This study adds insight regarding the occurrence and spread of SARS-CoV-2 Variants of Concern (VOCs) and Var-iants of Interest (VOIs) in Italy in October and November 2022, by testing urban wastewater collected through-out 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 similar to 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 se-quences 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 asso-ciated 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. Environ-mental surveillance proves to be a powerful tool for tracking the spread of SARS-CoV-2 variants/subvariants in the population.
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 / G., La Rosa; D., Brandtner; G., Bonanno Ferraro; C., Veneri; P., Mancini; M., Iaconelli; L., Lucentini; C., Del Giudice; L., Orlandi; Palma, Achille; Calabria, Adelaide; Carnevali, Agnese; Nehludoff, Albano; Stenico, Alberta; Izzotti, Alberto; Barca, Alessandra; Tosco, Alessandra; Porta, Amalia; Lombardi, Annalisa; Voli, Antonia; Franzetti, Andrea; Ciccaglione, Angela; Costa, Angela; D’Argenzio, Angelo; Romano, Angelo; Pariani, Anna; Carducci, Annalaura; Grucci, Annalisa; Prast, Anna-Maria; Agodi, Antonella; Cersini, Antonella; Giorgi, Antonella; Bertasi, Barbara; Griglio, Bartolomeo; Ancona, Carla; Massimo Maida, Carmelo; Montanaro, Carmen; Filizzolo, Chiara; Ottaviano, Claudio; Cocuzza, Clementina; Pignata, Cristina; Nasci, Daniele; Cereda, Danilo; Oliva, Desdemona; Antonella Giorgi, Doriana; Malacaria, Edoardo; Grasselli, Elena; Nicosia, Elena; Carraro, Elisabetta; Ammoni, Emanuela; Grange, Eric; Federici, Ermanno; Filippetti, Fabio; Tramuto, Fabio; Guarneri, Flavia; Serio, Flavia; Damasco, Florida; Palumbo, Franca; Apollonio, Francesca; Cutrupi, Francesca; Gucciardi, Francesca; Pennino, Francesca; Russo, Francesca; Triggiano, Francesco; Rigoli, Franco; Pietrella, Gabriele; Trani, Gabriella; Maria Rossolini, Gian; Bulotta, Giorgia; Fusco, Giovanna; La Vecchia, Giovanna; Alborali, Giovanni; Giammanco, Giovanni; Santoro, Giovanni; Pitter, Gisella; Purpari, Giuseppa; Aprea, Giuseppe; Di Vittorio, Giuseppe; Folino, Giuseppe; Lauria, Giuseppe; Federigi, Ileana; Amoruso, Irene; Ferrante, Irene; Tomesani, Irene; De Lellis, Laura; Pellegrinelli, Laura; Demetz, Lea; Gentili, Lisa; Richiardi, Lisa; Zago, Lorella; Masieri, Lorena; Decastelli, Lucia; Bolognini, Luigi; Cossentino, Luigi; Bianchi, Manila; Verani, Marco; Zampini, Marco; Ferrante, Margherita; Cadonna, Maria; Teresa Montagna, Maria; Teresa Scicluna, Maria; Arizzi, Mariaconcetta; Mariuz, Marika; Palermo, Mario; Bellisomi, Marta; Paniccià, Marta; Barchitta, Martina; Ramazzotti, Matteo; Postinghel, Mattia; Viscardi, Maurizio; Ruffier, Mauro; Petricciuolo, Maya; La Bianca, Michele; Colitti, Michele; Monfrinotti, Monica; Fontani, Nadia; Formenti, Nicoletta; Mongelli, Onofrio; De Giglio, Osvalda; Angelini, Paola; Foladori, Paola; Torlontano, Paolo; Calà, Piergiuseppe; Anna Cifarelli, Rosa; Binda, Sandro; Briscolini, Sara; Castiglioni, Sara; Bonetta, Silvia; Magi, Silvia; Scattolini, Silvia; Schiarea, Silvia; De Grazia, Simona; Rosatto, Stefano; Baldovin, Tatjana; Primache, Valeria; Groppi, Vanessa; Aniela Acciari, Vicdalia; Mazzucco, Walter; E., Suffredini. - In: SCIENCE OF THE TOTAL ENVIRONMENT. - ISSN 1879-1026. - STAMPA. - 873:(2023), pp. 16233901-16233910. [10.1016/j.scitotenv.2023.162339]
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
Francesca Cutrupi;Paola Foladori;
2023-01-01
Abstract
This study adds insight regarding the occurrence and spread of SARS-CoV-2 Variants of Concern (VOCs) and Var-iants of Interest (VOIs) in Italy in October and November 2022, by testing urban wastewater collected through-out 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 similar to 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 se-quences 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 asso-ciated 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. Environ-mental surveillance proves to be a powerful tool for tracking the spread of SARS-CoV-2 variants/subvariants in the population.| File | Dimensione | Formato | |
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