Computational protocol: Detection and molecular characterisation of bovine corona and toroviruses from Croatian cattle

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Protocol publication

[…] Sequences were aligned and compared to previously published BCoV N, BCoV S and BToV S sequences, respectively. Sequence identities of nucleotides as well as estimation of the evolutionary divergence between sequences were analyzed using BioEdit and Mega6 [] software, respectively. The neighbour-joining (NJ) trees were obtained using Mega6 program with the evolutionary model set to Tamura-Nei + Gamma for Spike gene analysis and Kimura-2 parametar for N gene. Estimation of best-fit model by hierarchical likelihood ratio tests (hLRTs) and approximate Akaike information criterion (AIC) was performed with jModelTest V.0.1.1. []. Reliabilities of phylogenetic relationships were evaluated using nonparametric bootstrap analysis with 1000 replicates for NJ analysis. Bootstrap values exceeding 70 were considered well supported.The dataset included the reference strains of BCoV: Mebus (GenBank accession number U00735), Quebec (AF220295) respiratory BCoV strains: LSU2 (AF058943), OK-3 (AF058944) and AH187 (FJ938065); Italian strains 179/07–11 (EU019216), 438/06-TN (EU814647) and 339/06 (EF445634); Korean strain KWD19 (DQ389660), Japanese strain Kakegawa (AB354579), Swedish strain SWE/I/08-3 (KF169933), Danish strain DEN03-2 (KF169914), Irish strain RVLC9 (KF272913), Human coronaviruses: Hu-OC43 (Z32769) and Hu-4408 (L07748; FJ415342). Reference strains of BToV: Breda1 (AY427798), NA7 (AB254073), Gifu-2007TI/E (AB526863), Hokkaido-2008TI/E (AB526864), Aichi/2004 (AB526866) and B145 (AJ575373). […]

Pipeline specifications

Software tools BioEdit, MEGA, jModelTest
Application Phylogenetics
Organisms Bos taurus, Bovine coronavirus
Diseases Infection, Respiratory Insufficiency
Chemicals Nucleotides