title: Whole genome sequence analysis of the arctic-lineage strain responsible for distemper in Italian wolves and dogs through a fast and robust next generation sequencing protocol.
abstract: Dynamic surveillance and characterization of canine distemper virus (CDV) circulating strains are essential against possible vaccine breakthroughs events. This study describes the setup of a fast and robust next-generation sequencing (NGS) Ion PGM™ protocol that was used to obtain the complete genome sequence of a CDV isolate (CDV2784/2013). CDV2784/2013 is the prototype of CDV strains responsible for severe clinical distemper in dogs and wolves in Italy during 2013. CDV2784/2013 was isolated on cell culture and total RNA was used for NGS sample preparation. A total of 112.3 Mb of reads were assembled de novo using MIRA version 4.0rc4, which yielded a total number of 403 contigs with 12.1% coverage. The whole genome (15,690 bp) was recovered successfully and compared to those of existing CDV whole genomes. CDV2784/2013 was shown to have 92% nt identity with the Onderstepoort vaccine strain. This study describes for the first time a fast and robust Ion PGM™ platform-based whole genome amplification protocol for non-segmented negative stranded RNA viruses starting from total cell-purified RNA. Additionally, this is the first study reporting the whole genome analysis of an Arctic lineage strain that is known to circulate widely in Europe, Asia and USA.
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy.
authors.forename: Maurilia
authors.initials: M
authors.lastname: Marcacci
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Ancora
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy.
authors.forename: Iolanda
authors.initials: I
authors.lastname: Mangone
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy.
authors.forename: Liana
authors.initials: L
authors.lastname: Teodori
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy.
authors.forename: Daria
authors.initials: D
authors.lastname: Di Sabatino
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: De Massis
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy.
authors.forename: Cesare
authors.initials: C
authors.lastname: Camma'
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Savini
authors.affiliation: National Reference Centre for Urban Hygiene and Non-Epidemic Emergencies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise "G. Caporale", 64100 Teramo, Italy. Electronic address: a.lorusso@izs.it.
authors.forename: Alessio
authors.initials: A
authors.lastname: Lorusso
mesh_terms: D000818:Animals; D004216:Distemper / Q000821:virology; D004217:Distemper Virus, Canine / Q000235:genetics* / Q000302:isolation & purification; D004285:Dogs; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D007558:Italy; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D014776:Virus Cultivation; D019596:Wolves / Q000821:virology
chemical_list: D012367:RNA, Viral
keywords: Arctic lineage; Canine distemper virus; Next generation sequencing; Whole genome