Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates
© The Author 2014. Background: Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. Methods: We performed whole-genome sequencing of 69 P. falciparum isolates from Ma...
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th-mahidol.348762018-11-09T10:06:34Z Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates Harold Ocholla Mark D. Preston Mwapatsa Mipando Anja T.R. Jensen Susana Campino Bronwyn Macinnis Daniel Alcock Anja Terlouw Issaka Zongo Jean Bosco Oudraogo Abdoulaye A. Djimde Samuel Assefa Ogobara K. Doumbo Steffen Borrmann Alexis Nzila Kevin Marsh Rick M. Fairhurst Francois Nosten Tim J.C. Anderson Dominic P. Kwiatkowski Alister Craig Taane G. Clark Jacqui Montgomery Malawi-Liverpool-Wellcome Trust Clinical Research Programme University of Malawi Liverpool School of Tropical Medicine London School of Hygiene & Tropical Medicine Wellcome Trust Sanger Institute Wellcome Trust Centre for Human Genetics Kobenhavns Universitet Copenhagen University Hospital Institut de Recherche en Sciences de la Santé University of Bamako Universitat Tubingen King Fahd University of Petroleum and Minerals Wellcome Trust Research Laboratories Nairobi National Institute of Allergy and Infectious Diseases Texas Biomedical Research Institute Nuffield Department of Clinical Medicine Mahidol University KEMRI/CDC Laboratories Pennsylvania State University Medicine © The Author 2014. Background: Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. Methods: We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used population genetics approaches to investigate genetic diversity and population structure and identify loci under selection. Results. High genetic diversity (π = 2.4 × 10<sup>-4</sup>), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known drugresistance loci, including pfcrt, pfdhps, pfmdr1, and pfgch1. Conclusions: The sequence variations observed at drug-resistance loci reflect differences in each country's historical use of antimalarial drugs and may be useful in formulating local malaria treatment guidelines. 2018-11-09T03:06:34Z 2018-11-09T03:06:34Z 2014-01-01 Article Journal of Infectious Diseases. Vol.210, No.12 (2014), 1991-2000 10.1093/infdis/jiu349 15376613 00221899 2-s2.0-84924468292 https://repository.li.mahidol.ac.th/handle/123456789/34876 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84924468292&origin=inward |
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Medicine Harold Ocholla Mark D. Preston Mwapatsa Mipando Anja T.R. Jensen Susana Campino Bronwyn Macinnis Daniel Alcock Anja Terlouw Issaka Zongo Jean Bosco Oudraogo Abdoulaye A. Djimde Samuel Assefa Ogobara K. Doumbo Steffen Borrmann Alexis Nzila Kevin Marsh Rick M. Fairhurst Francois Nosten Tim J.C. Anderson Dominic P. Kwiatkowski Alister Craig Taane G. Clark Jacqui Montgomery Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates |
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© The Author 2014. Background: Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. Methods: We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used population genetics approaches to investigate genetic diversity and population structure and identify loci under selection. Results. High genetic diversity (π = 2.4 × 10<sup>-4</sup>), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known drugresistance loci, including pfcrt, pfdhps, pfmdr1, and pfgch1. Conclusions: The sequence variations observed at drug-resistance loci reflect differences in each country's historical use of antimalarial drugs and may be useful in formulating local malaria treatment guidelines. |
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Malawi-Liverpool-Wellcome Trust Clinical Research Programme |
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Malawi-Liverpool-Wellcome Trust Clinical Research Programme Harold Ocholla Mark D. Preston Mwapatsa Mipando Anja T.R. Jensen Susana Campino Bronwyn Macinnis Daniel Alcock Anja Terlouw Issaka Zongo Jean Bosco Oudraogo Abdoulaye A. Djimde Samuel Assefa Ogobara K. Doumbo Steffen Borrmann Alexis Nzila Kevin Marsh Rick M. Fairhurst Francois Nosten Tim J.C. Anderson Dominic P. Kwiatkowski Alister Craig Taane G. Clark Jacqui Montgomery |
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Article |
author |
Harold Ocholla Mark D. Preston Mwapatsa Mipando Anja T.R. Jensen Susana Campino Bronwyn Macinnis Daniel Alcock Anja Terlouw Issaka Zongo Jean Bosco Oudraogo Abdoulaye A. Djimde Samuel Assefa Ogobara K. Doumbo Steffen Borrmann Alexis Nzila Kevin Marsh Rick M. Fairhurst Francois Nosten Tim J.C. Anderson Dominic P. Kwiatkowski Alister Craig Taane G. Clark Jacqui Montgomery |
author_sort |
Harold Ocholla |
title |
Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates |
title_short |
Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates |
title_full |
Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates |
title_fullStr |
Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates |
title_full_unstemmed |
Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates |
title_sort |
whole-genome scans provide evidence of adaptive evolution in malawian plasmodium falciparum isolates |
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2018 |
url |
https://repository.li.mahidol.ac.th/handle/123456789/34876 |
_version_ |
1763488225122320384 |