Parasite genomics

  • Article | | open

    Understanding genomic variation in Plasmodium falciparum parasites and inferring migration patterns can guide malaria elimination strategies. Using genome-wide data for 1722 parasites collected from 54 districts, the authors use identity-by-descent approaches to estimate regional parasite migration and spread of artemisinin drug resistance.

    • Amol C. Shetty
    • , Christopher G. Jacob
    • , Fang Huang
    • , Yao Li
    • , Sonia Agrawal
    • , David L. Saunders
    • , Chanthap Lon
    • , Mark M. Fukuda
    • , Pascal Ringwald
    • , Elizabeth A. Ashley
    • , Kay Thwe Han
    • , Tin Maung Hlaing
    • , Myaing M. Nyunt
    • , Joana C. Silva
    • , Kathleen E. Stewart
    • , Christopher V. Plowe
    • , Timothy D. O’Connor
    • , Shannon Takala-Harrison
    • , Harald Noedl
    • , Wasif A. Khan
    • , Paul Newton
    • , Myat P. Kyaw
    • , Nicholas J. White
    • , Arjen M. Dondorp
    • , Nicholas P. Day
    • , Charles J. Woodrow
    • , Mehul Dhorda
    • , M. Abul Faiz
    • , Rick M. Fairhurst
    • , Pharath Lim
    • , Rupam Tripura
    • , Mayfong Mayxay
    • , Ye Htut
    • , Francois Nosten
    • , Aung Pyae Phyo
    • , Sasithon Pukrittayakamee
    • , Tran Tinh Hien
    • , Nguyen Thanh Thuy Nhien
    • , Olugbenga A. Mokuolu
    • , Caterina I. Fanello
    •  & Marie A. Onyamboko
  • Article | | open

    Mechanisms underlying increasing artemisinin resistance of Plasmodium in Southeast Asia remain unclear. Here, Zhu et al. integrate TWAS, GWAS and eQTL analyses for 773 P. falciparum isolates and identify genetic and transcriptomic backgrounds to artemisinin resistance.

    • Lei Zhu
    • , Jaishree Tripathi
    • , Frances Maureen Rocamora
    • , Olivo Miotto
    • , Rob van der Pluijm
    • , Till S. Voss
    • , Sachel Mok
    • , Dominic P. Kwiatkowski
    • , François Nosten
    • , Nicholas P. J. Day
    • , Nicholas J. White
    • , Arjen M. Dondorp
    • , Zbynek Bozdech
    • , Aung Pyae Phyo
    • , Elizabeth A. Ashley
    • , Frank Smithuis
    • , Khin Lin
    • , Kyaw Myo Tun
    • , M Abul Faiz
    • , Mayfong Mayxay
    • , Mehul Dhorda
    • , Nguyen Thanh Thuy-Nhien
    • , Paul N. Newton
    • , Sasithon Pukrittayakamee
    • , Tin M. Hlaing
    • , Tran Tinh Hien
    •  & Ye Htut
  • Article | | open

    Increasing resistance of Plasmodium falciparum strains to piperaquine (PPQ) in Southeast Asia is of concern and resistance mechanisms are incompletely understood. Here, Ross et al. show that mutations in the P. falciparum chloroquine resistance transporter are rapidly increasing in prevalence in Cambodia and confer resistance to PPQ.

    • Leila S. Ross
    • , Satish K. Dhingra
    • , Sachel Mok
    • , Tomas Yeo
    • , Kathryn J. Wicht
    • , Krittikorn Kümpornsin
    • , Shannon Takala-Harrison
    • , Benoit Witkowski
    • , Rick M. Fairhurst
    • , Frederic Ariey
    • , Didier Menard
    •  & David A. Fidock
  • Article | | open

    Plasmodium vivax incidence in Malaysia has declined markedly over the last decade, despite evidence of chloroquine resistance. Here, Auburn et al. compare population structure of P. vivax in Malaysia to regions with intermediate and high transmission and identify genetic regions under putative selection.

