Computational protocol: Genomic Characterization of a Circovirus Associated with Fatal Hemorrhagic Enteritis in Dog, Italy

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Protocol publication

[…] The genome sequence of the DogCV was assembled and analysed using the Genious software package (http://www.geneious.com) and the NCBI's (htttp://www.ncbi.nlm.nih.gov) and EMBL's (http://www.ebi.ac.uk) analysis tools. The complete sequence was deposited in GenBank under accession no. KJ530972.The nt sequences of the different ORFs were aligned with cognate sequences of reference DogCV strains and of other circoviruses using a translation-based alignment. Phylogenetic and molecular evolutionary analyses were conducted using Mega4.1 Beta . Phylogenetic trees based on the full-length genome and on the nt sequences of the replicase and capsid protein genes were elaborated using both neighbor-joining and parsimony methods, supplying a statistical support with bootstrapping over 1000 replicates. The following reference circovirus strains were used in the phylogenetic analysis: DogCV 214 (JQ821392), UCD1 (NC_020904), UCD2 (KC241984) and UCD3 (KC241983); PCV-1 (AY660574); PCV-2 AUT1 (AY424401), CaCV (AJ301633), BFDV (AF071878), Columbid circovirus (CoCV) (AF252610), Goose circovirus (GoCV) (J30445), Duck circovirus (DuCV) 33753-52 (DQ100076), Raven circovirus (RaCV) strain 4–1131 (DQ146997), Starling circovirus (StCV) (DQ17290), Gull circovirus (GuCV) (DQ845074), Finch circovirus (FiCV) (DQ845075), Cygnus olor circovirus (SwCV) (EU056310), Barbel circovirus (Barbel CV) (GU799606), Cyclovirus (Cy) NG13 (GQ404856), Silurus glanis circovirus (Catfish CV) (JQ011378), CyCV TN25 (GQ404857), CyCV PK5034 (GQ404845), CyCV PK5006 (GQ404844), CyCV NGChicken8 (HQ738643). The distantly-related Gyrovirus Chicken anemia virus (CAV) (M55918) was used as outgroup. […]

Pipeline specifications

Software tools Geneious, MEGA
Application Phylogenetics
Organisms Canis lupus familiaris
Diseases Enteritis