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The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance

2022; Elsevier BV; Volume: 837; Linguagem: Inglês

10.1016/j.scitotenv.2022.155767

1879-1026

Giuseppina La Rosa, M. Iaconelli, Carolina Veneri, Pamela Mancini, Giusy Bonanno Ferraro, David Brandtner, Luca Lucentini, Lucia Bonadonna, Mirko Rossi, Mauro Grigioni, Achille Palma, Alberta Stenico, Alberto Antonelli, Alberto Izzotti, Alessandra Schiavuzzi, Alessandra Tosco, Amalia Porta, Andrea Franzetti, Andrea Turolla, Angela Costa, Angelo D’Argenzio, Angelo Romano, Anna Pariani, Annalaura Carducci, Anna-Maria Prast, Antonella Agodi, Antonella Cersini, Antonio Pizzolante, Arianna Azzellino, Barbara Bertasi, Bartolomeo Griglio, Carla Ancona, Carmelo Massimo Maida, Carmen Montanaro, Claudio Ottaviano, Clementina Cocuzza, Cristina Pignata, Daniele Nasci, Danilo Cereda, Desdemona Oliva, Doriana Antonella Giorgi, Elena Grasselli, Elena Mengon, Elena Nicosia, Elisabetta Carraro, Emanuela Ammoni, Enrica Ricci, Eric Grange, Ermanno Federici, Ettore Zuccato, Fabio Filippetti, Fabio Zuccon, Flavia Guarneri, Florida Damasco, Franca Palumbo, Francesca Apollonio, Francesca Borney, Francesca Ciuti, Francesca Cutrupi, Francesca Malpei, Francesca Pennino, Francesca Russo, Francesco Pizzo, Francesco Triggiano, Franco Rigoli, Gabriella Trani, Giancarlo Cecchini, Gianluca Borlone, Giorgia Allaria, Giorgio Bertanza, Giovanna Fusco, Giovanna La Vecchia, Giovanni Loris Alborali, Anna Giammanco, G. A. Santoro, Gisella Pitter, Giulia Lauretani, Giulia Nani, Giuseppa Purpari, Giuseppe Aprea, Giuseppe Bucciarelli, Giuseppe Di Vittorio, Giuseppe Lauria, Ileana Federigi, Irene Amoruso, Irene Ferrante, Laura De Lellis, Lisa Gentili, Lorella Zago, Lucia Decastelli, Luigi Bolognini, Luigi Cossentino, Manila Bianchi, Manuela Antonelli, Marco Guercio, Marco Verani, Marco Zampini, Margherita Ferrante, Maria Cadonna, Maria Grazia Cerroni, Maria Luisa Callegari, Maria Teresa Montagna, Maria Teresa Scicluna, Mariaconcetta Arizzi, Marika Mariuz, Marina Nadia Losio, Mario Palermo, Marta Paniccià, Maria Triassi, Martina Barchitta, Matteo Ramazzotti, Mattia Postinghel, Maria Carla Cravero, Mauro Ruffier, Maya Petricciuolo, Michele La Bianca, Michele Colitti, Monica Monfrinotti, Nadia Fontani, Nicola Ungaro, Nicoletta Formenti, Onofrio Mongelli, Osvalda De Giglio, Paola Angelini, Paola Foladori, Paolo Torlontano, Paola Montenegro, Pellegrinelli Laura, Piergiuseppe Calà, Renato Olivares, Renza Berruti, Rosa Anna Cifarelli, Rosanna Brienza, S. Binda, Sara Briscolini, Sara Castiglioni, Sara Muzio, Serena Manara, Silvia Bonetta, Silvia Magi, Silvia Riosa, Silvia Schiarea, Simona De Grazia, Sofia Barigelli, Stefano Rosatto, Tatjana Baldovin, Valeria Capparuccini, V. Prímache, Vanessa Groppi, Walter Mazzucco, Elisabetta Suffredini,

Biosensors and Analytical Detection

The SARS-CoV-2 Omicron variant emerged in South Africa in November 2021, and has later been identified worldwide, raising serious concerns. A real-time RT-PCR assay was designed for the rapid screening of the Omicron variant, targeting characteristic mutations of the spike gene. The assay was used to test 737 sewage samples collected throughout Italy (19/21 Regions) between 11 November and 25 December 2021, with the aim of assessing the spread of the Omicron variant in the country. Positive samples were also tested with a real-time RT-PCR developed by the European Commission, Joint Research Centre (JRC), and through nested RT-PCR followed by Sanger sequencing. Overall, 115 samples tested positive for Omicron SARS-CoV-2 variant. The first occurrence was detected on 7 December, in Veneto, North Italy. Later on, the variant spread extremely fast in three weeks, with prevalence of positive wastewater samples rising from 1.0% (1/104 samples) in the week 5-11 December, to 17.5% (25/143 samples) in the week 12-18, to 65.9% (89/135 samples) in the week 19-25, in line with the increase in cases of infection with the Omicron variant observed during December in Italy. Similarly, the number of Regions/Autonomous Provinces in which the variant was detected increased from one in the first week, to 11 in the second, and to 17 in the last one. The presence of the Omicron variant was confirmed by the JRC real-time RT-PCR in 79.1% (91/115) of the positive samples, and by Sanger sequencing in 66% (64/97) of PCR amplicons. In conclusion, we designed an RT-qPCR assay capable to detect the Omicron variant, which can be successfully used for the purpose of wastewater-based epidemiology. We also described the history of the introduction and diffusion of the Omicron variant in the Italian population and territory, confirming the effectiveness of sewage monitoring as a powerful surveillance tool.