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1. Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

Author

Veneri, C, Brandtner, D, Mancini, P, Bonanno Ferraro, G, Iaconelli, M, Suffredini, E, Petrillo, M, Leoni, G, Paracchini, V, Gawlik, B, Marchini, A, Torlontano, P, Aprea, G, Scattolini, S, Acciari, V, La Bianca, M, Cifarelli, R, Palma, A, Lauria, G, La Vecchia, G, Giordano, V, Cossentino, L, Pennino, F, Lombardi, A, Gentili, L, Angelini, P, Nasci, D, Alborali, G, Formenti, N, Guarneri, F, Fontani, N, Guercio, M, Mariuz, M, Trani, G, Pariani, A, De Lellis, L, Ancona, C, Barca, A, Serio, F, Giorgi, D, Ferrante, I, Capparuccini, V, Scicluna, M, Cersini, A, Pietrella, G, Nicosia, E, Grasselli, E, Izzotti, A, Tomesani, I, Bellisomi, M, Rosatto, S, Ammoni, E, Cereda, D, Bertasi, B, Losio, M, Oliva, D, Castiglioni, S, Schiarea, S, Binda, S, Primache, V, Pellegrinelli, L, Cocuzza, C, Musumeci, R, Bolognini, L, Filippetti, F, Paniccia', M, Briscolini, S, Magi, S, Grucci, A, Colitti, M, Ciccaglione, A, Montanaro, C, Griglio, B, Costa, A, Decastelli, L, Romano, A, Bianchi, M, Carraro, E, Pignata, C, Macrì, M, Bonetta, S, Albano, N, Di Vittorio, G, Mongelli, O, Apollonio, F, Triggiano, F, De Giglio, O, Montagna, M, Palermo, M, Maida, C, Mazzucco, W, Tramuto, F, De Grazia, S, Giammanco, G, Filizzolo, C, Purpari, G, Gucciardi, F, Ferrante, M, Agodi, A, Barchitta, M, Cala', P, Carducci, A, Verani, M, Federigi, I, Macrì, S, Federici, E, Petricciuolo, M, Carnevali, A, Russo, F, Pitter, G, Groppi, V, Rigoli, F, Zampini, M, Baldovin, T, Amoruso, I, Cadonna, M, Postinghel, M, Foladori, P, Zago, L, Stenico, A, Marco, M, Matteo, D, La Rosa, G, Veneri, C., Brandtner, D., Mancini, P., Bonanno Ferraro, G., Iaconelli, M., Suffredini, E., Petrillo, M., Leoni, G., Paracchini, V., Gawlik, B. M., Marchini, A., 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, 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., Veneri, C, Brandtner, D, Mancini, P, Bonanno Ferraro, G, Iaconelli, M, Suffredini, E, Petrillo, M, Leoni, G, Paracchini, V, Gawlik, B, Marchini, A, Torlontano, P, Aprea, G, Scattolini, S, Acciari, V, La Bianca, M, Cifarelli, R, Palma, A, Lauria, G, La Vecchia, G, Giordano, V, Cossentino, L, Pennino, F, Lombardi, A, Gentili, L, Angelini, P, Nasci, D, Alborali, G, Formenti, N, Guarneri, F, Fontani, N, Guercio, M, Mariuz, M, Trani, G, Pariani, A, De Lellis, L, Ancona, C, Barca, A, Serio, F, Giorgi, D, Ferrante, I, Capparuccini, V, Scicluna, M, Cersini, A, Pietrella, G, Nicosia, E, Grasselli, E, Izzotti, A, Tomesani, I, Bellisomi, M, Rosatto, S, Ammoni, E, Cereda, D, Bertasi, B, Losio, M, Oliva, D, Castiglioni, S, Schiarea, S, Binda, S, Primache, V, Pellegrinelli, L, Cocuzza, C, Musumeci, R, Bolognini, L, Filippetti, F, Paniccia', M, Briscolini, S, Magi, S, Grucci, A, Colitti, M, Ciccaglione, A, Montanaro, C, Griglio, B, Costa, A, Decastelli, L, Romano, A, Bianchi, M, Carraro, E, Pignata, C, Macrì, M, Bonetta, S, Albano, N, Di Vittorio, G, Mongelli, O, Apollonio, F, Triggiano, F, De Giglio, O, Montagna, M, Palermo, M, Maida, C, Mazzucco, W, Tramuto, F, De Grazia, S, Giammanco, G, Filizzolo, C, Purpari, G, Gucciardi, F, Ferrante, M, Agodi, A, Barchitta, M, Cala', P, Carducci, A, Verani, M, Federigi, I, Macrì, S, Federici, E, Petricciuolo, M, Carnevali, A, Russo, F, Pitter, G, Groppi, V, Rigoli, F, Zampini, M, Baldovin, T, Amoruso, I, Cadonna, M, Postinghel, M, Foladori, P, Zago, L, Stenico, A, Marco, M, Matteo, D, La Rosa, G, Veneri, C., Brandtner, D., Mancini, P., Bonanno Ferraro, G., Iaconelli, M., Suffredini, E., Petrillo, M., Leoni, G., Paracchini, V., Gawlik, B. M., Marchini, A., 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, 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, and La Rosa, G.

Abstract

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.

Published
2024

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, 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., Suffredini E., 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., 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., Suffredini E., 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., and Prast A. -M.

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

3. 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 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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., 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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

4. Trends in SARS-CoV-2 clinically confirmed cases and viral load in wastewater: A critical alignment for Padua city (NE Italy).

Author

Baldovin T, Amoruso I, Fonzo M, Bertoncello C, Groppi V, Pitter G, Russo F, and Baldo V

Abstract

Since the beginning of the COVID-19 pandemic, wastewater-based epidemiology (WBE) has been depicted as a promising environmental surveillance tool and early warning system. Predictive models for the estimate of COVID-19 cases from wastewater viral loads also earned lot of interest and are currently under development. Hereby a pilot study that compares WBE surveillance data with confirmed cases, total hospitalizations, doses of vaccine administered and predominance of coronavirus variants. Composite 24hrs wastewater samples were collected weekly between September 2021 and July 2022 from Padua wastewater treatment plant. Samples were processed following a previously published method. One-step RT-qPCR was performed for quantification, adapting an Orf1b-nsp14 gene assay. Variant replacement was derived from the monthly bulletins of the Italian National Health Institute. Aggregate data on vaccine doses administered and on COVID-19 prevalence and hospitalizations were retrieved from official reports. Eighty-two samples were processed. Viral loads highlighted 3 major peaks in January, April and July 2022. Quantitation of SARS-CoV-2 in wastewater and clinical surveillance resulted temporally juxtaposable. However, variation of the two curves is not proportional. SARS-CoV-2 showed its highest peak in April, whereas maximum COVID-19 prevalence was achieved in January. Total hospitalizations followed the prevalence trend. Omicron BA.1 started to replace the Delta variant in December 2021. Subsequently, the shift towards Omicron BA.2 occurred between February and April 2022. Finally, BA.4/5 attested around June, somehow preceding the summer peak. Emergence of Omicron BA.1 over Delta could be a possible driver of the increase in both clinical cases and wastewater viral load in January 2022. In late March 2022, Omicron BA.2 replaced BA.1: this reflected in a steep increase of wastewater viral load, but not of COVID-19 confirmed cases. When a dramatic drop in the testing capacity of clinical surveillance occurred, WBE was possibly capable of detecting a substantial increase in viral circulation., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

Published
2023
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