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Wastewater surveillance of SARS-CoV-2 variants in October–November 2022 in Italy: detection of XBB.1, BA.2.75 and rapid spread of the BQ.1 lineage

2023; Elsevier BV; Volume: 873; Linguagem: Inglês

10.1016/j.scitotenv.2023.162339

1879-1026

Giuseppina La Rosa, David Brandtner, Giusy Bonanno Ferraro, Carolina Veneri, Pamela Mancini, M. Iaconelli, Luca Lucentini, Claudia Del Giudice, Lidia Orlandi, Achille Palma, Adelaide Calabria, Agnese Carnevali, Albano Nehludoff, Alberta Stenico, Alberto Izzotti, Alessandra Barca, Alessandra Tosco, Amalia Porta, Annalisa Lombardi, Antonia Voli, Andrea Franzetti, Angela Ciccaglione, Angela Costa, Angelo D’Argenzio, Angelo Romano, Anna Pariani, Annalaura Carducci, Annalisa Grucci, Anna-Maria Prast, Antonella Agodi, Antonella Cersini, Antonella Giorgi, Barbara Bertasi, Bartolomeo Griglio, Carla Ancona, Carmelo Massimo Maida, Carmen Montanaro, Chiara Filizzolo, Claudio Ottaviano, Clementina Cocuzza, Cristina Pignata, Daniele Nasci, Danilo Cereda, Desdemona Oliva, Doriana Antonella Giorgi, Edoardo Malacaria, Elena Grasselli, Elena Nicosia, Elisabetta Carraro, Emanuela Ammoni, Eric Grange, Ermanno Federici, Fabio Filippetti, Fabio Tramuto, Flavia Guarneri, Flavia Serio, Florida Damasco, Franca Palumbo, Francesca Apollonio, Francesca Cutrupi, Francesca Gucciardi, Francesca Pennino, Francesca Russo, Francesco Triggiano, Franco Rigoli, Gabriele Pietrella, Gabriella Trani, Gian María Rossolini, Giorgia Bulotta, Giovanna Fusco, Giovanna La Vecchia, Giovanni Loris Alborali, Anna Giammanco, Graziano Santoro, Gisella Pitter, Giuseppa Purpari, Giuseppe Aprea, Giuseppe Di Vittorio, Giuseppe Folino, Giuseppe Lauria, Ileana Federigi, Irene Amoruso, Irene Ferrante, Irene Tomesani, Laura De Lellis, Laura Pellegrinelli, Lea Demetz, Lisa Gentili, Lisa Richiardi, Lorella Zago, Lorena Masieri, Lucia Decastelli, Luigi Bolognini, Luigi Cossentino, Manila Bianchi, Marco Verani, Marco Zampini, Margherita Ferrante, Maria Cadonna, Maria Teresa Montagna, Maria Teresa Scicluna, Mariaconcetta Arizzi, Marika Mariuz, Mario Palermo, Marta Bellisomi, Marta Paniccià, Martina Barchitta, Matteo Ramazzotti, Mattia Postinghel, Maurizio Viscardi, Mauro Ruffier, Maya Petricciuolo, Michele La Bianca, Michele Colitti, Monica Monfrinotti, Nadia Fontani, Nicoletta Formenti, Onofrio Mongelli, Osvalda De Giglio, Paola Angelini, Paola Foladori, Paolo Torlontano, Piergiuseppe Calà, Rosa Anna Cifarelli, S. Binda, Sara Briscolini, Sara Castiglioni, Silvia Bonetta, Silvia Magi, Silvia Scattolini, Silvia Schiarea, Simona De Grazia, Stefano Rosatto, Tatjana Baldovin, V. Prímache, Vanessa Groppi, Vicdalia Aniela Acciari, Walter Mazzucco, Elisabetta Suffredini,

Biosensors and Analytical Detection

This study adds insight regarding the occurrence and spread of SARS-CoV-2 Variants of Concern (VOCs) and Variants of Interest (VOIs) in Italy in October and November 2022, by testing urban wastewater collected throughout the country. A total of 332 wastewater samples were collected from 20 Italian Regions/Autonomous Provinces (APs) within the framework of national SARS-CoV-2 environmental surveillance. Of these, 164 were collected in the first week of October and 168 in the first week of November. A ∼1600 bp fragment of the spike protein was sequenced by Sanger (for individual samples) and long-read nanopore sequencing (for pooled Region/AP samples). In October, mutations characteristic of Omicron BA.4/BA.5 were detected in the vast majority (91 %) of the samples amplified by Sanger sequencing. A fraction of these sequences (9 %) also displayed the R346T mutation. Despite the low prevalence documented in clinical cases at the time of sampling, amino acid substitutions characteristic of sublineages BQ.1 or BQ.1.1 were detected in 5 % of sequenced samples from four Regions/APs. A significantly higher variability of sequences and variants was documented in November 2022, when the rate of sequences harbouring mutations of lineages BQ.1 and BQ1.1 increased to 43 %, and the number of Regions/APs positive for the new Omicron subvariant more than tripled (n = 13) compared to October. Moreover, an increase in the number of sequences with the mutation package BA.4/BA.5 + R346T (18 %), as well as the detection of variants never observed before in wastewater in Italy, such as BA.2.75 and XBB.1 (the latter in a Region where no clinical cases associated with this variant had ever been documented) was recorded. The results suggest that, as predicted by the ECDC, BQ.1/BQ.1.1 is rapidly becoming dominant in late 2022. Environmental surveillance proves to be a powerful tool for tracking the spread of SARS-CoV-2 variants/subvariants in the population.