Evaluation of physico-chemical factors affecting Wastewater-Based Epidemiology of SARS-CoV-2 in a southern Philippine sewershed

Wastewater-Based Epidemiology as a complementary Public Health Surveillance tool in Davao City proved useful as the basis of further improvements in disease surveillance. Weekly sampling from November to December in 2020 identified 91% sewer water samples with SARS-CoV-2 RNA despite the lack of reported positive clinical cases in areas identified as moderate to high risk for COVID-19 transmission. Detections of SARS-CoV-2 N, RdRP, and E genes concentrated from PEG-NaCl precipitation method and analyzed using RT-PCR were evaluated in conjunction with physico-chemical and fecal parameters, particularly coliform count, flow rate, surface water temperature, salinity, and total dissolved solids. The physico-chemical parameters provide insight on the preservation of organic matter and residence time of the waters that can impact the recovery of SARS-CoV-2. From whole genome sequencing, single nucleotide polymorphisms (SNPs) were detected and spatially clustered in areas with high population density and mobility. The mutations include previously reported and not yet detected to which the SNPs P383L and V21L in wastewater were detected a month before they were reported from clinical surveillance. Refining the sewershed map is highly recommended and is currently surveyed in more detail. For future improved WBE, the sites were narrowed down to fast flowing channels in densely populated areas with more established sewer lines. Acknowledgements This project was funded by USAID Partnerships for Enhanced Engagement in Research (subaward number 2000009924) “Baselining Persistent and Emerging Organic Pollutant Levels in Environmental and Engineered Systems for Healthy Philippines” and the University of the Philippines Mindanao in-house funding. We also thank Mr Chris Carl Toyado for assisting us with this paper.