Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination

Author summary Plasmodium vivax is a major global health threat particularly in Central and South America which experiences 700,000 P. vivax cases each year. Panama has greatly reduced P. vivax incidence, however, this progress has since plateaued. Understanding how the parasite moves throughout the country, uncovering pockets of focalized transmission, and identifying imported cases, is critical for Panama and other countries to succeed in their elimination efforts. Genomic epidemiology and population genomics tools can help provide this information needed to inform malaria control policy. In this study, we collected 100 Panamanian P. vivax samples from two time periods (2007-2009 and 2017-2019), of which 59 yielded usable sequencing data. We found that the majority (n = 47) samples belong to a single highly related lineage, termed CL1. This lineage has persisted since at least 2007. We also observed a second smaller completely clonal lineage of four parasites, termed CL2. Additionally, we observed four samples that shared no recent ancestry with any other Panamanian samples but clustered with samples collected in a previous study from Colombia. We highlight how genomic epidemiology can be used to spotlight parasites that may be imported as a result of human migration, as well as corroborate or refute the country of origin as suggested by the travel history of a patient. There is no evidence of outcrossing between these potentially imported parasites and the local Panamanian parasite population. This finding suggests that imported parasites are not driving ongoing malaria transmission in Panama. We note the need for sustained genomic surveillance of P. vivax in Panama to monitor transmission dynamics in the local population and to further flag potentially imported cases. The low diversity we observe in Panama indicates that this parasite population has been previously subject to a severe bottleneck and may be eligible for elimination. Malaria incidence in Panama has plateaued in recent years in spite of elimination efforts, with almost all cases caused by Plasmodium vivax. Notwithstanding, overall malaria prevalence remains low (fewer than 1 case per 1000 persons). We used selective whole genome amplification to sequence 59 P. vivax samples from Panama. The P. vivax samples were collected from two periods (2007-2009 and 2017-2019) to study the population structure and transmission dynamics of the parasite. Imported cases resulting from increased levels of human migration could threaten malaria elimination prospects, and four of the samples evaluated came from individuals with travel history. We explored patterns of recent common ancestry among the samples and observed that a highly genetically related lineage (termed CL1) was dominant among the samples (47 out of 59 samples with good sequencing coverage), spanning the entire period of the collection (2007-2019) and all regions of the country. We also found a second, smaller clonal lineage (termed CL2) of four parasites collected between 2017 and 2019. To explore the regional context of Panamanian P. vivax we conducted principal components analysis and constructed a neighbor-joining tree using these samples and samples collected worldwide from a previous study. Three of the four samples with travel history clustered with samples collected from their suspected country of origin (consistent with importation), while one appears to have been a result of local transmission. The small number of Panamanian P. vivax samples not belonging to either CL1 or CL2 clustered with samples collected from Colombia, suggesting they represent the genetically similar ancestral P. vivax population in Panama or were recently imported from Colombia. The low diversity we observe in Panama indicates that this parasite population has been previously subject to a severe bottleneck and may be eligible for elimination. Additionally, while we confirmed that P. vivax is imported to Panama from diverse geographic locations, the lack of impact from imported cases on the overall parasite population genomic profile suggests that onward transmission from such cases is limited and that imported cases may not presently pose a major barrier to elimination.