{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T08:53:14Z","timestamp":1790671994335,"version":"4.1.0"},"reference-count":41,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2019,9,3]],"date-time":"2019-09-03T00:00:00Z","timestamp":1567468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Progetto Bandiera Nanomax","award":["G42I12000180005"],"award-info":[{"award-number":["G42I12000180005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Lineage 2 West Nile virus (WNV) caused a vast epidemic in Europe in 2018, with the highest incidence being recorded in Italy. To reconstruct the evolutionary dynamics and epidemiological history of the virus in Italy, 53 envelope gene and 26 complete genome sequences obtained from human and animal samples were characterised by means of next-generation sequencing. Phylogenetic analysis revealed two Italian strains originating between 2010 and 2012: clade A, which apparently became extinct in 2013\u20132014, and clade B, which was responsible for the 2018 epidemic. The mean genetic distances in clade B increased over time and with the distance between sampling locations. Bayesian birth-death and coalescent skyline plots of the clade B showed that the effective number of infections and the effective reproduction number (Re) increased between 2015 and 2018. Our data suggest that WNV-2 entered Italy in 2011 as a result of one or a few penetration events. Clade B differentiated mainly as a result of genetic drift and purifying selection, leading to the appearance of multiple locally circulating sub-clades for different times. Phylodynamic analysis showed a current expansion of the infection among reservoir birds and\/or vectors.<\/jats:p>","DOI":"10.3390\/v11090814","type":"journal-article","created":{"date-parts":[[2019,9,3]],"date-time":"2019-09-03T03:06:14Z","timestamp":1567479974000},"page":"814","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["Evolutionary Dynamics of the Lineage 2 West Nile Virus That Caused the Largest European Epidemic: Italy 2011\u20132018"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2724-5871","authenticated-orcid":false,"given":"Carla","family":"Veo","sequence":"first","affiliation":[{"name":"Department of Biomedical and Clinical Sciences \u201cL.Sacco\u201d, University of Milan, 20157 Milano, Italy"},{"name":"CRC-Coordinated Research Center \u201cEpiSoMI\u201d, University of Milan, 20157 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carla","family":"della Ventura","sequence":"additional","affiliation":[{"name":"Department of Biomedical and Clinical Sciences \u201cL.Sacco\u201d, University of Milan, 20157 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8497-9708","authenticated-orcid":false,"given":"Ana","family":"Moreno","sequence":"additional","affiliation":[{"name":"Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna (IZSLER), 25124 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Rovida","sequence":"additional","affiliation":[{"name":"Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Percivalle","sequence":"additional","affiliation":[{"name":"Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabrina","family":"Canziani","sequence":"additional","affiliation":[{"name":"Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna (IZSLER), 25124 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debora","family":"Torri","sequence":"additional","affiliation":[{"name":"Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna (IZSLER), 25124 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7489-2556","authenticated-orcid":false,"given":"Mattia","family":"Calzolari","sequence":"additional","affiliation":[{"name":"Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna (IZSLER), 25124 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fausto","family":"Baldanti","sequence":"additional","affiliation":[{"name":"Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Massimo","family":"Galli","sequence":"additional","affiliation":[{"name":"Department of Biomedical and Clinical Sciences \u201cL.Sacco\u201d, University of Milan, 20157 Milano, Italy"},{"name":"CRC-Coordinated Research Center \u201cEpiSoMI\u201d, University of Milan, 20157 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gianguglielmo","family":"Zehender","sequence":"additional","affiliation":[{"name":"Department of Biomedical and Clinical Sciences \u201cL.Sacco\u201d, University of Milan, 20157 Milano, Italy"},{"name":"CRC-Coordinated Research Center \u201cEpiSoMI\u201d, University of Milan, 20157 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,9,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"30340","DOI":"10.2807\/1560-7917.ES.2016.21.37.30340","article-title":"West Nile virus transmission: Results from the integrated surveillance system in Italy, 2008 to 2015","volume":"21","author":"Rizzo","year":"2016","journal-title":"Euro. Surveill."