Direct Comparison of RT-ddPCR and Targeted Amplicon Sequencing for SARS-CoV-2 Mutation Monitoring in Wastewater

Monitoring of SARS-CoV-2 variant dynamics in wastewater by digital RT-PCR : from Alpha to Omicron BA.2 VOC

“…Wastewater-based epidemiology allows tracking the overall dynamics of the SARS-CoV-2 epidemic (Medema et al, 2020b; Randazzo et al, 2020; Wurtzer et al, 2022, 2020). Variant identification results from sequencing, but such approach faces limitations for application in wastewater with respect to RNA quality and quantity (Lou et al, 2022), but also mathematical tools to deconvolute isolated mutations to reconstruct the original genomes in a mixture of variants (Agrawal et al, 2022b; Jahn et al, 2021; Smyth et al, 2022). Different studies have shown that it is also possible to monitor specific mutations suggestive of VOC to identify the emergence of VOC in a territory and to explain the predominance of certain VOC in epidemic waves (Caduff et al, 2022; Carcereny et al, 2022; Erster et al, 2022; Wurtzer et al, 2022).…”

“…To overcome these limitations, targeted and specific RT-qPCR approaches have been proposed to detect certain mutations suggestive of variant presence or functional mutations whose evolution could reveal the spread of variants designated as VOC (Wurtzer et al, 2022). Different RT-PCR methods have been proposed based on either relative quantification of mutations to the total SARS-CoV-2 genomes (Erster et al, 2022; Wurtzer et al, 2022; Yaniv et al, 2021), either on wild-type and mutated allelic discrimination (Graber et al, 2021), quantification of mutations and total genomes by digital PCR (Boogaerts et al, 2022; Caduff et al, 2022; Heijnen et al, 2021; Lou et al, 2022). These approaches have been developed and applied to the emergence of Alpha and Delta VOC.…”