An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
Adam I., Alam MS., Alemu S., Amaratunga C., Amato R., Andrianaranjaka V., Anstey NM., Aseffa A., Ashley E., Assefa A., Auburn S., Barber BE., Barry A., Batista Pereira D., Cao J., Chau NH., Chotivanich K., Chu C., Dondorp AM., Drury E., Echeverry DF., Erko B., Espino F., Fairhurst R., Faiz A., Fernanda Villegas M., Gao Q., Golassa L., Goncalves S., Grigg MJ., Hamedi Y., Hien TT., Htut Y., Johnson KJ., Karunaweera N., Khan W., Krudsood S., Kwiatkowski DP., Lacerda M., Ley B., Lim P., Liu Y., Llanos-Cuentas A., Lon C., Lopera-Mesa T., Marfurt J., Michon P., Miotto O., Mohammed R., Mueller I., Namaik-larp C., Newton PN., Nguyen T-N., Nosten F., Noviyanti R., Pava Z., Pearson RD., Petros B., Phyo AP., Price RN., Pukrittayakamee S., Rahim AG., Randrianarivelojosia M., Rayner JC., Rumaseb A., Siegel SV., Simpson VJ., Thriemer K., Tobon-Castano A., Trimarsanto H., Urbano Ferreira M., Vélez ID., Wangchuk S., Wellems TE., White NJ., William T., Yasnot MF., Yilma D.
This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.