Journal Article

Wastewater-based epidemiology surveillance as an early warning system for SARS-CoV-2 in Indonesia

Bines, Julie E, Nuryastuti, Titik, Wiratama, Bayu Satria, McCarthy, David T., Donato, Celeste M., Thobari, Jarir At, Handley, Amanda, Supriyati, Endah, Laksono, Ida Safitri, Murni, Indah Kartika, Oktaria, Vicka, Dinari, Rizka

2024

Overview

Wastewater-based epidemiology (WBE) surveillance has been proposed as an early warning system (EWS) for community SARS-CoV-2 transmission. However, there is limited data from low-and middle-income countries (LMICs). This study aimed to assess the ability of WBE surveillance to detect SARS-CoV-2 in formal and informal environments in Indonesia using different methods of sample collection, to compare WBE data with patterns of clinical cases of COVID-19 within the relevant communities, and to assess the WBE potential to be used as an EWS for SARS-CoV-2 outbreaks within a community. We conducted WBE surveillance in three districts in Yogyakarta province, Indonesia, over eleven months (27 July 2021 to 7 January 2022 [Delta wave]; 18 January to 3 June 2022 [Omicron wave]). Water samples using grab, and/or passive sampling methods and soil samples were collected either weekly or fortnightly. RNA was extracted from membrane filters from processed water samples and directly from soil. Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the SARS-CoV-2 N and ORF1ab genes. A total of 1,582 samples were collected. Detection rates of SARS-CoV-2 in wastewater reflected the incidence of community cases, with rates of 85% at the peak to 2% at the end of the Delta wave and from 94% to 11% during the Omicron wave. A 2-week lag time was observed between the detection of SARS-CoV-2 in wastewater and increasing cases in the corresponding community. WBE surveillance for SARS-CoV-2 in Indonesia was effective in monitoring patterns of cases of COVID-19 and served as an early warning system, predicting the increasing incidence of COVID-19 cases in the community.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Biology and life sciences / COVID-19 / COVID-19 - diagnosis / COVID-19 - epidemiology / COVID-19 - virology / Disease transmission / DNA-directed RNA polymerase / Early warning systems / Earth Sciences / Ecology and Environmental Sciences / Epidemiology / Health aspects / Humans / Indonesia - epidemiology / Lag time / Medicine and health sciences / People and Places / Polymerase chain reaction / Public health / Real time / Ribonucleic acid / RNA / Sampling methods / SARS-CoV-2 - genetics / SARS-CoV-2 - isolation & purification / Severe acute respiratory syndrome coronavirus 2 / Social Sciences / Surveillance / Wastewater / Wastewater - virology / Wastewater-Based Epidemiological Monitoring / Water analysis / Water purification / Water sampling / Water treatment