The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.
Molecular tracing of SARS-CoV-2 in Italy in the first three months of the epidemic / Lai, A.; Bergna, A.; Caucci, S.; Clementi, N.; Vicenti, I.; Dragoni, F.; Cattelan, A. M.; Menzo, S.; Pan, A.; Callegaro, A.; Tagliabracci, A.; Caruso, A.; Caccuri, F.; Ronchiadin, S.; Balotta, C.; Zazzi, M.; Vaccher, E.; Clementi, M.; Galli, M.; Zehender, G.; Alessandrini, F; Andreoni, M; Antonelli, G; Babudieri, S; Bagnarelli, P; Bonora, S; Bruzzone, B; Brindicci, G; Carrer, P; Ceccherini, F; Codeluppi, M; Coluccello, A; Coppola, N; Cusi, Mg; C Della Ventura, ; DI SANTE, Laura; S Di Giambenedetto, ; G Di Perri, ; Fiore, V; Fiorentini, S; Francisci, D; Gandolfo, C; Gervasoni, C; Ghisetti, V; Greco, R; Guarona, G; Iannetta, M; L Li Puma, ; Malagnino, V.; Mancuso, G; Mastroianni, C; Menozzi, I; Milano, E; Miola, A; Morganti, M; Monno, L; Noberasco, G; Nunnari, G; Onofri, V; Orsi, A; Pierfranceschi, Mg; Pongolini, S; Ripamonti, D; Rubino, S; Ruggerone, L; Russignaga, D; Sagnelli, C; Sanguinetti, M; Sarmati, L; Sasset, L; Scaltriti, E; Schiavo, R; Schioppa, M; Testa, S; Turchi, C; Turriziani, O; E Venanzi Rollo, ; Zanussi, S; Zoncada, A. - In: VIRUSES. - ISSN 1999-4915. - 12:8(2020), p. 798. [10.3390/v12080798]
Molecular tracing of SARS-CoV-2 in Italy in the first three months of the epidemic
Caucci S.;Menzo S.;Tagliabracci A.;F Alessandrini;P Bagnarelli;Laura Di Sante;V Onofri;C Turchi;
2020-01-01
Abstract
The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
