Molecular surveillance over 14 years confirms reduction of Plasmodium vivax and falciparum transmission after implementation of Artemisinin-based combination therapy in Papua, Indonesia

Genetic epidemiology can provide important insights into parasite transmission that can inform public health interventions. The current study compared long-term changes in the genetic diversity and structure of co-endemic Plasmodium falciparum and P . vivax populations. The study was conducted in Papua Indonesia, where high-grade chloroquine resistance in P . falciparum and P . vivax led to a universal policy of Artemisinin-based Combination Therapy (ACT) in 2006. Microsatellite typing and population genetic analyses were undertaken on available isolates collected between 2004 and 2017 from patients with uncomplicated malaria (n = 666 P . falciparum and n = 615 P . vivax ). The proportion of polyclonal P . falciparum infections fell from 28% (38/135) before policy change (2004–2006) to 18% (22/125) at the end of the study (2015–2017); p<0.001. Over the same period, polyclonal P . vivax infections fell from 67% (80/119) to 35% (33/93); p <0.001. P . falciparum strains persisted for up to 9 years compared to 3 months for P . vivax , reflecting higher rates of outbreeding in the latter. Sub-structure was observed in the P . falciparum population, but not in P . vivax , confirming different patterns of outbreeding. The P . falciparum population exhibited 4 subpopulations that changed in frequency over time. Notably, a sharp rise was observed in the frequency of a minor subpopulation (K2) in the late post-ACT period, accounting for 100% of infections in late 2016–2017. The results confirm epidemiological evidence of reduced P . falciparum and P . vivax transmission over time. The smaller change in P . vivax population structure is consistent with greater outbreeding associated with relapsing infections and highlights the need for radical cure to reduce recurrent infections. The study emphasizes the challenge in disrupting P . vivax transmission and demonstrates the potential of molecular data to inform on the impact of public health interventions.