Analysis of Genomic Characteristics of SARS-CoV-2 in Italy, 29 January to 27 March 2020.

Alessandra Lo Presti,Stefano Palomba,Giovanni Rezza,Florigio Lista,Riccardo De Santis,Francesco Giordani,Concetta Fabiani,Giuseppina Di Mario,Marzia Facchini,Laura Calzoletti,Filippo Molinari,Antonella Fortunato,Anna Anselmo,Paola Stefanelli,Angela Di Martino,Silvia Fillo,Stefano Fiore,Giovanni Faggioni,Vanessa Vera Fain,Giancarlo Petralito

doi:10.3390/v14030472

Abstract

We performed next-generation sequencing (NGS), phylogenetic analysis, gene flows, and N- and O-glycosylation prediction on SARS-CoV-2 genomes collected from lab-confirmed cases from different Italian regions. To this end, a total of 111 SARS-CoV-2 genomes collected in Italy between 29 January and 27 March 2020 were investigated. The majority of the genomes belonged to lineage B.1, with some descendant lineages. The gene flow analysis showed that the spread occurred mainly from the north to the center and to the south of Italy, as confirmed by epidemiological data. The mean evolutionary rate estimated here was 8.731 × 10−4 (95% highest posterior density, HPD intervals 5.809 × 10−4 to 1.19 × 10−3), in line with values reported by other authors. The dated phylogeny suggested that SARS-CoV-2 lineage B.1 probably entered Italy between the end of January and early February 2020. Continuous molecular surveillance is needed to trace virus circulation and evolution.

Highlights

Human coronaviruses (CoV) are enveloped positive-stranded RNA viruses belonging to the order Nidovirales, mostly responsible for upper respiratory and digestive tract infections [1].An outbreak of a febrile respiratory illness due to the newly discovered coronavirus (officially named by the World Health Organization as SARS-CoV-2 (COVID-19)) occurred in mid-December 2019, in the city of Wuhan, Hubei province (China)
The genomes comprised in lineage B.1 are divided in several clusters (Table 1): two genomes located in the main clade
These results are in agreement with those of other authors [6,33,34] and with data showing lineage B.1 most commonly spreading in the UK, USA, and to a lesser extent in Turkey, France, and Canada [16]

Summary

Introduction

Human coronaviruses (CoV) are enveloped positive-stranded RNA viruses belonging to the order Nidovirales, mostly responsible for upper respiratory and digestive tract infections [1]. An outbreak of a febrile respiratory illness due to the newly discovered coronavirus (officially named by the World Health Organization as SARS-CoV-2 (COVID-19)) occurred in mid-December 2019, in the city of Wuhan, Hubei province (China). The virus spread across most countries on all continents, causing a pandemic event [2–4]. The first patients with confirmed COVID-19 diagnosed in Italy were two Chinese tourists hospitalized in Rome [5]. A case was identified on 20 February 2020 in Lombardy Region (Codogno), Northern Italy [6]. The virus spread through the country very rapidly, causing the first epidemic wave, which was characterized by a high number of cases and deaths [7]

Objectives

Methods

Results

Conclusion