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 2nd; Francis L de Los Reyes 3rd; Caroline Marie B Jaraula; Emmanuel S Baja; Dann Marie N Del Mundo

doi:10.3390/ijerph19148789

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

Int J Environ Res Public Health. 2022 Jul 19;19(14):8789. doi: 10.3390/ijerph19148789.

Authors

Maria Catherine B Otero^{1

2}, Lyre Anni E Murao^{3

4}, Mary Antoinette G Limen⁵, Daniel Rev A Caalim³, Paul Lorenzo A Gaite⁴, Michael G Bacus⁴, Joan T Acaso^{3

4}, Refeim M Miguel³, Kahlil Corazo^{6

7}, Ineke E Knot^{6

8}, Homer Sajonia 2nd⁶, Francis L de Los Reyes 3rd⁹, Caroline Marie B Jaraula⁵, Emmanuel S Baja^{1

10}, Dann Marie N Del Mundo¹¹

Affiliations

¹ Department of Clinical Epidemiology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines.
² College of Medicine Research Center, Davao Medical School Foundation, Inc., Bajada, Davao City 8000, Philippines.
³ Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines.
⁴ Philippine Genome Center Mindanao, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines.
⁵ Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon City 1101, Philippines.
⁶ Project Accessible Genomics.
⁷ Biology Department, Ateneo de Davao University, Roxas Avenue, Davao City 8000, Philippines.
⁸ Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX Amsterdam, The Netherlands.
⁹ Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27207, USA.
¹⁰ Institute of Clinical Epidemiology, National Institutes of Health, University of the Philippines Manila, Ermita, Manila 1000, Philippines.
¹¹ Department of Food Science and Chemistry, University of the Philippines Mindanao, Mintal, Davao City 8000, Philippines.

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; SARS-CoV-2; public health surveillance; wastewater-based epidemiology; whole genome sequencing.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

COVID-19* / epidemiology
Humans
Philippines / epidemiology
Pilot Projects
RNA, Viral
SARS-CoV-2* / genetics
Wastewater
Wastewater-Based Epidemiological Monitoring

Substances

RNA, Viral
Waste Water

Grants and funding

This project was supported by the University of the Philippines Mindanao In-House Research Grant (details), the Department of Science and Technology-Philippine Council for Health Research and Development (DOST-PCHRD) through the Philippine Genome Center Mindanao (award number not applicable), the Just One Giant Lab (JOGL) OpenCovid-19 Grant Round 4/5 through the Accessible Genomics Project, USAID Partners 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 DOST-PCHRD Niche Center for Research of the University of the Philippines Mindanao Center for Applied Modeling, Data Analytics, and Bioinformatics for Decision Support Systems in Health (UP Mindanao AMDABiDSS-Health) under the component project “Integrated Wastewater-Based Epidemiology and Data Analytics for Community Level Pathogen Surveillance and Genetic Tracking”.