Aim of the Study: Following the declaration of the end of the pandemic, surveillance efforts are limited due to a decline in swab testing and sequencing. This poses a significant challenge in tracking the emergence of new variants. The use of wastewater monitoring can provide a comprehensive approach to tracking the circulation and spread of different SARS-CoV-2 variants within a community or population. Among the most recent variants, Omicron BA.2.86 and its sublineages, including JN.1, have gained attention for their potential to evade the immune system. It was first detected in Denmark and Israel and has since become the prevalent variant, worldwide. This study aimed to comprehensively investigate the occurrence and dynamics of the BA.2.86* lineage in Italian wastewater from September 2023 to January 2024. Methods: A total of 507 wastewater samples were collected from 114 wastewater treatment plants across 16 regions and 2 autonomous provinces. These samples were subjected to viral concentration, nucleic acid extraction, and quantification of SARS-CoV-2 RNA using a newly designed digital RT-PCR targeting the BA.2.86* lineage. Additionally, a subset of samples underwent conventional RT-PCR and Sanger sequencing to confirm assay specificity and to identify specific sub-lineages, such as JN.1. Results: In total, 23% of samples tested positive for BA.2.86*, with viral concentrations ranging from 4.0 × 10^3 to 1.1×10^5 genome copies/L. The lineage was first detected in October 2023, with a minimum detection rate of 2%, and a rapid spread was observed over the following months, reaching a peak detection rate of 62% in January 2024. Subsequent sequencing confirmed the emergence and dominance of the JN.1 sub-lineage, characterised by the L455S mutation, highlighting its evolutionary advantage over the parental BA.2.86 variant. Conclusions: Environmental surveillance proved instrumental in elucidating the emergence and spread dynamics of BA.2.86* in Italy, providing critical insights into the evolution and spread of the variant. The RT-dPCR assay demonstrated its utility as a rapid and sensitive tool for variant detection in wastewater. These findings highlight the importance of sustained wastewater surveillance as a complementary approach to clinical surveillance, particularly in monitoring variant dynamics during periods of low virus circulation. Effective and timely surveillance efforts are essential for informing evidence-based public health interventions and mitigating the impact of emerging SARS-CoV-2 variants on public health. Acknowledgements: We wish to thank Dr. Paola Stefanelli (Istituto Superiore di Sanità, Department of Infectious Diseases) for sharing clinical omicron samples used as controls for specificity. This research was supported by EU funding within the NextGeneration EU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (Project no. PE00000007, PE13 INF-ACT).
SPREAD OF THE BA.2.86 LINEAGE OF SARS-CoV-2 IN ITALY BY ANALYSIS OF WASTEWATER / Veneri, C.; Brandtner, D.; Mancini, P.; Bonanno Ferraro, G.; Iaconelli, M.; Suffredini, E.; Petrillo, M.; Leoni, G.; Paracchini, V.; Gawlik, B. M.; Marchini, A.; Bucciarelli, Giuseppe; Torlontano, Paolo; Aprea, Giuseppe; Scattolini, Silvia; Scattolini, Silvia; D’Angelantonio, Daniela; Migliorati, Giacomo; La Bianca, Michele; Anna Cifarelli, Rosa; Palma, Achille; E Giuseppe Lauria, Giovanna La Vecchia; Brienza, Rosanna; Montenegro, Patrizia; Malacaria, Eduardo; Folino, Giuseppe; Iannone, Michelangelo; Casaburi, Filomena; Bulotta, Giorgia; Barillari, Emanuela; Dragone, Melania; Sacco, Iolanda; Tomaino, Carmine; Felicetta, Cristina; Calabria, Adelaide; Varcasia, Ottavia; Stefanizzi, Francesca; Vizza, Concetta; D’Argenzio, Angelo; Cossentino, Luigi; Olivares, Renato; Pizzolante, Antonio; Fusco, Giovanna; Tosco, Alessandra; Porta, Amalia; Pennino, Francesca; Maria, Triassi; Angelini, Paola; Gentili, Lisa; De Lellis, Laura; Nasci, Daniele; Alborali, Giovanni; Formenti, Nicoletta; Guarneri, Flavia; Fontani, Nadia; Nani, Giulia; Palumbo, Franca; Borlone, Gianluca; Guercio, Marco; Mariuz, Marika; Trani, Gabriella; Pariani, Anna; Ancona, Carla; Barca, Alessandra; Serio, Flavia; Antonella Giorgi, Doriana; Ferrante, Irene; Monfrinotti, Monica; Riosa, Silvia; Capparuccini, Valeria; Teresa Scicluna, Maria; Cersini, Antonella; Arizzi, Mariaconcetta; Cecchini, Giancarlo; Ottaviano, Claudio; Nicosia, Elena; Fontani, Nadia; Nani, Giulia; Palumbo, Franca; Borlone, Gianluca; Guercio, Marco; Grasselli, Elena; Allaria, Giorgia; Dondero, Lorenzo; Rispo, Francesca; Izzotti, Alberto; Maria Bertolotto, Rosa; Nicosia, Elena; Rosatto, Stefano; Bellisomi, Marta; Tomesani, Irene; Tiso, Micaela; Ammoni, Emanuela; Cereda, Danilo; Nadia Losio, Marina; Bertasi, Barbara; Oliva, Desdemona; Giovanna