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
- Creators
- La Rosa G.
- Brandtner D.
- Bonanno Ferraro G.
- Veneri C.
- Mancini P.
- Iaconelli M.
- Lucentini L.
- Del Giudice C.
- Orlandi L.
- Suffredini E.
- Torlontano P.
- Aprea G.
- Scattolini S.
- Acciari V. A.
- La Bianca M.
- Cifarelli R. A.
- Palma A.
- Lauria G.
- La Vecchia G.
- Malacaria E.
- Folino G.
- Calabria A.
- Bulotta G.
- D'Argenzio A.
- Cossentino L.
- Fusco G.
- Viscardi M.
- Tosco A.
- Porta A.
- Voli A.
- Pennino F.
- Lombardi A.
- Angelini P.
- Nasci D.
- Alborali G.
- Formenti N.
- Guarneri F.
- Fontani N.
- Palumbo F.
- Gentili L.
- Mariuz M.
- Trani G.
- Pariani A.
- De Lellis L.
- Ancona C.
- Barca A.
- Serio F.
- Giorgi D. A.
- Ferrante I.
- Monfrinotti M.
- Scicluna M. T.
- Cersini A.
- Pietrella G.
- Ottaviano C.
- Arizzi M.
- Nicosia E.
- Grasselli E.
- Izzotti A.
- Tomesani I.
- Bellisomi M.
- Rosatto S.
- Ammoni E.
- Cereda D.
- Bertasi B.
- Oliva D.
- Castiglioni S.
- Schiarea S.
- Binda S.
- Primache V.
- Pellegrinelli L.
- Cocuzza C.
- Franzetti A.
- Bolognini L.
- Filippetti F.
- Paniccia' M.
- Briscolini S.
- Magi S.
- Grucci A.
- Colitti M.
- Ciccaglione A.
- Montanaro C.
- Griglio B.
- Costa A.
- Decastelli L.
- Bianchi A. R. M.
- Carraro E.
- Pignata C.
- Richiardi L.
- Bonetta S.
- Albano N.
- Di Vittorio G.
- Mongelli O.
- Apollonio F.
- Triggiano F.
- De Giglio O.
- Montagna M. T.
- Palermo M.
- Maida C. M.
- 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.
- Ramazzotti M.
- Rossolini G. M.
- Santoro G.
- Federici E.
- Petricciuolo M.
- Carnevali A.
- Ruffier M.
- Masieri L.
- Grange E.
- Damasco F.
- Russo F.
- Pitter G.
- Groppi V.
- Rigoli F.
- Zampini M.
- Baldovin T.
- Amoruso I.
- Cadonna M.
- Postinghel M.
- Foladori P.
- Cutrupi F.
- Zago L.
- Stenico A.
- Lea D.
- Anna-Maria P.
- Others:
- La Rosa, G.
- Brandtner, D.
- Bonanno Ferraro, G.
- Veneri, C.
- Mancini, P.
- Iaconelli, M.
- Lucentini, L.
- Del Giudice, C.
- Orlandi, L.
- Suffredini, E.
- Torlontano, P.
- Aprea, G.
- Scattolini, S.
- Acciari, V. A.
- La Bianca, M.
- Cifarelli, R. A.
- Palma, A.
- Lauria, G.
- La Vecchia, G.
- Malacaria, E.
- Folino, G.
- Calabria, A.
- Bulotta, G.
- D'Argenzio, A.
- Cossentino, L.
- Fusco, G.
- Viscardi, M.
- Tosco, A.
- Porta, A.
- Voli, A.
- Pennino, F.
- Lombardi, A.
- Angelini, P.
- Nasci, D.
- Alborali, G.
- Formenti, N.
- Guarneri, F.
- Fontani, N.
- Palumbo, F.
- Gentili, L.
- Mariuz, M.
- Trani, G.
- Pariani, A.
- De Lellis, L.
- Ancona, C.
- Barca, A.
- Serio, F.
- Giorgi, D. A.
- Ferrante, I.
- Monfrinotti, M.
- Scicluna, M. T.
- Cersini, A.
- Pietrella, G.
- Ottaviano, C.
- Arizzi, M.
- Nicosia, E.
- Grasselli, E.
- Izzotti, A.
- Tomesani, I.
- Bellisomi, M.
- Rosatto, S.
- Ammoni, E.
- Cereda, D.
- Bertasi, B.
- Oliva, D.
- Castiglioni, S.
- Schiarea, S.
- Binda, S.
- Primache, V.
- Pellegrinelli, L.
- Cocuzza, C.
- Franzetti, A.
- Bolognini, L.
- Filippetti, F.
- Paniccia', M.
- Briscolini, S.
- Magi, S.
- Grucci, A.
- Colitti, M.
- Ciccaglione, A.
- Montanaro, C.
- Griglio, B.
- Costa, A.
- Decastelli, L.
- Bianchi, A. R. M.
- Carraro, E.
- Pignata, C.
- Richiardi, L.
- Bonetta, S.
- Albano, N.
- Di Vittorio, G.
- Mongelli, O.
- Apollonio, F.
- Triggiano, F.
- De Giglio, O.
- Montagna, M. T.
- Palermo, M.
- Maida, C. M.
- 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.
- Ramazzotti, M.
- Rossolini, G. M.
- Santoro, G.
- Federici, E.
- Petricciuolo, M.
- Carnevali, A.
- Ruffier, M.
- Masieri, L.
- Grange, E.
- Damasco, F.
- Russo, F.
- Pitter, G.
- Groppi, V.
- Rigoli, F.
- Zampini, M.
- Baldovin, T.
- Amoruso, I.
- Cadonna, M.
- Postinghel, M.
- Foladori, P.
- Cutrupi, F.
- Zago, L.
- Stenico, A.
- Lea, D.
- Anna-Maria, P.
Description
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.
Additional details
- URL
- https://hdl.handle.net/11567/1156588
- URN
- urn:oai:iris.unige.it:11567/1156588
- Origin repository
- UNIGE