Project: The Nice Promenade of the English Variant

About

We reported in August 2021 in the journal Lancet Regional Health Europe comment The spread of the "English" (alpha) variant of SARS-CoV-2 occurred within the city of Nice at the beginning of 2021. We obtained these results by analyzing wastewater from around twenty points in the city by RNA sequencing. This allowed us to draw up a map of the different variants present in the territory. Such approaches will certainly provide valuable epidemiological information on this virus or any other infectious material in the future.
The genome of the SARS-CoV-2 virus contains approximately 30,000 ribonucleotides. We have implemented a nanopore sequencing approach to monitor the different variants of the SARS-CoV-2 virus in the wastewater of the city of Nice, which makes it possible to quantify the concentration of the virus while also determining the nature of any variants. We have demonstrated that the quantifications carried out in the wastewater of different districts of a city made it possible to accurately reflect what was happening on the surface, after comparing the signals measured in the wastewater to measurements carried out on samples from patients collected during the same week. Measurements carried out on the sewerage networks thus provide a fairly precise picture of what may be happening at the scale of the entire population, by allowing the screening of symptomatic as well as asymptomatic people.
With the help of the sanitation services of the Nice Metropolitan Area, wastewater from 20 different districts of the city was collected. Very precise information on the different variants circulating was then able to be collected for 6 months, allowing the authorities to be alerted very early in 2021 to the presence of "at risk" variants in certain districts of the city.
Our measurements made it possible to detect in January 2021 the emergence in one of the city's districts of a particular variant of the alpha lineage, carrying an A522S mutation on the spicule. This variant had only been detected in less than 2% of all the B.1.1.7 viruses, but it is nevertheless this strain which quickly spread throughout the city to become largely the majority there from the month of February .