Computational protocol: Pestivirus infection in cattle dairy farms: E2 glycoprotein ELISA reveals the presence of bovine viral diarrhea virus type 2 in northwestern Italy

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Protocol publication

[…] PI animals were identified using an antigen ELISA (IDEXX BVDV Ag/Serum Plus, IDEXX, Westbrook, ME, USA). Two of the 5 PI animals (CN10.2015.813 and CN10.2015.821) were selected for viral strain characterization and blood serum was collected from both. The first animal died after developing MD during the study, and samples from the spleen and intestinal epithelium were collected. Tissue homogenates and blood serum from the animal were used to isolate the viral strain on MDBK culture. Viral RNA was extracted from homogenized tissues and infected cell culture supernatant using an EZ1 Virus kit v2.0 (Qiagen, Hilden, Germany). For each sample, the 5’UTR region was amplified as previously described []. Amplicons were purified using Nucleospin Gel and PCR Clean-up kit (Machery Nagel) and directly sequenced in both directions (BMR Genomics, Padua, Italy). Consensus sequences were aligned to homologous reference sequences available in the online databases (Clustal W algorithm embedded in Geneious software ver. 9.0.2), referring to the BVDV-2 classification proposed previously []. Phylogenetic analysis was conducted by selecting the best evolutionary model with jModelTest version 2.1.7 [] and applying the Bayesian heuristic search approach included in MrBayes software []. […]

Pipeline specifications

Software tools Clustal W, Geneious, jModelTest, MrBayes
Application Phylogenetics
Organisms Bovine viral diarrhea virus 1, Bos taurus, Bovine viral diarrhea virus 2
Diseases Hepatitis, Viral, Human, HIV Infections, Pestivirus Infections