Author:

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.