Since the end of 2020, the COVID-19 pandemic has experienced a major turning point with the appearance and rapid spread of new variants, causing a significant increase in the number of new cases requiring hospitalization. These so-called UK, South African or Brazilian variants are characterized by combinations of mutations which allow them to be distinguished from the variants which have circulated since the start of the epidemic. The impact of these variants on the functioning of healthcare systems requires monitoring the spread of these variants, which are more contagious, more lethal and may reinfect people who are already immune to a natural infection or to a vaccination. Monitoring the viral genome in wastewater has shown great value in early detection of the dynamics of virus spreading in populations. The sequencing of viral genomes is used in humans, but its application and interpretation on wastewater matrices are much more complex due to the diversity of circulating strains. Also this study demonstrates the possibility of following certain mutations found in these new variants by targeted RT-qPCR. This study is the first carried out in France demonstrating the spreading dynamics of the 69-70 deletion in the Spike protein of SARS-CoV-2.