Computational protocol: Emergence of Pathogenic Coronaviruses in Cats by Homologous Recombination between Feline and Canine Coronaviruses

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Protocol publication

[…] Homologies among strains were analyzed using GENETYX Ver.8 (GENETYX Corporation, Tokyo, Japan) and phylogenetic trees were constructed by the neighbor-joining method using MEGA5.0 software based on nucleotide pairwise distance. For construction of the phylogenetic tree, we referred to the following sequences; type II FCoV 79-1146 (accession no. DQ010921), 79-1683 (JN634064), DF-2 (JQ408981) and NTU156/P/2007 (GQ152141), type I FCoV C3663 (AB535528), Yayoi (AB695067 for S), UCD1 (AB088222 for S, AB086902 for N), Black (EU186072), NTU2/R/2003 (DQ160294), RM (FJ938051), UCD11a (FJ917519), UCD5 (FJ917522), UCD12 (FJ917521), UCD13 (FJ917523), UCD14 (FJ917524), UU2 (FJ938060), UU16 (FJ938058), UU18 (HQ012368), UU20 (HQ392471), UU21 (HQ012369), UU23 (GU553362), type II CCoV 1-71 (JQ404409), v1 (AY390342 for S, AY390345 for N), K378 (KC175340), NTU336/F/2008 (GQ477367), 5821 (AB017789 for S), TGEV Purdue (DQ811789), and PRCoV ISU-1 (DQ811787). Analysis of the similarity in the 3′-region of the genome, excluding poly A, was carried out using Simplot version 3.5.1 . […]

Pipeline specifications

Software tools MEGA, SimPlot
Application Phylogenetics
Organisms Canis lupus familiaris, Felis catus, Feline coronavirus
Diseases Coronavirus Infections