Environmental DNA and next-generation sequencing for post-elimination surveillance of neglected tropical diseases in the Philippines and the Western Pacific Region

Post-elimination surveillance remains one of the most difficult challenges in neglected tropical disease (NTD) control. As countries in the Western Pacific Region approach elimination targets, conventional diagnostic tools such as microscopy and antigen rapid tests, optimised for moderate-to-high prevalence settings, are insufficient to detect the rare, focal, or reintroduced transmission that characterises near-elimination settings. The WHO Global Report on Neglected Tropical Diseases 2025 identifies weak surveillance systems and insufficient diagnostic innovation as primary threats to sustaining gains toward the 2030 road map, yet no operational framework exists for deploying environmental genomic surveillance in resource-limited post-elimination settings. The COVID-19 pandemic demonstrated the transformative potential of next-generation sequencing (NGS)-based wastewater surveillance for population-level pathogen detection, yet environmental NGS remains substantially underused for NTDs. In the Philippines, where lymphatic filariasis and Schistosoma japonicum approach elimination while soil-transmitted helminthiases, foodborne trematodes and rabies persist at low, focal prevalence, climate-driven rainfall and flooding concentrate pathogen burden within specific watersheds, drainage systems and habitats. Effective surveillance therefore requires frameworks that go beyond assay sensitivity and specificity to address how surveillance objectives, low-prevalence conditions, sampling strategy, and resource constraints jointly determine what can realistically be detected. This narrative review synthesises evidence on targeted and metagenomic NGS across the three locations in which an NTD signal can be recovered: environmental matrices, vectors and intermediate hosts, and animal reservoirs, using lymphatic filariasis, schistosomiasis, rabies, and related NTDs in the Philippines as a case example. We organise diseases by transmission route and the resulting signal location, which together determine the sampling matrix and the appropriate NGS approach (metabarcoding versus shotgun metagenomics). We argue that the principal remaining gap is not detection but integration: calibrating the environmental signal to infection prevalence and linking it with vector, host and clinical data to guide programmatic decisions, aligned with the 2030 NTD road map.