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1. 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

Author

G. La Rosa, D. Brandtner, G. Bonanno Ferraro, C. Veneri, P. Mancini, M. Iaconelli, L. Lucentini, C. Del Giudice, L. Orlandi, E. Suffredini, 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 Maria Rossolini, Giorgia Bulotta, Giovanna Fusco, Giovanna La Vecchia, Giovanni Alborali, Giovanni Giammanco, Giovanni 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, Sandro Binda, Sara Briscolini, Sara Castiglioni, Silvia Bonetta, Silvia Magi, Silvia Scattolini, Silvia Schiarea, Simona De Grazia, Stefano Rosatto, Tatjana Baldovin, Valeria Primache, Vanessa Groppi, Vicdalia Aniela Acciari, Walter Mazzucco, La Rosa, G, Brandtner, D, Bonanno Ferraro, G, Veneri, C, Mancini, P, Iaconelli, M, Lucentini, L, Del Giudice, C, Orlandi, L, Suffredini, E, Cocuzza, C, Franzetti, A, La Rosa, G., Brandtner, D., Bonanno Ferraro, G., Veneri, C., Mancini, P., Iaconelli, M., Lucentini, L., Del Giudice, C., Orlandi, L., Suffredini, E., Pennino, F., Lombardi, A., Maida, CM, Mazzucco, W, and Tramuto, F

Subjects
BA2.75, Environmental Engineering, Surveillance, MED/42 - IGIENE GENERALE E APPLICATA, Omicron, SARS-CoV-2, BQ.1, Wastewater, XBB.1, BIO/19 - MICROBIOLOGIA GENERALE, Pollution, MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, BA2.75, BQ.1, Omicron, SARS-CoV-2, Surveillance, Wastewater, XBB.1, Environmental Chemistry, Waste Management and Disposal
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.

