Over 60 countries have integrated wastewater-based epidemiology (WBE) in their COVID-19 surveillance programs, focusing on wastewater treatment plants (WWTP). In this paper, we piloted the assessment of SARS-CoV-2 WBE as a complementary public health surveillance method in susceptible communities in a highly urbanized city without WWTP in the Philippines by exploring the extraction and detection methods, evaluating the contribution of physico-chemical–anthropogenic factors, and attempting whole-genome sequencing (WGS). Weekly wastewater samples were collected from sewer pipes or creeks in six communities with moderate-to-high risk of COVID-19 transmission, as categorized by the City Government of Davao from November to December 2020. Physico-chemical properties of the wastewater and anthropogenic conditions of the sites were noted. Samples were concentrated using a PEG-NaCl precipitation method and analyzed by RT-PCR to detect the SARS-CoV-2 N, RdRP, and E genes. A subset of nine samples were subjected to WGS using the Minion sequencing platform. SARS-CoV-2 RNA was detected in twenty-two samples (91.7%) regardless of the presence of new cases. Cycle threshold values correlated with RNA concentration and attack rate. The lack of a sewershed map in the sampled areas highlights the need to integrate this in the WBE planning. A combined analysis of wastewater physico-chemical parameters such as flow rate, surface water temperature, salinity, dissolved oxygen, and total dissolved solids provided insights on the ideal sampling location, time, and method for WBE, and their impact on RNA recovery. The contribution of fecal matter in the wastewater may also be assessed through the coliform count and in the context of anthropogenic conditions in the area. Finally, our attempt on WGS detected single-nucleotide polymorphisms (SNPs) in wastewater which included clinically reported and newly identified mutations in the Philippines. This exploratory report provides a contextualized framework for applying WBE surveillance in low-sanitation areas.

Highly Urbanized Cities (HUCs) in the Philippines were at the forefront of public health surveillance and response during the COVID-19 pandemic. With the rapid spread of COVID-19 to Philippine cities, local government units continuously assessed, adapted, and implemented public health interventions (PHIs) and depended on available open-source government data (OSGD). This study consolidated PHIs in selected HUCs in the Philippines using high-quality OSGD to create a timeline of interventions and document good practices in local COVID-19 control. OSGD resources were collected from February 2020 to January 2023, and the data quality of OSGD was evaluated using the Journal of the American Medical Association (JAMA) benchmarks. A total of 180 metadata sources that met at least two core standards (Authorship and Currency) were included in the analysis. COVID-19 control strategies were analyzed vis-à-vis the rise of COVID-19 cases and types of PHIs, including the control of imported cases, case management, contact management, behavioral modification, and pharmaceutical intervention. Travel bans and hard lockdowns in Luzon early in the pandemic delayed the introduction of COVID-19 to other parts of the country. Good practices of LGUs for local COVID-19 control, such as quarantine passes, curfews and liquor bans, using QR-based contact tracing, massive community testing in high-risk communities, and free public swabbing centers, were implemented to slow down the local spread of COVID-19. With the evolving scenarios in city-level COVID-19 epidemics, local risk assessments based on available OSGD drove the adoption of relevant and innovative control strategies in HUCs in the Philippines. Lessons learned must be integrated into epidemic preparedness and response programs against future emerging or re-emerging infectious diseases.

Highly Urbanized Cities (HUCs) in the Philippines were at the forefront of public health surveillance and response during the COVID-19 pandemic response. With the rapid spread of COVID-19 to Philippine cities, local government units continuously assessed, adapted, and implemented public health interventions (PHIs), and depended on available open-source government data (OSGD). This study consolidated PHIs in selected HUCs in the Philippines using high quality OSGD to create a timeline of interventions and document good practices in local COVID-19 control. OSGD resources were collected from February 2020 to January 2023, and data quality of OSGD was evaluated using the JAMA benchmarks. A total of 180 metadata sources were included in the analysis. All OSGD sources achieved at least two core standards with a mean (±SD) JAMA score of 3.03 (±0.90) indicating these are high-quality resources. COVID-19 control strategies were analyzed vis-à-vis the rise of COVID-19 cases and types of PHIs, including control of imported cases, case management, contact management, behavioral modification, and pharmaceutical intervention. Travel bans and hard lockdowns in Luzon early in the pandemic delayed the introduction of COVID-19 to other parts of the country. Good practices of LGUs for local COVID-19 control, such as quarantine passes, curfews and liquor bans, using QR-based contact tracing, massive community testing in high-risk communities, and free public swabbing centers, were implemented to slow down the local spread of COVID-19. The COVID-19 pandemic has shown the importance of OSGD for community and public health, especially for quick action and control, and post-pandemic assessments. Lessons learned must be integrated in epidemic preparedness and response programs against future emerging or re-emerging infections.