Implementing a SARS-CoV-2 Early Warning System in Valencia (Spain) and its Correlation with Epidemiological Indicators

PURPOSE: To implement a SARS-CoV-2 wastewater surveillance system in Valencia and study the correlation between SARS-CoV-2 concentration levels and epidemiological indicators. METHODS & MATERIALS: The working strategy developed in the municipality of Valencia consisted of monitoring wastewater effluents collected by 790,000 people. The city was divided into 24 different hydraulic sectors. 3,023 samples of untreated wastewater were collected and analysed between May 2020 and May 2021. RNA extraction from sewage material was carried out using the NucleoSpin RNA virus Kit. SARS-CoV-2 RNA detection was performed by RT-qPCR using One-Step PrimeScript™ RT-PCR Kit (Perfect Real Time), targeting the nucleoprotein (N), N1 and N2 fragments, and envelope protein (E) gene. Mengovirus RNA recovery rates were used as quality assurance parameters according to ISO 15216-1:2017. RESULTS: A total of 2,169 samples were positive for SARS-CoV-2 RNA material. SARS-CoV-2 variations were detected throughout the entire study evidencing trends during the first, second and third wave. As the National State of Emergency ended (June 2020), SARS-CoV-2 values began to increase reaching the first and most significant concentration spike of the study (20th-26th of July 2020), with a weekly average aggregate concentration of 34,5M GC/L (an increase of 2 units in the log scale). This translated in the worsening of epidemiological indicators (number of cases, hospitalizations, deaths and cumulative incidence (CI)), which maintained a stable increase until a second spike was detected during an important bank holiday in October (9th-12th), where the concentration changed from 28M GC/L to 345M GC/L in a 3-day period while the city was registering 1,100 new weekly cases and a CI of 200 cases/100,000 residents. Finally, a third wave placed Valencia with the worst historical epidemiological data (6,545 new cases; 1,000 new hospitalizations; CI= 1,318,04 cases/100,000 inhabitants) with a weekly SARS-CoV-2 average aggregate concentration of 967M GC/L, leading health officials to implement new restrictive measures. CONCLUSION: Wastewater surveillance could be used as a complimentary tool to estimate the presence and prevalence of COVID-19 in communities and can be used for preventive purposes, as an increasing SARS-CoV-2 trend in wastewater could be a signal of the possible re-emergence of the pandemic.