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Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia

View ORCID ProfileDavid J. Winter, View ORCID ProfileM. Andreína Pacheco, View ORCID ProfileAndres F. Vallejo, View ORCID ProfileRachel S. Schwartz, View ORCID ProfileMyriam Arevalo-Herrera, View ORCID ProfileSocrates Herrera, View ORCID ProfileReed A. Cartwright, View ORCID ProfileAnanias A. Escalante
doi: https://doi.org/10.1101/025338
David J. Winter
1The Biodesign Institute, Arizona State University, Tempe, AZ, USA
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  • For correspondence: djwinter@asu.edu Ananias.Escalante@temple.edu
M. Andreína Pacheco
1The Biodesign Institute, Arizona State University, Tempe, AZ, USA
2Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA
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Andres F. Vallejo
3Caucaseco Scientific Research Center, Cali, Colombia
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Rachel S. Schwartz
1The Biodesign Institute, Arizona State University, Tempe, AZ, USA
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Myriam Arevalo-Herrera
3Caucaseco Scientific Research Center, Cali, Colombia
4Faculty of Health, Universidad del Valle, Cali, Colombia
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Socrates Herrera
3Caucaseco Scientific Research Center, Cali, Colombia
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Reed A. Cartwright
1The Biodesign Institute, Arizona State University, Tempe, AZ, USA
5The School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Ananias A. Escalante
1The Biodesign Institute, Arizona State University, Tempe, AZ, USA
2Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA
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  • For correspondence: djwinter@asu.edu Ananias.Escalante@temple.edu
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Abstract

Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations is affects. Its control and eventual elimination are a global health priority. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission.

Here we analyze whole genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this parasite. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 microsatellite loci that are polymorphic and easy to score and can thus be used in epidemiological investigations in South America.

Author Summary Although P. vivax is not as deadly as the more widely studied P. falciparum, it remains a pressing global health problem. Here we report the results of a whole genome study of P. vivax from Cordóba, Colombia, in South America. This parasite is the most prevalent in this region. We show that the parasite population is genetically diverse, contrary the expectations from earlier studies from the Americas. We also find molecular evidence that resistance to an anti-malarial drug has arisen recently in this region. This selective sweep indicates that the parasite has been exposed to a drug that is not used as first line treatment for this malaria parasite. In addition to extensive SNP and microsatellite polymorphism, we report 18 new genetic loci that might be helpful for fine-scale studies of this species in the Americas.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 23, 2015.
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Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia
David J. Winter, M. Andreína Pacheco, Andres F. Vallejo, Rachel S. Schwartz, Myriam Arevalo-Herrera, Socrates Herrera, Reed A. Cartwright, Ananias A. Escalante
bioRxiv 025338; doi: https://doi.org/10.1101/025338
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Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia
David J. Winter, M. Andreína Pacheco, Andres F. Vallejo, Rachel S. Schwartz, Myriam Arevalo-Herrera, Socrates Herrera, Reed A. Cartwright, Ananias A. Escalante
bioRxiv 025338; doi: https://doi.org/10.1101/025338

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