. Gene. 2008; 410: 105-112 [OpenAIRE] [PubMed]

Barry, AE, Waltmann, A, Koepfli, C, Barnadas, C, Mueller, I. Uncovering the transmission dynamics of Plasmodium vivax using population genetics. Pathog Glob Health. 2015; 109: 142-152 [OpenAIRE] [PubMed]

Koepfli, C. Plasmodium vivax diversity and population structure across four continents. PLoS Negl Trop Dis. 2015; 9: e0003872 [OpenAIRE] [PubMed]

Carlton, JM. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 2008; 455: 757-763 [OpenAIRE] [PubMed]

Dharia, NV. Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes. Proc Natl Acad Sci U S A. 2010; 107: 20045-50 [OpenAIRE] [PubMed]

Hester, J. De novo assembly of a field isolate genome reveals novel Plasmodium vivax erythrocyte invasion genes. PLoS Negl Trop Dis. 2013; 7: e2569 [OpenAIRE] [PubMed]

Chan, ER. Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax. PLoS Negl Trop Dis. 2012; 6: e1811 [OpenAIRE] [PubMed]

Neafsey, DE. The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet. 2012; 44: 1046-1050 [OpenAIRE] [PubMed]

56 references, page 1 of 4
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