Phylogeny of Duck Enteritis Virus: Evolutionary Relationship in the Family <i>Herpesviridae</i>

Abstract

Objective: To understand the evolutionary relationship of duck enteritis virus (DEV) in the family Herpesviridae and the genome organization of DEV. Methods: A modified ‘targeted gene walking PCR’ method was used to amplify the unknown gene of DEV Clone-03 strain adjacent to a short stretch of known sequence. The assembled unknown fragment was confirmed to be a homologue of herpesviruses by BLAST analysis and comparison with other herpesviruses homologues. Open reading frames (ORFs) were determined and analyzed by Gene Runner software and an online transcriptional element search engine. Two evolutionary analysis approaches were used to conduct phylogenetic trees of DEV in relation to herpesviruses based on the deduced amino acid sequences. Results: A genomic fragment encompassing 25,625 nt and containing 16 ORFs was amplified, determined, and compared with homologues in other herpesviruses. Phylogenetic trees indicated that DEV and other herpesviruses generated from one ancestor and DEV were grouped into the subfamily Alphaherpesvirinae. In most cases, DEV showed a close relationship with the genus Mardivirus, but formed a single branch. Conclusion: Partial genomic organization and phylogenetic analysis in the present study provides evidence that DEV was a member of the subfamily Alphaherpesvirinae and should be assigned as a single group.

Identification of a spliced gene from duck enteritis virus encoding a protein homologous to UL15 of herpes simplex virus 1

“…This phenomenon might be the result of an evolutionary event: the terminase-related UL15 coding sequence remained conserved for its importance in herpesvirus biology, while genes within the intron evolved via recombination and gene transfer between virus and vertebrate hosts since these events are common in herpesviruses [33]. In this interpretation, the fact that the pattern of ORF organization within the DEV UL15 intron is very similar to that of the corresponding regions of other alphaherpesviruses is another piece of direct evidence that DEV is a member of the subfamily Alphaherpesvirinae , which is in accordance with pervious findings [4,6,7,34]. …”

Different linkages in the long and short regions of the genomes of duck enteritis virus Clone-03 and VAC Strains

“…Genes in the UL region of DEV and their arrangement have been reported by our laboratory, and the results generally showed more similarity with Mardiviruses [8-13]. Another report showed that the LORF11 gene of the VAC strain is located at the leftmost end of the DEV genome, and that the LORF11 gene encoded a putative protein of 275 amino acids in the VAC strain [14]; both of these results differ from our previous results [12]. Meanwhile, several genes in the US region have also been reported [15-18]; however, the length of the putative proteins encoded by the US10 gene and US7 gene has been debated.…”

“…The genome structure and the gene layout of this fragment are depicted in Figure 1. The fragment contained part of the sequence of the LORF11 gene [12], the rightmost part of the L region, the US region and its flanking sequences, and inverted repeats of the short region (IRS and TRS). The L region and IRS were interrupted by a set of tandem repeat sequences designated as α-type-like sequences [13], as in the case of the two regions in herpes simplex virus (HSV) [19].…”

“…However, some differences were detected by comparison of parts of our DEV Clone-03 strain with those of the DEV VAC strain. Herein, we presented the sequence of a 42,897-bp fragment anchored in the LORF11 gene of the DEV genome which was located at the rightward end of the UL region [12], by using the method of 'targeted gene walking PCR' (Figure 1). Comparison of the sequence of the fragment with that of the DEV VAC strain showed that our Clone-03 strain of DEV had a different gene order from that of the DEV VAC strain in this region.…”

“…A pair of specific primers, L1 and L2, was designed on the basis of the partial sequence of DEV LORF11 published in GenBank (GenBank no. EU294364) [12]. The PCR was carried out by using L1 and L2 as forward primers; the four nonspecific primers were used as reverse primers.…”