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Background   Plasmodium vivax  poses a significant challenge to malaria elimination due to its ability to cause relapsed infections from reactivation of dormant liver parasites called hypnozoites. We analyzed 69  P .  vivax  whole genome sequences obtained from subjects residing in three different villages along the Peruvian Amazon. This included 23 paired  P .  vivax  samples from subjects who experienced recurrent  P .  vivax  parasitemia following observed treatment with chloroquine and primaquine.    Methods  Genomic DNA was extracted from whole blood samples collected from subjects.  P .  vivax  DNA was enriched using selective whole genome amplification and whole genome sequencing. We used single nucleotide polymorphisms (SNPs) from the core  P .  vivax  genome to determine characteristics of the parasite population using discriminant analysis of principal components, maximum likelihood estimation of individual ancestries, and phylogenetic analysis. We estimated the relatedness of the paired samples by calculating the number of segregating sites and using a hidden Markov model approach to estimate identity by descent.    Results  We present a comprehensive dataset of population genetics of  Plasmodium vivax  in the Peruvian Amazonian. We define the parasite population structure in this region and demonstrate a novel method for distinguishing homologous relapses from reinfections or heterologous relapses with improved accuracy. The parasite population in this area was quite diverse with an estimated five subpopulations and evidence of a highly heterogeneous ancestry of some of the isolates, similar to previous analyses of  P .  vivax  in this region. Pairwise comparison of recurrent infections determined that there were 12 homologous relapses and 3 likely heterologous relapses with highly related parasites. To the best of our knowledge, this is the first large-scale study to evaluate recurrent  P .  vivax  infections using whole genome sequencing.    Conclusions  Whole genome sequencing is a high-resolution tool that can identify  P .  vivax  homologous relapses with increased sensitivity, while also providing data about drug resistance and parasite population genetics. This information is important for evaluating the efficacy of known and novel antirelapse medications in endemic areas and thus advancing the campaign to eliminate malaria.    Electronic supplementary material  The online version of this article (10.1186/s13073-018-0563-0) contains supplementary material, which is available to authorized users.

Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing