Comparative analysis of the genes UL1 through UL7 of the duck enteritis virus and other herpesviruses of the subfamily Alphaherpesvirinae

Li, Huixin; Liu, Shengwang; Han, Zongxi; Shao, Yufeng; Chen, Shuhong; Kong, Xiangang

doi:10.1590/s1415-47572009005000003

Cited by 9 publications

(17 citation statements)

References 28 publications

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“…The DEV gene arrangement and content in this region ( fig. 2 ) showed differences from other genes in previously reported UL regions [10][11][12][13][14] .…”

Section: Discussionmentioning

confidence: 82%

“…Generally, the arrangement of partial genes in the UL region of the DEV genome is collinear with homologues in HSV-1, and phylogenetic analysis of most b genes in the DEV UL region has shown that DEV has a close relationship to members of Mardivirus [10][11][12][13][14] . In the present study, we report sequences in the leftmost region of DEV UL and the molecular characteristics of predicted genes in this region.…”

Section: Discussionmentioning

confidence: 99%

“…Briefly, a pair of primers, L1 and L2, were designed based on the partial DEV UL1 sequence from GenBank (GenBank accession No. EF449516) [12] . The 1st fragment (F1) was amplified in the direction opposite to the UL1 gene.…”

Section: Virus Propagationmentioning

confidence: 99%

“…DEV has a genome of approximately 180 kb [9] . The complete gene sequences of the unique long (UL) region have been sequenced and determined in our laboratory [10][11][12][13][14] , and several other genes in the unique short (US) region have also been reported [15][16][17] . The results demonstrate that DEV has a similar, but not the same, genomic organization as other herpesviruses.…”

Section: Introductionmentioning

confidence: 99%

“…The results demonstrate that DEV has a similar, but not the same, genomic organization as other herpesviruses. In general, DEV has a closer evolutionary relationship to members of Mardivirus than to other herpesviruses [10][11][12][13][14] . Like other herpesviruses, DEV has a large DNA genome, but little is known about the genomic structure and the sequences in the terminus of the unique region.…”

Section: Introductionmentioning

confidence: 99%

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Unique Sequence Characteristics of Genes in the Leftmost Region of Unique Long Region in Duck Enteritis Virus

Liu

Liu²,

Li³

et al. 2009

Intervirology

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Objective: Our objective was to further understand the evolutionary position of duck enteritis virus (DEV) in the family Herpesviridae and to determine the genomic structure in the leftmost region of the unique long region (UL) of DEV. Methods: ‘Targeted gene walking PCR’ was used to amplify the unknown gene of DEV clone-03 strain adjacent to known sequences in the UL region. Open reading frames (ORFs) were determined by Gene Runner and an online transcriptional element search engine. The phylogenetic tree was constructed by DNAStar based on the deduced amino acid sequences. Results: A fragment of 13,947 bp, containing 5 ORFs (designated ICP4, ORF1, ORF2, LORF2 and LORF3, respectively), was amplified from the DEV clone-03 strain genome. In addition, a tandem repeat region of α-type-like sequences was detected between ICP4 and LORF2. Phylogenetic analysis of ICP4 indicated that DEV ICP4 should be clustered into Varicellovirus. DEV ORF1 and ORF2 were unique among herpesviruses. Additionally, the existence and characteristics of LORF2 and LORF3 indicated a close relationship with Mardivirus members. Conclusion: The characteristics and gene content in the leftmost end of the UL region of the DEV genome showed that the DEV genome is different from those of other herpesviruses.

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“…The DEV gene arrangement and content in this region ( fig. 2 ) showed differences from other genes in previously reported UL regions [10][11][12][13][14] .…”

Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Section: Virus Propagationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Unique Sequence Characteristics of Genes in the Leftmost Region of Unique Long Region in Duck Enteritis Virus

Liu

Liu²,

Li³

et al. 2009

Intervirology

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An attempt to develop a detection method specific for virulent duck plague virus strains based on the UL2 gene B fragment

et al. 2017

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A comparison of the unique long region 2 (UL2) gene sequences between 10 virulent and 11 attenuated duck plague virus (DPV) strains (including all DPV UL2 gene sequences registered in GenBank) showed that the UL2 genes in the attenuated DPV strains had a 528 bp deletion in the B fragment. Primers were designed based on the B fragment sequence of the UL2 gene in an attempt to establish a fluorescence quantitative polymerase chain reaction (PCR) and a conventional PCR detection method that could specifically detect virulent DPV strains (i.e. positive detection for virulent DPV strains and negative detection for attenuated DPV strains). Additionally, PCR products were cloned for sequence analysis. These two methods detected five attenuated DPV strains in addition to the virulent DPV strains. Sequence analysis of the PCR products showed that the amplified products were the B fragments of the UL2 gene. These results indicated that detection methods specific for virulent DPV strains could not be established using primers designed based on the UL2 gene B fragment.

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Comparative Genomic Analysis of Duck Enteritis Virus Strains

Cheng

Wang

et al. 2012

J Virol

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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...

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Comparative analysis of the genes UL1 through UL7 of the duck enteritis virus and other herpesviruses of the subfamily Alphaherpesvirinae

Cited by 9 publications

References 28 publications

Unique Sequence Characteristics of Genes in the Leftmost Region of Unique Long Region in Duck Enteritis Virus

Unique Sequence Characteristics of Genes in the Leftmost Region of Unique Long Region in Duck Enteritis Virus

An attempt to develop a detection method specific for virulent duck plague virus strains based on the UL2 gene B fragment

Comparative Genomic Analysis of Duck Enteritis Virus Strains

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