Human mobility and the dispersal of malaria parasite lineages in the main transmission hotspot of Brazil

Abstract Background Despite continued control efforts, malaria due to Plasmodium vivax and P. falciparum remains endemic across the Amazon Basin. Here, we sought to understand how malaria parasites spread between sources and sinks within the upper Juruá Valley region of northwestern Brazil, the country’s main residual transmission hotspot, to inform more effective control and elimination strategies. Methods We combined the analysis of nearly 70,000 case notifications between 2018 and 2021 with high-resolution molecular genotyping data from 207 P. vivax and 117 P. falciparum isolates to map malaria parasite movement across the Juruá Valley hotspot. We introduce the C50 metric to estimate parasite connectivity within clusters of genetically related parasites, or molecular clusters. Results We found that 16–18% of infections were acquired outside participants’ localities of residence. Genotyping of P. vivax and P. falciparum revealed large molecular clusters comprising parasites of each species collected across rural-urban boundaries over four years, with some pairs of genetically related parasites originating from distant localities within Juruá Valley. We found a large variation in C50 values, with a few parasites serving as main hubs within large molecular clusters. Imported P. vivax isolates were significantly more connected than locally acquired infections. Conclusions We suggest that the combined use of routine epidemiological surveillance data and molecular genotyping can help to map human mobility and parasite lineage dispersal across space and time, aiming to inform specific interventions tailored for local populations that move malaria parasites between source and sink localities in residual transmission settings in the Amazon.