Comparative Genomic Analysis of Duck Enteritis Virus Strains

Abstract

cThe icosahedral virion of duck enteritis virus (DEV) is roughly spherical and approximately 150 nm in diameter. Here, we describe the genomic features of DEV CHv together with a draft genome sequence and its annotation, highlighting the homogeneity and heterogeneity of this genome in comparison with its reference genomes. Duck enteritis virus (DEV) is an epornitic agent. It causes considerable economic losses to the commercial duck industry and poses a continuous threat to wild and migratory waterfowl populations (20). Many DEV genes have been published in molecular biology studies (1, 3-18, 21, 22, 23, 25-35). However, research into DEV still lags relatively far behind that of other members of herpesvirus due to the limited genomic information.The construction of DEV libraries and the sequencing of the DEV genome were performed as previously described (2). There are three complete genomic sequences of DEV strains available in GenBank: the attenuate vaccine (VAC), the European virulent strain (2085), and the Chinese virulent DEV strain (DEV CHv) (24). Here, we report the comparative analysis of the DEV genome, which may provide insight into the differences between these strains.The DEV CHv genome contains a linear double-stranded DNA of 162,175 bp. It is larger than that of VAC (158,091 bp) or 2085 (160,649 bp). The GϩC levels of all three strains are nearly identical (CHv, 44.89%; VAC, 44.91%; 2085, 44.93%). NCBI BLAST results indicated 99% identity between the CHv, VAC, and 2085 genomes at the nucleotide level. Further analysis showed DEV to have a typical type D herpesvirus genome arrangement: UL-IRS-US-TRS. However, the orientation of the US segment within strain 2085 was found to be opposite that of CHv and VAC. This kind of inversion occasionally happens in type D herpesvirus genomes, since the short component inverts relatively easy to the long (19).NCBI BLAST showed 100% identity among 16 open reading frames (ORFs) in the UL region and 4 ORFs in the US region across all three strains. This may mean that these ORFs are conserved in DEV strains and cannot be the cause of VAC attenuation or the regional bias of 2085. Functional prediction indicated that these gene products are structural proteins and may be involved in viral DNA metabolism. The LORF3 and US7 ORFs both exhibited minor nucleotide-level variability and 98% similarity of the nucleotides. The LORF3 segment of the 2085 strain was found to lack a 33-bp nucleotide repeat present in both CHv and VAC. Geographic differences between Asian DEV (CHv, VAC) and European (2085) strains might explain this. Sequence analysis identified one insertion in the VAC US7 gene. It caused a frameshift and premature termination of transcription. Although US7 is not considered essential to viral growth, it might be related to the attenuation of the VAC strain. The strains were found to vary greatly within LORF5, called LORF11 in VAC and 2085. Although these three strains share a 60-amino-acid domain at the carboxyl terminus, another 181-amino-acid domain is completely...

Duck virus enteritis (duck plague) – a comprehensive update

“…A significant difference may also be seen in arrangement of inverted and directly repeated sequences (Hayward et al 1975;Wadsworth et al 1976). Partial or complete genomic sequences of DEVs are rapidly accumulating and its analyses demonstrated that, although similar to other herpes viruses, the DEV genome also varies Wang et al 2011;Wu et al 2012a;Wu et al 2012b;Yang et al 2013). The Chinese DEV is a wild type virulent strain of DEV (Gao et al 2015).…”

Duck enteritis virus (DEV) UL54 protein, a novel partner, interacts with DEV UL24 protein

“…DEV is a linear, double-stranded DNA virus, the genome size of which is approximately 158–162 kb [3–6]. The entire genome of DEV is composed of a unique long (UL), a unique short (US) and two inverted repeated sequences (IRS and TRS) [6].…”

Complete Genome Sequence of an Attenuated Duck Enteritis Virus Obtained by In Vitro Serial Passage

“…There is very high identity between the 63rd-passage strain and DEV strain VAC (5), with a difference of only 44 single-nucleotide polymorphisms. Compared with the virulent DEV strains CHv (6, 7) and 2085 (8), the 63rd-passage strain had a 3,513-bp deletion and a 2,497-bp deletion, respectively, after nucleotide 2715, causing a frameshift in long ORF 11 (LORF11). Additionally, there was a 528-bp deletion that caused the deletion of 176 amino acids in the frame of unique long region 2 (UL2).…”