UCA GenomiX tracks SARS-CoV-2 variants in waste water

The UCA GenomiX (IPMC) platform has been developing for several months a method to measure the levels of the different forms of the SARS-CoV-2 virus circulating in the wastewater of the Nice area. The detection of high levels of SARS-CoV2 in patients’ faeces has indeed suggested the interest of monitoring its levels in wastewater treatment facilities. The emergence of new variants makes the sequencing approach particularly interesting, as it allows easy detection. The entire viral genome (30,000 nucleotides) is sequenced using an Oxford Nanopore technique on a set of amplicons from sewage extracts.  In September 2020, UCA GenomiX started to establish a partnership with the City of Nice to carry out the sequencing of samples collected in twenty different districts, providing a precise quantification of the different variants present in the region. This collection by district enabled to alert the Nice Metropôle very quickly on the circulation of certain “at-risk” variants in particular districts of the city. While continuing this monitoring, the team is now working with the company Véolia, which wants to industrialise this approach, building on the expertise developed by UCA GenomiX. The first analyses required the implementation of a complete processing chain, from sample collection to library production, sequencing and bioinformatics analysis. This initiative was followed by others, such as the Ôbépine monitoring unit (https://www.reseau-obepine.fr/), to be extended to the whole of France.

IPMC staff involved in the project: Géraldine Rios, CNRS Assistant Engineer; Rainer Waldmann, INSERM researcher; Caroline Lacoux (Bernard Mari team), CNRS researcher; Kévin Lebrigand, CNRS engineer; Anna Diamant, Master student; Pascal Barbry, CNRS Research Director.