Guiso, Maria; Ferrari, Fabio; Mundo, Maria; Martines, Antonino; Castiglioni, Sara; Schiarea, Silvia; Salmoiraghi, Giulia; Antonelli, Manuela; Azzellino, Arianna; Malpei, Francesca; Turolla, Andrea; Binda, Sandro; Laura, Pellegrinelli; Primache, Valeria; Cocuzza, Clementina; Franzetti, Andrea; Musumeci, Rosario; Martinelli, Marianna; Bertanza, Giorgio; Luisa Callegari, Maria; Bolognini, Luigi; Filippetti, Fabio; Paniccia', Marta; Ciuti, Francesca; Briscolini, Sara; Magi, Silvia; Colitti, Michele; Montanaro, Carmen; Aprea, Giuseppe; Scattolini, Silvia; D’Angelantonio, Daniela; Migliorati, Giacomo; Grazia Cerroni, Maria; Griglio, Bartolomeo; Berruti, Renza; Cravero, Mauro; Costa, Angela; Bianchi, Manila; Decastelli, Lucia; Romano, Angelo; Tramuta, Clara; Carraro, Elisabetta; Pignata, Cristina; Bonetta, Silvia; Richiardi, Lisa; Di Vittorio, Giuseppe; Mongelli, Onofrio; De Giglio, Osvalda; Apollonio, Francesca; Triggiano, Francesco; Teresa Montagna, Maria; Ungaro, Nicola; Palermo, Mario; Massimo Maida, Carmelo; Mazzucco, Walter; De Grazia, Simona; Giammanco, Giovanni; Purpari, Giuseppa; Ferrante, Margherita; Agodi, Antonella; Barchitta, Martina; Cala', Piergiuseppe; Carducci, Annalaura; Verani, Marco; Federigi, Ileana; Lauretani, Giulia; Muzio, Sara; Ramazzotti, Matteo; Antonelli, Alberto; Santoro, Giovanni; Federici, Ermanno; Petricciuolo, Maya; Barigelli, Sofia; Ruffier, Mauro; Borney, Francesca; Grange, Eric; Damasco, Florida; Russo, Francesca; Pitter, Gisella; Groppi, Vanessa; Rigoli, Franco; Zampini, Marco; Baldovin, Tatjana; Amoruso, Irene; Zago, Lorella; Stenico, Alberta; Demetz, Lea; Pizzo, Francesco; Schiavuzzi, Alessandra; Mengon, Elena; Cadonna, Maria; Postinghel, Mattia; Cutrupi, Francesca; Foladori, Paola; Manara, Serena; La Rosa, G.. - ELETTRONICO. - (2024), pp. 289-289. (Intervento presentato al convegno 8. National Congress of the Italian Society of Virology tenutosi a Bologna nel 7-9 luglio 2024).
SPREAD OF THE BA.2.86 LINEAGE OF SARS-CoV-2 IN ITALY BY ANALYSIS OF WASTEWATER
Paola Foladori;
2024-01-01
Abstract
Aim of the Study: Following the declaration of the end of the pandemic, surveillance efforts are limited due to a decline in swab testing and sequencing. This poses a significant challenge in tracking the emergence of new variants. The use of wastewater monitoring can provide a comprehensive approach to tracking the circulation and spread of different SARS-CoV-2 variants within a community or population. Among the most recent variants, Omicron BA.2.86 and its sublineages, including JN.1, have gained attention for their potential to evade the immune system. It was first detected in Denmark and Israel and has since become the prevalent variant, worldwide. This study aimed to comprehensively investigate the occurrence and dynamics of the BA.2.86* lineage in Italian wastewater from September 2023 to January 2024. Methods: A total of 507 wastewater samples were collected from 114 wastewater treatment plants across 16 regions and 2 autonomous provinces. These samples were subjected to viral concentration, nucleic acid extraction, and quantification of SARS-CoV-2 RNA using a newly designed digital RT-PCR targeting the BA.2.86* lineage. Additionally, a subset of samples underwent conventional RT-PCR and Sanger sequencing to confirm assay specificity and to identify specific sub-lineages, such as JN.1. Results: In total, 23% of samples tested positive for BA.2.86*, with viral concentrations ranging from 4.0 × 10^3 to 1.1×10^5 genome copies/L. The lineage was first detected in October 2023, with a minimum detection rate of 2%, and a rapid spread was observed over the following months, reaching a peak detection rate of 62% in January 2024. Subsequent sequencing confirmed the emergence and dominance of the JN.1 sub-lineage, characterised by the L455S mutation, highlighting its evolutionary advantage over the parental BA.2.86 variant. Conclusions: Environmental surveillance proved instrumental in elucidating the emergence and spread dynamics of BA.2.86* in Italy, providing critical insights into the evolution and spread of the variant. The RT-dPCR assay demonstrated its utility as a rapid and sensitive tool for variant detection in wastewater. These findings highlight the importance of sustained wastewater surveillance as a complementary approach to clinical surveillance, particularly in monitoring variant dynamics during periods of low virus circulation. Effective and timely surveillance efforts are essential for informing evidence-based public health interventions and mitigating the impact of emerging SARS-CoV-2 variants on public health. Acknowledgements: We wish to thank Dr. Paola Stefanelli (Istituto Superiore di Sanità, Department of Infectious Diseases) for sharing clinical omicron samples used as controls for specificity. This research was supported by EU funding within the NextGeneration EU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (Project no. PE00000007, PE13 INF-ACT).I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione
