The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia

Abstract

Background: Wastewater-based epidemiology (WBE) surveillance as an early warning system (EWS) for monitoring community transmission of SARS-CoV-2 in low- and middle-income country (LMIC) settings, where diagnostic testing capacity is limited, needs further exploration. We explored the feasibility to conduct a WBE surveillance in Indonesia, one of the global epicenters of the COVID-19 pandemic in the middle of 2021, with the fourth largest population in the world where sewer and non-sewered sewage systems are implemented. The feasibility and resource capacity to collect samples on a weekly or fortnightly basis with grab and/or passive sampling methods, as well as to conduct qualitative and quantitative identification of SARS-CoV-2 ribonucleic acid (RNA) using real-time RT-PCR (RT-qPCR) testing of environmental samples were explored.

Materials and methods: We initiated a routine surveillance of wastewater and environmental sampling at three predetermined districts in Special Region of Yogyakarta Province. Water samples were collected from central and community wastewater treatment plants (WWTPs), including manholes flowing to the central WWTP, and additional soil samples were collected for the near source tracking (NST) locations (i.e., public spaces where people congregate).

Results: We began collecting samples in the Delta wave of the COVID-19 pandemic in Indonesia in July 2021. From a 10-week period, 54% (296/544) of wastewater and environmental samples were positive for SARS-CoV-2 RNA. The sample positivity rate decreased in proportion with the reported incidence of COVID-19 clinical cases in the community. The highest positivity rate of 77% in week 1, was obtained for samples collected in July 2021 and decreased to 25% in week 10 by the end of September 2021.

Conclusion: A WBE surveillance system for SARS-CoV-2 in Indonesia is feasible to monitor the community burden of infections. Future studies testing the potential of WBE and EWS for signaling early outbreaks of SARS-CoV-2 transmissions in this setting are required.

Fig 1. Flowchart of sample strategy.

We selected ten sub-districts from three out of five districts in Special region of Yogyakarta Province (Yogyakarta city, Bantul, and Sleman districts). Samples from three sub-districts were taken weekly (identified by blue arrows), while others were taken fortnightly. Detailed type and number of samples in each sub-district are illustrated in the figure.

Fig 2. Nucleocapsid (N) gene positivity by sample types.

Fig 3. Distribution maps of SARS-CoV-2 in Special Region of Yogyakarta province, comparing detection targeting N gene to community confirmed cases.

(A) In week 1–2 of the sample collection. (B) In week 5–6 of the sample collection. (C) In week 9–10 of the sample collection. Community COVID-19 confirmed cases were represented by blue color, the lighter the fewer cases. Detected cases in sampling locations were represented by red colored dots/triangles/pentagons, while non-detected cases were represented by green colored dots/triangles/pentagons. With circles denoting manholes, pentagons denoting river and triangles denoting NST water.