Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics

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 and Ric N. Price ()
Additional contact information
Sarah Auburn: Menzies School of Health Research and Charles Darwin University
Ernest D. Benavente: London School of Hygiene and Tropical Medicine
Olivo Miotto: Li Ka Shing Centre for Health Information and Discovery
Richard D. Pearson: Li Ka Shing Centre for Health Information and Discovery
Roberto Amato: Li Ka Shing Centre for Health Information and Discovery
Matthew J. Grigg: Menzies School of Health Research and Charles Darwin University
Bridget E. Barber: Menzies School of Health Research and Charles Darwin University
Timothy William: Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit
Irene Handayuni: Menzies School of Health Research and Charles Darwin University
Jutta Marfurt: Menzies School of Health Research and Charles Darwin University
Hidayat Trimarsanto: Eijkman Institute for Molecular Biology
Rintis Noviyanti: Eijkman Institute for Molecular Biology
Kanlaya Sriprawat: Mahidol University
Francois Nosten: Mahidol University
Susana Campino: London School of Hygiene and Tropical Medicine
Taane G. Clark: London School of Hygiene and Tropical Medicine
Nicholas M. Anstey: Menzies School of Health Research and Charles Darwin University
Dominic P. Kwiatkowski: Li Ka Shing Centre for Health Information and Discovery
Ric N. Price: Menzies School of Health Research and Charles Darwin University

Nature Communications, 2018, vol. 9, issue 1, 1-12

Abstract: Abstract The incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination.

Date: 2018
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DOI: 10.1038/s41467-018-04965-4

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