Duck enteritis virus (DEV) infects ducks, geese, and swans,causing heavy economic loss [5]. The virus belongs to the species Anatid alphaherpesvirus 1, in the genus Mardivirus, subfamily Alphaherpesvirinae, family Herpesviridae (https://www.ictvonline.org). The DEV genome is approximately 160 kb long, composed of a unique long (UL) region and a unique short (US) region, each flanked by an inverted repeat (IR) and a terminal repeat (TR) [4, 8, 9, 11, 12]. In previous studies, we sequenced the complete genome of the Chinese standard challenge strain of DEV (DEV CSC) isolated in 1962, its passaged variant DEV C20E85, and a live vaccine strain, DEV K p63 (Table 1) [9,10,11, 13]. DEV is currently circulating in ducks in China, but no genomic information is available for the circulating strains. In this report, we describe the complete genome sequence of a DEV strain isolated recently in China.

Table 1 Lengths of various regions in the DEV genomes
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DEV SD was isolated in 2012 from a duck farm in Shandong Province, China. The liver of a dead duck was collected, homogenized, and inoculated into duck embryos. After two passages, all inoculated duck embryos died within 5 days.

Four susceptible 2-month-old ducks were inoculated intramuscularly with 105 EID50 of DEV SD, and as a control, two 2-month old ducks were inoculated with M199 medium. They were housed in two isolators. The ducks were observed for signs of disease for 14 days after inoculation. All ducks inoculated with DEV SD developed pyrexia and died at 5–7 days post-inoculation (dpi) with typical symptoms of infection, whilst the control ducks remained healthy.

To identify genetic mutations, whole-genome sequencing was done. DEV SD genomic DNA was extracted using a TaKaRa MiniBEST Viral RNA/DNA Extraction Kit Ver. 5.0 (Dalian, China). Primers were designed based on the DEV CSC genome sequence (GenBank no. JQ673560) and synthesized by BGI (Beijing, China). The PCR amplicons were purified and sequenced by the Sanger method (BGI, Beijing, China). All of the sequences were assembled and compared using Seqman and MegAlign of DNASTAR (V5.01). The DEV CSC sequence was used as the reference for mapping and annotation. The DEV SD sequence was deposited in the GenBank database under accession number MN518864.

The assembled complete genome sequence of DEV SD was 160,945 bp in length, which is shorter than that of the DEV CSC (Table 1), due to three discontinuous deletions of 101 bp, 48 bp, and 417 bp, within the noncoding inverted repeats. Whether these deletions influence the pathogenicity of the virus has yet to be established.

Similar deletions in the non-coding inverted repeats have also been observed in other alphaherpesviruses. A German isolate (DEV 2085) also had two deletions (48 bp and 104 bp) in the inverted repeats [7] (Fig. 1). Equine herpesvirus 1 strain RacL11, isolated from an aborted foal, had 354-bp, 25-bp and 119-bp deletions in the inverted repeats compared with strain Ab4 [6]. Notable nucleotide insertions and deletions have also been reported in the inverted repeats of different bovine herpesvirus type 1.1 isolates [1]. The length of the inverted repeats has been shown to vary significantly among different infectious laryngotracheitis virus strains [2, 3].

Fig. 1
figure 1

Schematic illustration of deletions in the internal repeat sequence of the genomes of DEV strains SD and 2085. The DEV CSC sequence was used as the reference for mapping and annotation. The deletions are shown as red dashed boxes. Numbers under boxes represent fragment length. Vertical dashed lines represent positions in the DEV CSC genome

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The amino acid (aa) sequences of all ORFs of the CSC and SD isolates were compared, and the results showed that there was an 11-aa deletion, two single-aa deletions, and one single-aa deletion in LORF3, UL47, UL4 of DEV SD, respectively. In addition, 38 single-aa variations were detected in 24 different ORFs (Table 2). The other ORFs were completely conserved among the sequences of SD and CSC.

Table 2 Amino acid sequence differences in the proteins encoded by DEV strains CSC and SD
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In summary, the complete DEV SD genome sequence was determined and found to have discontinuous deletions (101 bp, 48 bp and 417 bp) within the inverted repeats. These results will further advance our understanding of the genes involved in evolution.