Title: Characterization of the Whole Genome of Equid Herpesvirus 3 by Next-Generation Sequencing
Authors: Sijmons, Steven
Vissani, Aldana
Silva Tordoya, Maria
Muylkens, Benoît
Thiry, Etienne
Maes, Piet
Matthijnssens, Jelle
Barrandeguy, Maria
Van Ranst, Marc
Issue Date: 2013
Conference: Annual International Herpesvirus Workshop edition:38 location:Grand Rapids, Michigan, USA date:20-24 July 2013
Abstract: Equid herpesvirus 3 (EHV-3) is a member of the subfamily Alphaherpesvirinae that infects horses and causes equine coital exanthema.
Although the whole genome of four equine alphaherpesviruses (EHV-1, EHV-4, EHV-8 and EHV-9) has been published, the sequence
knowledge for EHV-3 is limited to fragments of the DNA polymerase, the DNA packaging protein and the glycoprotein G. We therefore
determined the complete genome sequence of EHV-3. EHV-3 was grown on equine dermal cells and purified with sucrose gradient
ultracentrifugation. Subsequently, residual equine DNA was degraded through nuclease digestion after which viral DNA was extracted.
Viral DNA was amplified using multiple displacement amplification and sequenced using 454 and Illumina next-generation sequencing
platforms. Sequence reads were mapped on the equine genome and unmapped reads were collected for further assembly. De novo
assemblies were conducted separately using 454 and Illumina datasets (with Newbler and Velvet respectively) and contigs were
merged using Phrap. This resulted in 12 contigs that could be extended and joined by an iterative mapping of the sequence reads on
the contig sequences. The resulting EHV-3 genome sequence is 152kb in size. EHV-3 ORFs are arranged in the same order as in the
other known equine alphaherpesviruses with no proof of additional ORFs. ORF76, however, is positioned inside the internal/terminal
repeat and encodes only the carboxy-terminal half compared to other equine alphaherpesviruses. Consequently, EHV-3 is predicted to
encode 76 distinct genes, four of which are duplicated (ORFs 64, 65, 66 and 76) in the internal/terminal repeat, resulting in a total of
80 genes. Genetic comparison demonstrated that EHV-3 is the most divergent of the equine alphaherpesviruses, possessing nucleotide
similarities ranging from 62.4 to 65.4% with EHV-1, EHV-4, EHV-8 and EHV-9.
Publication status: published
KU Leuven publication type: IMa
Appears in Collections:Laboratory of Clinical and Epidemiological Virology (Rega Institute)
Department of Health and Technology - UC Leuven

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