Application of wastewater-based epidemiological monitoring of COVID-19 for disease surveillance in the city

Highlights

● A continuous wastewater-based monitoring of SARS-CoV-2 was conducted.

● Positive correlation between RNA concentrations and reported cases was observed.

● Similar genetic diversity patterns in wastewater and patient source were observed.

● Wastewater-based surveillance aided the early warning of the COVID-19 pandemic.

● Wastewater-based surveillance in the post-pandemic era was evaluated.

Abstract

Wastewater-based surveillance serves as a supplementary approach to clinical surveillance of COVID-19 during the epidemic. This study aimed to track the prevalence of the disease and the viral genetic variability through wastewater-based surveillance in the post-epidemic era. Between January to December 2023, samples were collected from the influent lines of two wastewater treatment plants (WWTPs), concentrated using PEG8000, and subjected to detection of the target genes ORF 1ab and N of SARS-CoV-2 via reverse transcriptional quantitative PCR (RT-qPCR). For next-generation sequencing (NGS), high-quality samples from both wastewater and clinical patients were selected. Weekly analysis were performed using R software to evaluate the correlation between the SARS-CoV-2 RNA concentrations in wastewater and positive rate of reported cases, indicating a positive correlation. Genetic diversity patterns of SARS-CoV-2 in wastewater resembled those in the patient source based on Principal Coordinates Analysis (PCoA) with three clusters for different stages. The rise of RNA concentration in wastewater indicates the growth of cases and the emergence of new variants, serving as an early warning of potential viral mutations, disease outbreaks even possible epidemics. Furthermore, the genomic surveillance of wastewater could help identify new variants that may not be captured through population monitoring, especially when sample sizes are insufficient. Consequently, surveillance of SARS-CoV-2 in municipal wastewater has emerged as a reliable, early-warning monitoring system for COVID-19 in the post-epidemic era.

Keywords

Wastewater-based epidemiology / Monitoring / COVID-19 / Post-epidemic era

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Acknowledgements

The colleagues who participated in epidemiological investigations, sample collection, laboratory testing, and data analysis and the patients who provided consent to donate their swab samples for detection are acknowledged. This work was supported by the Key Technology Research and Development Program of the Science and Technology Department of Sichuan Province (China) (2021YFS0064), the Youth Innovation Research Project by the Sichuan Medical Association (China) (Q22017), and the Science Foundation of the Health and Family Planning Commission of Chengdu (China) (22056).

Declaration of Competing Interests

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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