key: cord-0873484-e5nxkvo7 authors: Giovanetti, Marta; Benvenuto, Domenico; Angeletti, Silvia; Ciccozzi, Massimo title: The first two cases of 2019‐nCoV in Italy: Where they come from? date: 2020-02-12 journal: J Med Virol DOI: 10.1002/jmv.25699 sha: 0345bb885e850845164b45ae6a2cfefe83335b51 doc_id: 873484 cord_uid: e5nxkvo7 A novel Coronavirus, 2019‐nCoV, has been identified as the causal pathogen of an ongoing epidemic, with the first cases reported in Wuhan, China, last December 2019, and has since spread to other countries worldwide, included Europe and very recently Italy. In this short report, phylogenetic reconstruction was used to better understand the transmission dynamics of the virus from its first introduction in China focusing on the more recent evidence of infection in a couple of Chinese tourists arrived in Italy on 23rd January 2020 and labeled as Coronavirus Italian cases. A maximum clade credibility tree has been built using a dataset of 54 genome sequences of 2019‐nCoV plus two closely related bat strains (SARS‐like CoV) available in GenBank. Bayesian time‐scaled phylogenetic analysis was implemented in BEAST 1.10.4. The Bayesian phylogenetic reconstruction showed that 2019‐2020 nCoV firstly introduced in Wuhan on 25 November 2019, started epidemic transmission reaching many countries worldwide, including Europe and Italy where the two strains isolated dated back 19 January 2020, the same that the Chinese tourists arrived in Italy. Strains isolated outside China were intermixed with strains isolated in China as evidence of likely imported cases in Rome, Italy, and Europe, as well. In conclusion, this report suggests that further spread of 2019‐nCoV epidemic was supported by human mobility and that quarantine of suspected or diagnosed cases is useful to prevent further transmission. Viral genome phylogenetic analysis represents a useful tool for the evaluation of transmission dynamics and preventive action. symptoms of coronavirus diseases, the couple has been admitted to Rome's Spallanzani Hospital, which is specialized in infectious diseases. In Italy, a state of emergency has been declared as a consequence of these two confirmed cases of infection that have been labeled as the first cases of Coronavirus transmission described in Italy. In this report, phylogenetic and evolutionary analysis has been applied to characterize the 2019-nCoV virus identified in Italy and better understand the transmission dynamics of the two cases diagnosed in Rome. The dataset used for phylogenetic analysis included (n = 54) genomes sequences from the current 2019-nCoV epidemic plus (n = 2) closely related bat strains (SARS-like CoV) retrieved from NCBI (http:// www.ncbi.nlm.nih.gov/genbank/) and GISAID (https://www.gisaid. org/) databases. Sequences were aligned using MAFFT software 5 and manually edited by BioEdit program v7.0.5. 6 By IQ-TREE 1.6.8 software the maximum likelihood (ML) phylogeny was reconstructed under the HKY nucleotide substitution model with 4 gamma categories (HKY+G4) which were inferred in jModelTest (https://github.com/ddarriba/jmodeltest2) as the best fitting model. 7 To investigate the temporal signal, from the ML tree, we regressed root-to-tip genetic distances against sample collection dates using TempEst v 1.5.1 (http://tree.bio.ed.ac.uk). 8 A novel coronavirus from patients with pneumonia in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health-the latest 2019 novel coronavirus outbreak in Wuhan, China The 2019-new coronavirus epidemic: evidence for virus evolution MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT jModelTest 2: more models, new heuristics and parallel computing Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Accurate model selection of relaxed molecular clocks in bayesian phylogenetics Relaxed phylogenetics and dating with confidence Posterior summarization in Bayesian phylogenetics using Tracer 1.7 Emerging understandings of 2019-nCoV The first two cases of 2019-nCoV in Italy: Where they come from