| Autor: |
Otero MCB; Department of Clinical Epidemiology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines.; College of Medicine Research Center, Davao Medical School Foundation, Inc., Bajada, Davao City 8000, Philippines., Murao LAE; Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines.; Philippine Genome Center Mindanao, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines., Limen MAG; Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon City 1101, Philippines., Caalim DRA; Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines., Gaite PLA; Philippine Genome Center Mindanao, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines., Bacus MG; Philippine Genome Center Mindanao, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines., Acaso JT; Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines.; Philippine Genome Center Mindanao, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines., Miguel RM; Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines., Corazo K; Project Accessible Genomics.; Biology Department, Ateneo de Davao University, Roxas Avenue, Davao City 8000, Philippines., Knot IE; Project Accessible Genomics.; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX Amsterdam, The Netherlands., Sajonia H 2nd; Project Accessible Genomics., de Los Reyes FL 3rd; Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27207, USA., Jaraula CMB; Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon City 1101, Philippines., Baja ES; Department of Clinical Epidemiology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines.; Institute of Clinical Epidemiology, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines., Del Mundo DMN; Department of Food Science and Chemistry, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines. |
| Abstrakt: |
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. |
