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.