SARS-CoV-2 RNA was extracted using the Kit QIAsymphony DSP Virus/Pathogen Midi kit on the QIAsymphony automated platform (QIAGEN, Hilden, Germany) (n = 11), the NucleoMag 96 Virus (Macherey–Nagel, Dueren, Germany) on automated KingFisher ml Magnetic Particle Processors (Thermo Fisher Scientific, Waltham, MA, USA) (n = 44) and manually with QIAamp Viral RNA Mini Kit (QIAGEN, Hilden, Germany) (n = 137). Full genome sequences were obtained with different protocols, by amplifying 26 fragments as previously described (n = 137)10 (link) or by Ion AmpliSeq SARS-CoV-2 Research Panel (Thermo Fisher Scientific, Waltham, Massachusetts, USA) (n = 11) or by CleanPlex SARS-CoV-2 Panel (Paragon Genomics Inc, Hayward, CA, USA) (n = 44). Sequencing was performed on Illumina Miseq platform for all samples except for 11 that were sequenced with Ion GeneStudioS5 System instrument. The results were mapped and aligned to the reference genome obtained from GISAID (https://www.gisaid.org/, accession ID: EPI_ISL_406800) using Geneious Prime software v. 9.1.5 (Biomatters, Auckland, New Zealand) (http://www.geneious.com) or Torrent Suite v. 5.10.1 (Euformatics Oy, Espoo, Finland) or BWA-mem and rescued using Samtools alignment/Map (Hinxton, UK) (v. 1.9).
Lai A., Bergna A., Toppo S., Morganti M., Menzo S., Ghisetti V., Bruzzone B., Codeluppi M., Fiore V., Rullo E.V., Antonelli G., Sarmati L., Brindicci G., Callegaro A., Sagnelli C., Francisci D., Vicenti I., Miola A., Tonon G., Cirillo D., Menozzi I., Caucci S., Cerutti F., Orsi A., Schiavo R., Babudieri S., Nunnari G., Mastroianni C.M., Andreoni M., Monno L., Guarneri D., Coppola N., Crisanti A., Galli M, & Zehender G. (2022). Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. Scientific Reports, 12, 5736.
Other organizations :
Luigi Sacco Hospital, University of Milan, University of Padua, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Marche Polytechnic University, Ospedale Amedeo di Savoia, Ospedale Policlinico San Martino, Guglielmo da Saliceto Hospital, University of Sassari, University of Messina, Policlinico Umberto I, Sapienza University of Rome, University of Rome Tor Vergata, University of Bari Aldo Moro, Ospedale Papa Giovanni XXIII, University of Campania "Luigi Vanvitelli", University of Perugia, University of Siena, IRCCS Ospedale San Raffaele, University of Genoa, Foundation Jewish Contemporary Documentation Center, Fondazione Edmund Mach, University of Turin, I.R.C.C.S. Oasi Maria SS
Bioinformatics tools: Geneious Prime, Torrent Suite, BWA-mem and Samtools
controls
Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned
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