Published
2023

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

Author

La Rosa, G., Iaconelli, M., Veneri, C., Mancini, P., Bonanno Ferraro, G., Brandtner, D., Lucentini, L., Bonadonna, L., Rossi, M., Grigioni, M., Suffredini, E., Giuseppe, Bucciarelli, Paolo, Torlontano, Giuseppe, Michele La Bianca, Rosa Anna Cifarelli, Achille, Palma, Giovanna La Vecchia, Giuseppe, Lauria, Rosanna, Brienza, Patrizia, Montenegro, Angelo, D'Argenzio, Luigi, Cossentino, Renato, Olivares, Antonio, Pizzolante, Giovanna, Fusco, Alessandra, Tosco, Amalia, Porta, Francesca, Pennino, Triassi, Maria, Paola, Angelini, Laura De Lellis, Daniele, Nasci, Giovanni, Alborali, Nicoletta, Formenti, Flavia, Guarneri, Nadia, Fontani, Giulia, Nani, Franca, Palumbo, Gianluca, Borlone, Marco, Guercio, Lisa, Gentili, Marika, Mariuz, Gabriella, Trani, Anna, Pariani, Carla, Ancona, Doriana Antonella Giorgi, Irene, Ferrante, Monica, Monfrinotti, Silvia, Riosa, Valeria, Capparuccini, Maria Teresa Scicluna, Antonella, Mariaconcetta, Arizzi, Giancarlo, Cecchini, Claudio, Ottaviano, Elena, Nicosia, Elena, Grasselli, Giorgia, Allaria, Alberto, Izzotti, Stefano, Rosatto, Emanuela, Ammoni, Danilo, Cereda, Marina Nadia Losio, Barbara, Bertasi, Andrea, Aliscioni, Desdemona, Oliva, Sara, Castiglioni, Silvia, Schiarea, Ettore, Zuccato, Manuela, Antonelli, Arianna, Azzellino, Francesca, Malpei, Andrea, Turolla, Sandro, Binda, Pellegrinelli, Laura, Valeria, Primache, Clementina, Cocuzza, Andrea, Franzetti, Giorgio, Bertanza, Maria Luisa Callegari, Luigi, Bolognini, Fabio, Filippetti, Marta, Paniccia, Francesca, Ciuti, Sara, Briscolini, Silvia, Magi, Michele, Colitti, Carmen, Montanaro, Giuseppe, Aprea, Maria Grazia Cerroni, Bartolomeo, Griglio, Renza, Berruti, Mauro, Cravero, Angela, Costa, Manila, Bianchi, Lucia, Decastelli, Angelo, Romano, Fabio, Zuccon, Elisabetta, Carraro, Cristina, Pignata, Silvia, Bonetta, Giuseppe Di Vittorio, Onofrio, Mongelli, Osvalda De Giglio, Francesca, Apollonio, Francesco, Triggiano, Maria Teresa Montagna, Nicola, Ungaro, Mario, Palermo, Carmelo Massimo Maida, Walter, Mazzucco, Simona De Grazia, Giovanni, Giammanco, Giuseppa, Purpari, Margherita, Ferrante, Antonella, Agodi, Martina, Barchitta, Piergiuseppe, Cala’, Carducci, Annalaura, Verani, Marco, Federigi, Ileana, Giulia, Lauretani, Sara, Muzio, Matteo, Ramazzotti, Alberto, Antonelli, Enrica, Ricci, Giovanni, Santoro, Ermanno, Federici, Maya, Petricciuolo, Sofia, Barigelli, Mauro, Ruffier, Francesca, Borney, Eric, Grange, Florida, Damasco, Francesca, Russo, Gisella, Pitter, Vanessa, Groppi, Franco, Rigoli, Marco, Zampini, Tatjana, Baldovin, Irene, Amoruso, Elena, Mengon, Maria, Cadonna, Mattia, Postinghel, Francesco, Pizzo, Alessandra, Schiavuzzi, Francesca, Cutrupi, Paola, Foladori, Serena, Manara, Lorella, Zago, Alberta, Stenico, Anna-Maria, Prast., La Rosa, G, Iaconelli, M, Veneri, C, Mancini, P, Bonanno Ferraro, G, Brandtner, D, Lucentini, L, Bonadonna, L, Rossi, M, Grigioni, M, Suffredini, E, Bucciarelli, G, Torlontano, P, Aprea, G, La Bianca, M, Cifarelli, R, Palma, A, La Vecchia, G, Lauria, G, Brienza, R, Montenegro, P, D'Argenzio, A, Cossentino, L, Olivares, R, Pizzolante, A, Fusco, G, Tosco, A, Porta, A, Pennino, F, Maria, T, Angelini, P, De