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1006\/viro.2002.1449","article-title":"Complete genome sequences and phylogenetic analysis of West Nile virus strains isolated from the United States, Europe, and the Middle East","volume":"298","author":"Lanciotti","year":"2002","journal-title":"Virology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.vetmic.2013.03.005","article-title":"Explosive spread of a neuroinvasive lineage 2 West Nile virus in Central Europe, 2008\/2009","volume":"165","author":"Bakonyi","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"618","DOI":"10.3201\/eid1204.051379","article-title":"Lineage 1 and 2 strains of encephalitic West Nile virus, central Europe","volume":"12","author":"Bakonyi","year":"2006","journal-title":"Emerg. Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.3201\/eid1710.110525","article-title":"Outbreak of West Nile virus infection in Greece, 2010","volume":"17","author":"Danis","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"ref_6","first-page":"29","article-title":"Genotyping of West Nile fever virus strains circulating in southern Russia as an epidemiological investigation method: Principles and results","volume":"2","author":"Platonov","year":"2011","journal-title":"Zh. Mikrobiol. Epidemiol. Immunobiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.3201\/eid0812.020234","article-title":"West Nile virus epidemic in horses, Tuscany region, Italy","volume":"8","author":"Autorino","year":"2002","journal-title":"Emerg. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1111\/j.1863-2378.2009.01303.x","article-title":"West Nile virus transmission in 2008 in north-eastern Italy","volume":"57","author":"Calistri","year":"2010","journal-title":"Zoonoses Public Health"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"19002","DOI":"10.2807\/ese.13.41.19002-en","article-title":"First human case of West Nile virus neuroinvasive infection in Italy, September 2008\u2014Case report","volume":"13","author":"Rossini","year":"2008","journal-title":"Euro. Surveill."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"19353","DOI":"10.2807\/ese.14.40.19353-en","article-title":"West Nile virus transmission with human cases in Italy, August\u2013September 2009","volume":"14","author":"Rizzo","year":"2009","journal-title":"Euro. Surveill."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"E545","DOI":"10.1111\/1469-0691.12018","article-title":"Circulation of West Nile virus lineage 1 and 2 during an outbreak in Italy","volume":"18","author":"Magurano","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1800427","DOI":"10.2807\/1560-7917.ES.2018.23.32.1800427","article-title":"An early start of West Nile virus seasonal transmission: The added value of One Heath surveillance in detecting early circulation and triggering timely response in Italy, June to July 2018","volume":"23","author":"Riccardo","year":"2018","journal-title":"Euro. Surveill."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Djikeng, A., Halpin, R., Kuzmickas, R., Depasse, J., Feldblyum, J., Sengamalay, N., Afonso, C., Zhang, X., Anderson, N.G., and Ghedin, E. (2008). Viral genome sequencing by random priming methods. BMC Genomics, 9.","DOI":"10.1186\/1471-2164-9-5"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"vev003","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: Detection and analysis of recombination patterns in virus genomes","volume":"1","author":"Martin","year":"2015","journal-title":"Virus. Evol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1093\/bioinformatics\/bth490","article-title":"RDP2: Recombination detection and analysis from sequence alignments","volume":"21","author":"Martin","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"13757","DOI":"10.1073\/pnas.241370698","article-title":"Evaluation of methods for detecting recombination from DNA sequences: Computer simulations","volume":"98","author":"Posada","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/bioinformatics\/16.7.573","article-title":"Sister-scanning: A Monte Carlo procedure for assessing signals in recombinant sequences","volume":"16","author":"Gibbs","year":"2000","journal-title":"Bioinformatics"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1006\/viro.1999.0056","article-title":"Possible emergence of new geminiviruses by frequent recombination","volume":"265","author":"Padidam","year":"1999","journal-title":"Virology"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1534\/genetics.106.068874","article-title":"An exact nonparametric method for inferring mosaic structure in sequence triplets","volume":"176","author":"Boni","year":"2007","journal-title":"Genetics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1007\/BF00182389","article-title":"Analyzing the mosaic structure of genes","volume":"34","author":"Smith","year":"1992","journal-title":"Journal of molecular evolution"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"Drummond","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1093\/molbev\/msn083","article-title":"jModelTest: Phylogenetic model averaging","volume":"25","author":"Posada","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1093\/molbev\/mss084","article-title":"Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty","volume":"29","author":"Baele","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"Drummond","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments","volume":"21","author":"Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Lemey, P., Rambaut, A., Drummond, A.J., and Suchard, M.A. (2009). Bayesian phylogeography finds its roots. PLoS. Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000520"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1093\/molbev\/msp274","article-title":"Bayesian inference of species trees from multilocus data","volume":"27","author":"Heled","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1073\/pnas.1207965110","article-title":"Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)","volume":"110","author":"Stadler","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Zehender, G., Veo, C., Ebranati, E., Carta, V., Rovida, F., Percivalle, E., Moreno, A., Lelli, D., Calzolari, M., and Lavazza, A. (2017). Reconstructing the recent West Nile virus lineage 2 epidemic in Europe and Italy using discrete and continuous phylogeography. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0179679"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"20172","DOI":"10.2807\/ese.17.20.20172-en","article-title":"Epidemiological surveillance of West Nile neuroinvasive diseases in Italy, 2008 to 2011","volume":"17","author":"Rizzo","year":"2012","journal-title":"Euro. Surveill."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Calzolari, M., Pautasso, A., Montarsi, F., Albieri, A., Bellini, R., Bonilauri, P., Defilippo, F., Lelli, D., Moreno, A., and Chiari, M. (2015). West Nile Virus Surveillance in 2013 via Mosquito Screening in Northern Italy and the Influence of Weather on Virus Circulation. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0140915"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/j.vetmic.2012.02.018","article-title":"Evidence of West Nile virus lineage 2 circulation in Northern Italy","volume":"158","author":"Savini","year":"2012","journal-title":"Vet. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"20002","DOI":"10.2807\/ese.16.43.20002-en","article-title":"Human case of autochthonous West Nile virus lineage 2 infection in Italy, September 2011","volume":"16","author":"Bagnarelli","year":"2011","journal-title":"Euro. Surveill."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.virol.2011.06.006","article-title":"Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999\u20132008","volume":"417","author":"Armstrong","year":"2011","journal-title":"Virology"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1186\/1743-422X-6-165","article-title":"Recombination in West Nile Virus: Minimal contribution to genomic diversity","volume":"6","author":"Pickett","year":"2009","journal-title":"Virol J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/j.chom.2016.03.002","article-title":"Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching","volume":"19","author":"Grubaugh","year":"2016","journal-title":"Cell Host Microbe."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.rvsc.2011.01.008","article-title":"2009 West Nile disease epidemic in Italy: First evidence of overwintering in Western Europe?","volume":"91","author":"Monaco","year":"2011","journal-title":"Res. Vet. Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1186\/s13071-017-2399-7","article-title":"West Nile virus in overwintering mosquitoes, central Europe","volume":"10","author":"Rudolf","year":"2017","journal-title":"Parasit. Vectors"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"6088","DOI":"10.1038\/s41598-018-24133-4","article-title":"Overwintering of West Nile virus in a bird community with a communal crow roost","volume":"8","author":"Barker","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1842","DOI":"10.3201\/eid1112.050997","article-title":"Host range and emerging and reemerging pathogens","volume":"11","author":"Woolhouse","year":"2005","journal-title":"Emerg. Infect. Dis."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1946","DOI":"10.1016\/S0140-6736(12)61151-9","article-title":"Drivers, dynamics, and control of emerging vector-borne zoonotic diseases","volume":"380","author":"Kilpatrick","year":"2012","journal-title":"Lancet"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/11\/9\/814\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:16:14Z","timestamp":1760188574000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/11\/9\/814"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,3]]},"references-count":41,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2019,9]]}},"alternative-id":["v11090814"],"URL":"https:\/\/doi.org\/10.3390\/v11090814","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9,3]]}}}