Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020

Lai, A.; Bergna, A.; Toppo, S.; Morganti, M.; Menzo, S.; Ghisetti, V.; Bruzzone, B.; Codeluppi, M.; Fiore, V.; Rullo, E.V.; Antonelli, G.; Sarmati, L.; Brindicci, G.; Callegaro, A.; Sagnelli, C.; Francisci, D.; Vicenti, I.; Miola, A.; Tonon, G.; Cirillo, D.; Menozzi, I.; Caucci, S.; Cerutti, F.; Orsi, A.; Schiavo, R.; Babudieri, S.; Nunnari, G.; Mastroianni, C.M.; Andreoni, M.; Monno, L.; Guarneri, D.; Coppola, N.; Crisanti, A.; Galli, M.; Zehender, G.; Balotta, C.; Ventura, C.; Schiuma, M.; Lavezzo, E.; Fontana, P.; Bianco, L.; Bertolotti, L.; Manuto, L.; Grazioli, M.; Bianca, F.; Del Vecchio, C.; Franchin, E.; Onelia, F.; Spitaleri, A.; Saluzzo, F.; Lorenzin, G.; Pongolini, S.; Scaltriti, E.; Soliani, L.; Bagnarelli, P.; Turchi, C.; Onofri, V.; Melchionda, F.; Tagliabracci, A.; Burdino, E.; Milia, M.G.; Caligiuri, P.; De Pace, V.; Ricucci, V.; Domnich, A.; Boccotti, S.; Cristina, L.M.; Cascio, G.L.; Rubino, S.; Lai, V.; Rocca, G.; Govoni, R.; Mancuso, G.; Campagna, R.; Mazzuti, L.; Oliveto, G.; Turriziani, O.; Campogiani, L.; Compagno, M.; Coppola, L.; Crea, A.M.A.; De Simone, G.; Di Lorenzo, A.; Ferrari, L.; Iannetta, M.; Malagnino, V.; Mulas, T.; Rossi, B.; Spalliera, I.; Tedde, S.; Teti, E.; Vitale, P.; Zordan, M.; Milano, E.; Lagioia, A.; Gallitelli, R.; Starace, M.; Minichini, C.; Di Fraia, A.; Schioppa, M.; Greco, R.; Gidari, A.; Zazzi, M.; Dragoni, F.; Puma, L.L.; Ronchiadin, S.; Ruggerone, L.; Russignaga, D.

doi:10.1038/s41598-022-09738-0

The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including < 80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.

Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020 / A. Lai, A. Bergna, S. Toppo, M. Morganti, S. Menzo, V. Ghisetti, B. Bruzzone, M. Codeluppi, V. Fiore, E.V. Rullo, G. Antonelli, L. Sarmati, G. Brindicci, A. Callegaro, C. Sagnelli, D. Francisci, I. Vicenti, A. Miola, G. Tonon, D. Cirillo, I. Menozzi, S. Caucci, F. Cerutti, A. Orsi, R. Schiavo, S. Babudieri, G. Nunnari, C.M. Mastroianni, M. Andreoni, L. Monno, D. Guarneri, N. Coppola, A. Crisanti, M. Galli, G. Zehender, C. Balotta, C. Ventura, M. Schiuma, E. Lavezzo, P. Fontana, L. Bianco, L. Bertolotti, L. Manuto, M. Grazioli, F. Bianca, C. Del Vecchio, E. Franchin, F. Onelia, A. Spitaleri, F. Saluzzo, G. Lorenzin, S. Pongolini, E. Scaltriti, L. Soliani, P. Bagnarelli, C. Turchi, V. Onofri, F. Melchionda, A. Tagliabracci, E. Burdino, M.G. Milia, P. Caligiuri, V. De Pace, V. Ricucci, A. Domnich, S. Boccotti, L.M. Cristina, G.L. Cascio, S. Rubino, V. Lai, G. Rocca, R. Govoni, G. Mancuso, R. Campagna, L. Mazzuti, G. Oliveto, O. Turriziani, L. Campogiani, M. Compagno, L. Coppola, A.M.A. Crea, G. De Simone, A. Di Lorenzo, L. Ferrari, M. Iannetta, V. Malagnino, T. Mulas, B. Rossi, I. Spalliera, S. Tedde, E. Teti, P. Vitale, M. Zordan, E. Milano, A. Lagioia, R. Gallitelli, M. Starace, C. Minichini, A. Di Fraia, M. Schioppa, R. Greco, A. Gidari, M. Zazzi, F. Dragoni, L.L. Puma, S. Ronchiadin, L. Ruggerone, D. Russignaga. - In: SCIENTIFIC REPORTS. - ISSN 2045-2322. - 12:1(2022 Dec), pp. 5736.1-5736.12. [10.1038/s41598-022-09738-0]

Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020

A. Lai^{Primo

Investigation};A. Bergna^{Secondo

Investigation};Toppo S.;Morganti M.;Menzo S.;Ghisetti V.;Bruzzone B.;Codeluppi M.;Fiore V.;Rullo E. V.;Antonelli G.;Sarmati L.;Brindicci G.;Callegaro A.;Sagnelli C.;Francisci D.;Vicenti I.;Miola A.;Tonon G.;Cirillo D.;Menozzi I.;Caucci S.;Cerutti F.;Orsi A.;Schiavo R.;Babudieri S.;Nunnari G.;Mastroianni C. M.;Andreoni M.;Monno L.;Guarneri D.;Coppola N.;Crisanti A.;M. Galli^{Conceptualization};G. Zehender^{Conceptualization};Balotta C.;Ventura C.;Schiuma M.;Lavezzo E.;Fontana P.;Bianco L.;Bertolotti L.;Manuto L.;Grazioli M.;Bianca F.;Del Vecchio C.;Franchin E.;Onelia F.;A. Spitaleri;Saluzzo F.;Lorenzin G.;Pongolini S.;Scaltriti E.;Soliani L.;Bagnarelli P.;Turchi C.;Onofri V.;Melchionda F.;Tagliabracci A.;Burdino E.;Milia M. G.;Caligiuri P.;De Pace V.;Ricucci V.;Domnich A.;Boccotti S.;Cristina L. M.;Cascio G. L.;Rubino S.;Lai V.;Rocca G.;Govoni R.;Mancuso G.;Campagna R.;Mazzuti L.;Oliveto G.;Turriziani O.;Campogiani L.;Compagno M.;Coppola L.;Crea A. M. A.;De Simone G.;Di Lorenzo A.;Ferrari L.;Iannetta M.;Malagnino V.;Mulas T.;Rossi B.;Spalliera I.;Tedde S.;Teti E.;Vitale P.;Zordan M.;Milano E.;Lagioia A.;Gallitelli R.;Starace M.;Minichini C.;Di Fraia A.;Schioppa M.;Greco R.;Gidari A.;Zazzi M.;Dragoni F.;Puma L. L.;Ronchiadin S.;Ruggerone L.;Russignaga D.

2022

Abstract

The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including < 80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.

Scheda breve

Scheda completa

Scheda completa (DC)

	Settori scientifico-disciplinari dell'articolo (sola visualizzazione)
	
				Settore MED/42 - Igiene Generale e Applicata
Settore MED/07 - Microbiologia e Microbiologia Clinica
Settore MED/17 - Malattie Infettive
			
	Data di pubblicazione
	
				dic-2022
			
	Data ahead of print o data di stampa
	
				6-apr-2022
			
	Rivista in ANCE
	
				SCIENTIFIC REPORTS
			
	DOI
	
				https://dx.doi.org/10.1038/s41598-022-09738-0
			
	Tipologia
	
				Article (author)
			
	Appare nelle tipologie:
	
				01 - Articolo su periodico

File in questo prodotto:

File	Dimensione	Formato
s41598-022-09738-0.pdf accesso aperto Tipologia: Publisher's version/PDF Dimensione 1.5 MB Formato Adobe PDF Visualizza/Apri	1.5 MB	Adobe PDF	Visualizza/Apri

Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/952683

Citazioni

5

6

6

IRIS Institutional Research Information System - AIR Archivio Istituzionale della Ricerca