title: Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections.
abstract: Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25-40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Mary Lynn
authors.initials: ML
authors.lastname: Baniecki
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Aubrey L
authors.initials: AL
authors.lastname: Faust
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Schaffner
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Park
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Kevin
authors.initials: K
authors.lastname: Galinsky
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Rachel F
authors.initials: RF
authors.lastname: Daniels
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Hamilton
authors.affiliation: Department of Parasitology, University of São Paulo, São Paulo, Brazil.
authors.forename: Marcelo U
authors.initials: MU
authors.lastname: Ferreira
authors.affiliation: Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
authors.forename: Nadira D
authors.initials: ND
authors.lastname: Karunaweera
authors.affiliation: Department of Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America.
authors.forename: David
authors.initials: D
authors.lastname: Serre
authors.affiliation: Department of International Health, Biology and Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Zimmerman
authors.affiliation: Laboratory of Malaria and Vector Research, Malaria Genetics Section, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: Juliana M
authors.initials: JM
authors.lastname: Sá
authors.affiliation: Laboratory of Malaria and Vector Research, Malaria Genetics Section, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Wellems
authors.affiliation: Department of Parasitology, Institute Pasteur de la Guyane, Cayenne, French Guiana.
authors.forename: Lise
authors.initials: L
authors.lastname: Musset
authors.affiliation: Department of Parasitology, Institute Pasteur de la Guyane, Cayenne, French Guiana.
authors.forename: Eric
authors.initials: E
authors.lastname: Legrand
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Melnikov
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Neafsey
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America; Broad Institute, Cambridge, Massachusetts, United States of America; School of Nursing and Health Sciences, Simmons College, Boston, Massachusetts, United States of America.
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Volkman
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America; Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Dyann F
authors.initials: DF
authors.lastname: Wirth
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America; Broad Institute, Cambridge, Massachusetts, United States of America; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Pardis C
authors.initials: PC
authors.lastname: Sabeti
mesh_terms: D000349:Africa / Q000453:epidemiology; D001208:Asia / Q000453:epidemiology; D001483:Base Sequence; D002874:Chromosome Mapping; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D016054:DNA, Protozoan / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D006801:Humans; D016780:Malaria, Vivax / Q000453:epidemiology / Q000469:parasitology*; D010963:Plasmodium falciparum / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D010966:Plasmodium vivax / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D020641:Polymorphism, Single Nucleotide; D013020:South America / Q000453:epidemiology
chemical_list: D016054:DNA, Protozoan; D005819:Genetic Markers