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.
Subject
Virology,Infectious Diseases
Reference52 articles.
1. Coronaviruses: An overview of their replication and pathogenesis;Fehr;Methods Mol. Biol.,2015
2. A new coronavirus associated with human respiratory disease in China
3. Statement on the Second Meeting of the International Health Regulations (2005) Emergency Committee Regarding the Outbreak of Novel Coronavirus (2019-nCoV). 30 January 2020https://www.who.int/news/item/30-01-2020-statement-on-the-second-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak-of-novel-coronavirus-(2019-ncov)
4. WHO Director—General’s Opening Remarks at the Media Briefing on COVID-19. 11 March 2020https://www.who.int/director-general/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020
5. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy
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