key: cord-0958660-3xusxrij
authors: Licastro, Danilo; Rajasekharan, Sreejith; Dal Monego, Simeone; Segat, Ludovica; D’Agaro, Pierlanfranco; Marcello, Alessandro
title: Isolation and Full-Length Genome Characterization of SARS-CoV-2 from COVID-19 Cases in Northern Italy
date: 2020-05-18
journal: J Virol
DOI: 10.1128/jvi.00543-20
sha: 15b5168bb07f6dcb08f66bd05f0c89629085e3c6
doc_id: 958660
cord_uid: 3xusxrij

In December 2019, the novel coronavirus Severe Acquired Respiratory Syndrome SARS-CoV-2 emerged in the city of Wuhan in the Hubei province, People's Republic of China, as the etiologic agent of coronavirus disease 2019 (COVID-19), which has hence spread worldwide causing a global pandemic (1-3).….

available at 03-16-2020 (6) . Bootstrap support values were calculated from 500 pseudoreplicate trees of the whole data set (Fig. 2) .

Despite a high burden of COVID-19 in Italy, very little information is available to date from full-length high-quality sequences. The first sequences deposited in GISAID (EPI_ISL_410545 and EPI_ISL_410546) were collected in Rome from a Chinese tourist from Hubei province who got infected before visiting Italy, and another one (EPI_ ISL_412974) was from a test-positive Italian citizen returning from China. Only two sequences were reported from the Lombardy cluster (EPI_ISL_412973 and EPI_ ISL_413489). In this report four additional sequences from cases epidemiologically linked to northern Italy have been examined. All infected individuals were connected to the city of Udine; S1 and S5 were from the same cluster of closely related cases, while S9 got infected probably in Lombardy and S8 visited Udine from a neighboring city (Table 1) . Sequence analysis showed a good coverage along the SARS-CoV-2 genome for all four isolates (Fig. 1) . Based on the marker variant S D614G, all four sequences grouped in the Bavarian rooted subclade G, which is dominant in Europe, including the sequence from Lombardy, but distinct from the three sequences mentioned above originating directly from China (7) . Intriguingly, the new isolates were more closely related to EPI_ISL_412973, while EPI_ISL_413489 was more distant (Fig. 2) . No evidence could be found for the putative 382-nucleotide (nt) deletion in ORF8 detected in Singapore, which has been proposed to indicate an attenuated phenotype (8) .

These findings strongly urge the need for comprehensive studies that combine genomic data with epidemiological data and clinical records of symptoms from patients with COVID-19. Data availability. The longer sequences were named hCoV-19/Italy/FVG/ICGEB_S1, _S5, _S8, and _S9 and were deposited in GISAID (https://www.gisaid.org/) with accession numbers EPI_ISL_417418, EPI_ISL_417419, EPI_ISL_417421, and EPI_ISL_417423, respectively (9) .

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Work was financed through intramural funds of the ICGEB, University of Trieste, ASUGI and the ARGO, MIUR-MISE-Region FVG Agreement Protocol signed by MIUR-MISE-Region FVG and managed by Area Science Park.We thank Elena Samar, Fabia Petronio, and Ilaria Sandron for their excellent technical assistance.The