title: 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.
authors.affiliation: The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: David J
authors.initials: DJ
authors.lastname: Winter
authors.affiliation: The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.|Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America.
authors.forename: M Andreína
authors.initials: MA
authors.lastname: Pacheco
authors.affiliation: Caucaseco Scientific Research Center, Cali, Colombia.
authors.forename: Andres F
authors.initials: AF
authors.lastname: Vallejo
authors.affiliation: The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: Rachel S
authors.initials: RS
authors.lastname: Schwartz
authors.affiliation: Caucaseco Scientific Research Center, Cali, Colombia.|Faculty of Health, Universidad del Valle, Cali, Colombia.
authors.forename: Myriam
authors.initials: M
authors.lastname: Arevalo-Herrera
authors.affiliation: Caucaseco Scientific Research Center, Cali, Colombia.
authors.forename: Socrates
authors.initials: S
authors.lastname: Herrera
authors.affiliation: The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.|The School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: Reed A
authors.initials: RA
authors.lastname: Cartwright
authors.affiliation: The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.|Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America.
authors.forename: Ananias A
authors.initials: AA
authors.lastname: Escalante
mesh_terms: D000293:Adolescent; D000962:Antimalarials / Q000627:therapeutic use; D001483:Base Sequence; D002648:Child; D003105:Colombia / Q000453:epidemiology; D004338:Drug Combinations; D004351:Drug Resistance; D005260:Female; D014644:Genetic Variation; D018503:Genome, Protozoan / Q000235:genetics*; D055106:Genome-Wide Association Study; D006801:Humans; D016780:Malaria, Vivax / Q000188:drug therapy / Q000453:epidemiology / Q000469:parasitology*; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D010966:Plasmodium vivax / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D011739:Pyrimethamine / Q000627:therapeutic use; D017422:Sequence Analysis, DNA; D013413:Sulfadoxine / Q000627:therapeutic use
chemical_list: D000962:Antimalarials; D004338:Drug Combinations; C001205:fanasil, pyrimethamine drug combination; D013413:Sulfadoxine; D011739:Pyrimethamine