    • Sarah Auburn
    • , Ernest D. Benavente
    • , Olivo Miotto
    • , Richard D. Pearson
    • , Roberto Amato
    • , Matthew J. Grigg
    • , Bridget E. Barber
    • , Timothy William
    • , Irene Handayuni
    • , Jutta Marfurt
    • , Hidayat Trimarsanto
    • , Rintis Noviyanti
    • , Kanlaya Sriprawat
    • , Francois Nosten
    • , Susana Campino
    • , Taane G. Clark
    • , Nicholas M. Anstey
    • , Dominic P. Kwiatkowski
    •  & Ric N. Price
  • Article | | open

    Unlike chimpanzees and gorillas, bonobos have not been found infected by malaria parasites in the wild. Here, Liu et al. report more thorough survey and sequencing results showing that bonobos host malaria parasites, including a yet-unknown species, but only in the eastern-most part of their range.

    • Weimin Liu
    • , Scott Sherrill-Mix
    • , Gerald H. Learn
    • , Erik J. Scully
    • , Yingying Li
    • , Alexa N. Avitto
    • , Dorothy E. Loy
    • , Abigail P. Lauder
    • , Sesh A. Sundararaman
    • , Lindsey J. Plenderleith
    • , Jean-Bosco N. Ndjango
    • , Alexander V. Georgiev
    • , Steve Ahuka-Mundeke
    • , Martine Peeters
    • , Paco Bertolani
    • , Jef Dupain
    • , Cintia Garai
    • , John A. Hart
    • , Terese B. Hart
    • , George M. Shaw
    • , Paul M. Sharp
    •  & Beatrice H. Hahn
  • Article | | open

    African apes harbour six Plasmodium species, one of which gave rise to the human malaria parasite. Here, Sundaraman et al. use selective whole-genome amplification to determine genome sequences from two chimpanzee Plasmodium species, shedding light on the evolutionary origin of the human parasite.

    • Sesh A. Sundararaman
    • , Lindsey J. Plenderleith
    • , Weimin Liu
    • , Dorothy E. Loy
    • , Gerald H. Learn
    • , Yingying Li
    • , Katharina S. Shaw
    • , Ahidjo Ayouba
    • , Martine Peeters
    • , Sheri Speede
    • , George M. Shaw
    • , Frederic D. Bushman
    • , Dustin Brisson
    • , Julian C. Rayner
    • , Paul M. Sharp
    •  & Beatrice H. Hahn
  • Article | | open

    The Asian liver fluke is a parasitic worm that is linked to an increased risk of malignant cancer. Here, the authors sequence the draft genome and transcriptome of this fluke and provide insight into how the species has adapted to be able to survive in the bile duct.

    • Neil D. Young
    • , Niranjan Nagarajan
    • , Suling Joyce Lin
    • , Pasi K. Korhonen
    • , Aaron R. Jex
    • , Ross S. Hall
    • , Helena Safavi-Hemami
    • , Worasak Kaewkong
    • , Denis Bertrand
    • , Song Gao
    • , Qihui Seet
    • , Sopit Wongkham
    • , Bin Tean Teh
    • , Chaisiri Wongkham
    • , Pewpan Maleewong Intapan
    • , Wanchai Maleewong
    • , Xinhua Yang
    • , Min Hu
    • , Zuo Wang
    • , Andreas Hofmann
    • , Paul W. Sternberg
    • , Patrick Tan
    • , Jun Wang
    •  & Robin B. Gasser
  • Article | | open

    Tracing the source of malarial infections is an important step towards monitoring and controlling the disease. Here, Preston et al. analyse sequence data from 711 isolates and design a genetic barcode based on combined mitochondrial and apicoplast genomes that is able to distinguish between malaria parasites isolated from different geographical regions.

    • Mark D. Preston
    • , Susana Campino
    • , Samuel A. Assefa
    • , Diego F. Echeverry
    • , Harold Ocholla
    • , Alfred Amambua-Ngwa
    • , Lindsay B. Stewart
    • , David J. Conway
    • , Steffen Borrmann
    • , Pascal Michon
    • , Issaka Zongo
    • , Jean-Bosco Ouédraogo
    • , Abdoulaye A. Djimde
    • , Ogobara K. Doumbo
    • , Francois Nosten
    • , Arnab Pain
    • , Teun Bousema
    • , Chris J. Drakeley
    • , Rick M. Fairhurst
    • , Colin J. Sutherland
    • , Cally Roper
    •  & Taane G. Clark