Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia
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Issued Date
2023-12-01
Resource Type
eISSN
20452322
Scopus ID
2-s2.0-85177857710
Journal Title
Scientific Reports
Volume
13
Issue
1
Rights Holder(s)
SCOPUS
Bibliographic Citation
Scientific Reports Vol.13 No.1 (2023)
Suggested Citation
Kebede A.M., Sutanto E., Trimarsanto H., Benavente E.D., Barnes M., Pearson R.D., Siegel S.V., Erko B., Assefa A., Getachew S., Aseffa A., Petros B., Lo E., Mohammed R., Yilma D., Rumaseb A., Nosten F., Noviyanti R., Rayner J.C., Kwiatkowski D.P., Price R.N., Golassa L., Auburn S. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia. Scientific Reports Vol.13 No.1 (2023). doi:10.1038/s41598-023-47889-w Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/91315
Title
Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia
Author's Affiliation
Faculty of Tropical Medicine, Mahidol University
Mahidol Oxford Tropical Medicine Research Unit
Ethiopian Public Health Institute
Cambridge Institute for Medical Research
University of Gondar
Jimma University
Armauer Hansen Research Institute
Addis Ababa University
Eijkman Institute for Molecular Biology
University Medical Center Utrecht
Menzies School of Health Research
Drexel University College of Medicine
Nuffield Department of Medicine
Wellcome Sanger Institute
Exeins Health Initiative
MilliporeSigma
Mahidol Oxford Tropical Medicine Research Unit
Ethiopian Public Health Institute
Cambridge Institute for Medical Research
University of Gondar
Jimma University
Armauer Hansen Research Institute
Addis Ababa University
Eijkman Institute for Molecular Biology
University Medical Center Utrecht
Menzies School of Health Research
Drexel University College of Medicine
Nuffield Department of Medicine
Wellcome Sanger Institute
Exeins Health Initiative
MilliporeSigma
Other Contributor(s)
Abstract
Ethiopia has the greatest burden of Plasmodium vivax in Africa, but little is known about the epidemiological landscape of parasites across the country. We analysed the genomic diversity of 137 P. vivax isolates collected nine Ethiopian districts from 2012 to 2016. Signatures of selection were detected by cross-country comparisons with isolates from Thailand (n = 104) and Indonesia (n = 111), representing regions with low and high chloroquine resistance respectively. 26% (35/137) of Ethiopian infections were polyclonal, and 48.5% (17/35) of these comprised highly related clones (within-host identity-by-descent > 25%), indicating frequent co-transmission and superinfection. Parasite gene flow between districts could not be explained entirely by geographic distance, with economic and cultural factors hypothesised to have an impact on connectivity. Amplification of the duffy binding protein gene (pvdbp1) was prevalent across all districts (16–75%). Cross-population haplotype homozygosity revealed positive selection in a region proximal to the putative chloroquine resistance transporter gene (pvcrt-o). An S25P variant in amino acid transporter 1 (pvaat1), whose homologue has recently been implicated in P. falciparum chloroquine resistance evolution, was prevalent in Ethiopia (96%) but not Thailand or Indonesia (35–53%). The genomic architecture in Ethiopia highlights circulating variants of potential public health concern in an endemic setting with evidence of stable transmission.