Identification of SARS-CoV-2 variants by MiSeq sequencing in sewers using passive sampling.
The objective of this study was to adapt a protocol to amplify and sequence the complete genome of the SARS-COV-2 and to compare the diversity of the variants observed following a passive sampling and a punctual sampling.Passive sampling and occasional wastewater sampling was carried out in parallel in the sewers of two French metropolises in April and May 2022, in regions where the incidence rate was contrasting.The devices were immersed for 24 hours on eleven sites, and the sampling was repeated once two days apart.Nucleic acids were extracted from the two types of samples according to suitable protocols.The virus was quantified by RT-QPCR and the complete genome was amplified by Multiplex PCR Artic and sequenced by Illumina MISEQ.The bioinformatics analysis was carried out using the Aspicov pipeline