Parasite population dynamics shaped P. falciparum pfhrp2 and pfhrp3 deletion expansion in the Peruvian Amazon.

Plasmodium falciparum populations in the Peruvian Amazon have undergone changes in the last 20 years, coinciding with the implementation of the PAMAFRO malaria control program (2005-2011). In this context, parasites with deletions of the pfhrp2 and pfhrp3 (pfhrp2/3) genes, involved in rapid diagnostic test (RDT) failure, have been increasingly predominant in Peru since 2012. Here, we investigated population genomic processes shaping P. falciparum populations in the Peruvian Amazon, using the PAMAFRO program as a reference point. We analyzed the genomic changes over 102 isolates between 2006 and 2018, grouped in two periods: 33 samples from 2006 to 2011 (Period 1, before PAMAFRO) and 69 from 2012 to 2018 (Period 2, after PAMAFRO). We found a reduction in the parasite population structure complexity, a significant decrease in genetic diversity and a clonal population structure in Period 2. The pfhrp2/3 deletion profiles differed significantly between periods, with the double pfhrp2/3 deletion being predominant in only Period 2 (68%). Importantly, no evidence of positive selection was found on the pfhrp2/3 loci. Together, these results indicate that P. falciparum populations in Peru experienced a bottleneck associated with PAMAFRO, followed by the clonal expansion of the parasites carrying pfhrp2/3 deletions. In contrast to the Horn of Africa, the deletion of the pfhrp2/3 genes were not selected in Peru, and their expansion is better explained by a different evolutionary process, such as genetic drift. These results highlight the importance of population genomic analysis in uncovering the patterns shaping the parasite population in Peru, which impacts malaria diagnostics and other control strategies.