Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis
Authors: Veneri C. , Brandtner D. , Mancini P. , Bonanno Ferraro G. , Iaconelli M. , Suffredini E. , Petrillo M. , Leoni G. , Paracchini V. , Gawlik B. M. , Marchini A. ,   the SARI Network, Torlontano Paolo , Aprea Giuseppe , Scattolini Silvia , Acciari Vicdalia Aniela , La Bianca Michele , Cifarelli Rosa Anna , Palma Achille , Lauria Giuseppe , La Vecchia Giovanna , Giordano Vincenzo , Cossentino Luigi , Pennino Francesca , Lombardi Annalisa , Gentili Lisa , Angelini Paola , Nasci Daniele , Alborali Giovanni , Formenti Nicoletta , Guarneri Flavia , Fontani Nadia , Guercio Marco , Mariuz Marika , Trani Gabriella , Pariani Anna , De Lellis Laura , Ancona Carla , Barca Alessandra , Serio Flavia , Giorgi Doriana Antonella , Ferrante Irene , Capparuccini Valeria , Scicluna Maria Teresa , Cersini Antonella , Pietrella Gabriele , Nicosia Elena , Fontani Nadia , Guercio Marco , Grasselli Elena , Izzotti Alberto , Tomesani Irene , Bellisomi Marta , Rosatto Stefano , Ammoni Emanuela , Cereda Danilo , Bertasi Barbara , Losio Marina Nadia , Oliva Desdemona , Castiglioni Sara , Schiarea Silvia , Binda Sandro , Primache Valeria , Pellegrinelli Laura , Cocuzza Clementina , Musumeci Rosario , Bolognini Luigi , Filippetti Fabio , Paniccia’ Marta , Briscolini Sara , Magi Silvia , Grucci Annalisa , Colitti Michele , Ciccaglione Angela , Montanaro Carmen , Griglio Bartolomeo , Costa Angela , Decastelli Lucia , Romano Angelo , Bianchi Manila , Carraro Elisabetta , Pignata Cristina , Macrì Manuela , Bonetta Silvia , Albano Nehludoff , Di Vittorio Giuseppe , Mongelli Onofrio , Apollonio Francesca , Triggiano Francesco , De Giglio Osvalda , Montagna Maria Teresa , Palermo Mario , Maida Carmelo Massimo , Mazzucco Walter , Tramuto Fabio , De Grazia Simona , Giammanco Giovanni Maurizio , Filizzolo Chiara , Purpari Giuseppa , Gucciardi Francesca , Ferrante Margherita , Agodi Antonella , Barchitta Martina , Cala’ Piergiuseppe , Carducci Annalaura , Verani Marco , Federigi Ileana , Macrì Salvatore , Federici Ermanno , Petricciuolo Maya , Carnevali Agnese , Russo Francesca , Pitter Gisella , Groppi Vanessa , Rigoli Franco , Zampini Marco , Baldovin Tatjana , Amoruso Irene , Cadonna Maria , Postinghel Mattia , Foladori Paola , Zago Lorella , Stenico Alberta , Marco Morelli , Matteo Dossena , La Rosa G. 
Published: June 2024

The emergence of new SARS-CoV-2 variants poses challenges to global surveillance efforts, necessitating swift actions in their detection, evaluation, and management. Among the most recent variants, Omicron BA.2.86 and its sub-lineages have gained attention due to their potential immune evasion properties. This study describes the development of a digital PCR assay for the rapid detection of BA.2.86 and its descendant lineages, in wastewater samples. By using this assay, we analyzed wastewater samples collected in Italy from September 2023 to January 2024. Our analysis revealed the presence of BA.2.86 lineages already in October 2023 with a minimal detection rate of 2% which then rapidly increased, becoming dominant by January 2024, accounting for a prevalence of 62%. The findings emphasize the significance of wastewater-based surveillance in tracking emerging variants and underscore the efficacy of targeted digital PCR assays for environmental monitoring.