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Droplet Digital RT-PCR to detect SARS-CoV-2 variants of concern in wastewater

Wastewater monitoring has developed into a valuable and efficient tool to assess the prevalence of COVID-19 in the community. The occurrence of new SARS-CoV-2 variants (“Variants of Concern”, VoC) has recently gained attention. There is a need for improved detection methods that provide specific and timely information to address the emergence of VoC.

Within the Wastewater4covid project, we recently investigated RT-ddPCR on wastewater samples for the specific detection of mutation N501Y. The use of this assay enabled simultaneous enumeration of variants with the 501Y mutation and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Data from sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method could determine both the concentrations and the proportions of WT and N501Y containing SARS-CoV-2 RNA in wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater corresponded with the emergence of B.1.1.7 in the Dutch population. These results indicate that RT-ddPCR of wastewater samples could be a tool in monitoring the emergence of the N501Y mutation in the community. The RT-ddPCR method could provide sensitive and accurate monitoring of current (like K417N, E484K) or future mutations present in SARS-CoV-2 variants of concern. Monitoring the emergence of these mutations in the community via wastewater is rapid, efficient and valuable in supporting public health decision-making.

The Wastewater4COVID project was financed by TKI Health Holland in EUREKA project WASTEWATER4COVID.