Leveraging Wastewater: Validating the National-Scale SARS-CoV-2 Surveillance System in Cyprus for Elevated Public Health Surveillance and Enhanced Epidemiological Insight

The validation of a cross-country, national-scale SARS-CoV-2 wastewater surveillance system for the monitoring of public health in the Republic of Cyprus, took place during October 2021-September 2022. The chronicle of SARS-CoV-2 genetic marker concentrations and prevailing Variants of Concern (VoCs) in all large Wastewater Treatment Plants (WWTPs) of Cyprus for a continuous period of 1 year, was recorded through an integrated, multi-disciplinary sewage-based surveillance system set up to track, visualize and make the collected information and statistical analysis outcomes, publicly available. Composite sampling and physicochemical parameter normalization of Population Equivalents (PE) and SARS-CoV-2 genetic marker concentration loads were utilized.Chemical Oxygen Demand (COD) was selected for normalization of genetic fragment loads. The selection of a normalization method should be tailored according to the characteristics of each individual city/WWTP population structure, flows and wastewater origin. Metagenomic sequencing showed the transition of the SARS-CoV-2 genome from the Delta to the Omicron variant prevalence, in agreement with changes in wastewater gene concentrations. Differences in the early detection of SARS-CoV-2 genetic markers were found among cities. The established system was able to track and monitor the trend of SARS-CoV-2, even in times of absence of other public health measures such as tracing of confirmed COVID-19 cases, showing the capacity of the wastewater system to quickly capture shifts in infections.The work done in the framework of this project, confirmed the ability of the national-scale system to timely observe pandemic trends, evaluate effects of control measures implemented and monitor the burden of infected patients that shed SARS-CoV-2 fragments.