Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy
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Near‑complete nucleotide sequence of a border disease virus genotype BDV‑7 isolate from Italy Moira Bazzucchi1 · Ilaria Pierini1 · Monica Giammarioli1 · Gian Mario De Mia1 Received: 17 July 2020 / Accepted: 7 September 2020 / Published online: 6 October 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract To gain further insight into the genomic features of border disease virus (BDV), we determined the nearly complete genome sequence of isolate TO/121/04 from an aborted ovine fetus. Its genome contains a single open reading frame (ORF), which comprises 11,681 nucleotides encoding a polyprotein of 3893 amino acids. Phylogenetic analysis of the near full-length genome sequence showed that the BDV isolate differed significantly from all ovine pestiviruses identified so far, thus reaffirming the presence in Italy of this novel genetic group, termed BDV-7. Border disease virus (BDV) is a member of the genus Pestivirus in the family Flaviviridae and causes abortion, stillbirths, and birth of weak lambs that show tremors, abnormal body shape, and hairy fleece in sheep and goats. The pestivirus genome is a positive-sense single-stranded RNA molecule that is approximately 12.3 kb in length and contains a single open reading frame (ORF) flanked by two untranslated regions (5′-UTR and 3′-UTR). In Italy, previous studies on the genetic diversity of BDV have provided evidence for the presence of at least six genotypes, namely BDV-1, BDV-3, BDV-5, BDV-6 (data not shown), BDV-7, and BDV-8 [1, 2]. Molecular analysis of an Italian caprine BDV isolated in 2002 revealed the presence of an atypical pestivirus, which may be the first member of a putative novel pestivirus genotype [3]. Further comparative analysis of the 5′-UTR and N pro genomic regions in ovine pestiviruses isolated after this study revealed that four additional BDV isolates clustered together with the caprine BDV strain into a novel phylogenetic group tentatively termed BDV-7 [4]. As an extension of this study, we describe the first fulllength sequence of a BDV strain belonging to this distinct cluster. We also analyzed the genomic information and the Handling Editor: Tim Skern. * Gian Mario De Mia [email protected] 1
Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, via G. Salvemini, 1, 06126 Perugia, Italy
phylogenetic relationship of this strain to other reported pestiviruses. The non-cytopathogenic BDV strain TO/121/04 was isolated in 2004 from an ovine fetus using the SFT-R cell line. Total RNA was extracted from the cell culture supernatant using a QIAamp Viral RNA Mini Kit (QIAGEN, Valencia, CA, USA) following the manufacturer’s instructions, and an RNeasy Mini Kit (QIAGEN, Valencia, CA, USA) was then used for the cleanup. The quality of total RNA was verified using a 2200 TapeStation RNA Screen Tape device (Agilent, Santa Clara, CA, USA), and its concentration was determined using an ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). Double-stranded cDNA was prepared using
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