COVID-19 wastewater based epidemiology: long-term monitoring of 10 WWTP in France reveals the importance of the sampling context

SARS-CoV-2 wastewater-based epidemiology (WBE) has been advanced as a relevant indicator of distribution of COVID-19 in communities, supporting classical testing and tracing epidemiological approaches. An extensive sampling campaign, including ten municipal wastewater treatment plants, has been conducted in different cities of France over a 20-week period, encompassing the second peak of COVID-19 outbreak in France. A well-recognised ultrafiltration – RNA extraction – RT-qPCR protocol was used and qualified, showing 5.5 +/− 0.5% recovery yield on heat-inactivated SARS-CoV-2. Importantly the whole, solid and liquid, fraction of wastewater was used for virus concentration in this study. Campaign results showed medium- to strong- correlation between SARS-CoV-2 WBE data and COVID-19 prevalence. To go further, statistical relationships between WWTP inlet flow rate and rainfall were studied and taken into account for each WWTP in order to calculate contextualized SARS-CoV-2 loads. This metric presented improved correlation strengths with COVID-19 prevalence for WWTP particularly submitted and sensitive to rain. Such findings highlighted that SARS-CoV-2 WBE data ultimately require to be contextualized for relevant interpretation. HIGHLIGHTS First study monitoring inlet of 10 WWTPs located in France for SARS-CoV-2 RNA quantification over a 20-week period encompassing the second peak of COVID-19 outbreak.; Viral recovery yield was 5.5% +/− 0.5% using heat-inactivated SARS-CoV-2.; Medium to high Spearman's correlation strength was observed between SARS-CoV-2 WBE and COVID-19 prevalence data.; Considering sampling context (i.e. rain events) improved data consistency and correlation strength.