Multifaceted Assessment of Wastewater-Based Epidemiology for SARS-CoV-2 in Selected Urban Communities in Davao City, Philippines: A Pilot Study

Maria Catherine B. Otero, Lyre Anni E. Murao, Mary Antoinette G. Limen, Daniel Rev A. Caalim, Paul Lorenzo A. Gaite, Michael G. Bacus, Joan T. Acaso, Refeim M. Miguel, Kahlil Corazo, Ineke E. Knot, Homer Sajonia, Francis L. de los Reyes, Caroline Marie B. Jaraula, Emmanuel S. Baja and Dann Marie N. Del Mundo
Additional contact information
Maria Catherine B. Otero: Department of Clinical Epidemiology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines
Lyre Anni E. Murao: Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines
Mary Antoinette G. Limen: Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon City 1101, Philippines
Daniel Rev A. Caalim: Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines
Paul Lorenzo A. Gaite: Philippine Genome Center Mindanao, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines
Michael G. Bacus: Philippine Genome Center Mindanao, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines
Joan T. Acaso: Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines
Refeim M. Miguel: Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines
Kahlil Corazo: Project Accessible Genomics
Ineke E. Knot: Project Accessible Genomics
Homer Sajonia: Project Accessible Genomics
Francis L. de los Reyes: Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27207, USA
Caroline Marie B. Jaraula: Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon City 1101, Philippines
Emmanuel S. Baja: Department of Clinical Epidemiology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines
Dann Marie N. Del Mundo: Department of Food Science and Chemistry, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines

IJERPH, 2022, vol. 19, issue 14, 1-24

Abstract: 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.

Keywords: COVID-19; Philippines; public health surveillance; SARS-CoV-2; wastewater-based epidemiology; whole genome sequencing (search for similar items in EconPapers)
JEL-codes: I I1 I3 Q Q5 (search for similar items in EconPapers)
Date: 2022
References: View complete reference list from CitEc
Citations: View citations in EconPapers (1)

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