Lellis, L, Nasci, D, Alborali, G, Formenti, N, Guarneri, F, Fontani, N, Nani, G, Palumbo, F, Borlone, G, Guercio, M, Gentili, L, Mariuz, M, Trani, G, Pariani, A, Ancona, C, Giorgi, D, Ferrante, I, Monfrinotti, M, Riosa, S, Capparuccini, V, Scicluna, M, Cersini, A, Arizzi, M, Cecchini, G, Ottaviano, C, Nicosia, E, Grasselli, E, Allaria, G, Izzotti, A, Rosatto, S, Ammoni, E, Cereda, D, Losio, M, Bertasi, B, Aliscioni, A, Oliva, D, Castiglioni, S, Schiarea, S, Zuccato, E, Antonelli, M, Azzellino, A, Malpei, F, Turolla, A, Binda, S, Laura, P, Primache, V, Cocuzza, C, Franzetti, A, Bertanza, G, Callegari, M, Bolognini, L, Filippetti, F, Paniccia', M, Ciuti, F, Briscolini, S, Magi, S, Colitti, M, Montanaro, C, Cerroni, M, Griglio, B, Berruti, R, Cravero, M, Costa, A, Bianchi, M, Decastelli, L, Romano, A, Zuccon, F, Carraro, E, Pignata, C, Bonetta, S, Di Vittorio, G, Mongelli, O, De Giglio, O, Apollonio, F, Triggiano, F, Montagna, M, Ungaro, N, Palermo, M, Maida, C, Mazzucco, W, De Grazia, S, Giammanco, G, Purpari, G, Ferrante, M, Agodi, A, Barchitta, M, Cala', P, Carducci, A, Verani, M, Federigi, I, Lauretani, G, Muzio, S, Ramazzotti, M, Antonelli, A, Ricci, E, Santoro, G, Federici, E, Petricciuolo, M, Barigelli, S, Ruffier, M, Borney, F, Grange, E, Damasco, F, Russo, F, Pitter, G, Groppi, V, Rigoli, F, Zampini, M, Baldovin, T, Amoruso, I, Mengon, E, Cadonna, M, Postinghel, M, Pizzo, F, Schiavuzzi, A, Cutrupi, F, Foladori, P, Manara, S, Zago, L, Stenico, A, Prast, A, La Rosa G., Iaconelli M., Veneri C., Mancini P., Bonanno Ferraro G., Brandtner D., Lucentini L., Bonadonna L., Rossi M., Grigioni M., Bucciarelli G., Torlontano P., Aprea G., La Bianca M., Cifarelli R.A., Palma A., La Vecchia G., Lauria G., Brienza R., Montenegro P., D'Argenzio A., Cossentino L., Olivares R., Pizzolante A., Fusco G., Tosco A., Porta A., Pennino F., Maria T., Angelini P., De Lellis L., Nasci D., Alborali G., Formenti N., Guarneri F., Fontani N., Nani G., Palumbo F., Borlone G., Guercio M., Gentili L., Mariuz M., Trani G., Pariani A., Ancona C., Giorgi D.A., Ferrante I., Monfrinotti M., Riosa S., Capparuccini V., Scicluna M.T., Cersini A., Arizzi M., Cecchini G., Ottaviano C., Nicosia E., Grasselli E., Allaria G., Izzotti A., Rosatto S., Ammoni E., Cereda D., Losio M.N., Bertasi B., Aliscioni A., Oliva D., Castiglioni S., Schiarea S., Zuccato E., Antonelli M., Azzellino A., Malpei F., Turolla A., Binda S., Laura P., Primache V., Cocuzza C., Franzetti A., Bertanza G., Callegari M.L., Bolognini L., Filippetti F., Paniccia' M., Ciuti F., Briscolini S., Magi S., Colitti M., Montanaro C., Cerroni M.G., Griglio B., Berruti R., Cravero M., Costa A., Bianchi M., Decastelli L., Romano A., Zuccon F., Carraro E., Pignata C., Bonetta S., Di Vittorio G., Mongelli O., De Giglio O., Apollonio F., Triggiano F., Montagna M.T., Ungaro N., Palermo M., Maida C.M., Mazzucco W., De Grazia S., Giammanco G., Purpari G., Ferrante M., Agodi A., Barchitta M., Cala' P., Carducci A., Verani M., Federigi I., Lauretani G., Muzio S., Ramazzotti M., Antonelli A., Ricci E., Santoro G., Federici E., Petricciuolo M., Barigelli S., Ruffier M., Borney F., Grange E., Damasco F., Russo F., Pitter G., Groppi V., Rigoli F., Zampini M., Baldovin T., Amoruso I., Mengon E., Cadonna M., Postinghel M., Pizzo F., Schiavuzzi A., Cutrupi F., Foladori P., Manara S., Zago L., Stenico A., Prast A.-M., Suffredini E., and Triassi, M

Subjects
Omicron, RT-qPCR, SARS-CoV-2, Sewage, Variant, Wastewater-based epidemiology, Wastewater-Based Epidemiological Monitoring, Environmental Engineering, COVID-19, Wastewater, Pollution, Humans, RNA, Viral, Waste Water, SARS-Cov2, Environmental Chemistry, RNA, Viral, wastewater based epidemiology, Waste Management and Disposal, Human, Omicron, RT-qPCR, SARS-CoV-2, Sewage, Variant, Wastewater-based epidemiology
Abstract

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.

Published
2022

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