Asymptomatic parasitaemia in a malaria pre-elimination setting in the Putumayo area of the Ecuadorian Amazon basin

Background: Ecuador is approaching malaria elimination, but its Amazonian Putumayo canton borders regions in Colombia and Peru with high transmission intensity. This ‘frontier’ setting represents a critical vulnerability where asymptomatic infections may sustain transmission, undetected by routine surveillance. Methods: In a repeated cross-sectional study during the 2023 rainy season, we surveyed 293 asymptomatic individuals in four riverine communities in Putumayo. We used a tiered diagnostic approach: rapid diagnostic tests (RDTs), expert microscopy, and real-time qPCR targeting the 18S rRNA gene. Results: No infections were detected by RDT (0/293). Microscopy identified three P. vivax infections (1.0%, 95% CI 0.2–2.4%). qPCR detected five positive cases (1.7%, 95% CI 0.6–3.9%), revealing two additional submicroscopic infections. The failure of a subsequent species-specific PCR and high Cq values (mean 32.6) indicated very low parasite densities. Infections were found only in the mid-to-late rainy season, predominantly in males. Conclusions: Molecular surveillance revealed a low-density, asymptomatic malaria reservoir missed entirely by RDTs, and partially by microscopy. This hidden burden represents a critical blind spot for Ecuador’s elimination program. To achieve and sustain elimination, surveillance in such border regions must incorporate highly sensitive molecular tools and be supported by robust cross-border collaboration.