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

Abstract Plasmodium vivax 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 P. vivax are global health priorities. 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 species. 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 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. Author SummaryAlthough 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, which is contrary to 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 single nucleotide and microsatellite polymorphism, we report 18 new genetic loci that might be helpful for fine-scale studies of this species in the Americas.