Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in <i>Plasmodium vivax</i> from Colombia

<div><p><i>Plasmodium vivax</i> is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of <i>P. vivax</i> are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of <i>P. vivax</i> 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 <i>P. vivax</i> 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 species. These results indicate that <i>P. vivax</i> 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 <i>Plasmodium</i> species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America.</p>