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Volume 26, Number 8—August 2020
Dispatch

SARS-CoV-2 Phylogenetic Analysis, Lazio Region, Italy, February–March 2020

Barbara Bartolini, Martina Rueca, Cesare Ernesto Maria Gruber, Francesco Messina, Fabrizio Carletti, Emanuela Giombini, Eleonora Lalle, Licia Bordi, Giulia Matusali, Francesca Colavita, Concetta Castilletti, Francesco Vairo, Giuseppe Ippolito, Maria Rosaria Capobianchi, and Antonino Di CaroComments to Author 
Author affiliations: National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy

Main Article

Figure

Phylogenetic analysis of 150 severe acute respiratory syndrome coronavirus 2 representative genome sequences, including genomes collected in Italy (blue) and sequences identified for this study at the National Institute for Infectious Diseases (red). Available genomes were retrieved from GISAID (https://www.gisaid.org) on April 10, 2020; we discarded sequences with low coverage depth (low amount of read sequenced) or low coverage length (not complete genome sequences). Representative sequences f

Figure. Phylogenetic analysis of 150 severe acute respiratory syndrome coronavirus 2 representative genome sequences, including genomes collected in Italy (blue) and sequences identified for this study at the National Institute for Infectious Diseases (red). Available genomes were retrieved from GISAID (https://www.gisaid.org) on April 10, 2020; we discarded sequences with low coverage depth (low amount of read sequenced) or low coverage length (not complete genome sequences). Representative sequences from every B lineage (A. Rambaut et al., unpub. data, https://doi.org/10.1101/2020.04.17.046086v1), together with all genome sequences collected in Italy so far, were selected for further analysis. Multiple sequence alignment was obtained with MAFFT version 7.271 (https://mafft.cbrc.jp/alignment/software). Phylogenetic analysis was performed with IQ-TREE (http://www.iqtree.org): transition model with empirical base frequencies and invariable sites was selected with ModelFinder, and the best tree was found performing 1,000 bootstrap ultrafast replicates. Bootstrap values of >80% are reported on each branch. Lineages according to the description by Rambaut et al. are marked to the right of the tree. Scale bar represents number of substitutions per site.

Main Article

Page created: May 20, 2020
Page updated: July 18, 2020
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