Complete genome sequence of virulent duck enteritis virus (DEV) strain 2085 and comparison with genome sequences of virulent and attenuated DEV strains

Abstract

We here report the complete genome sequence of the duck enteritis virus (DEV) wild-type strain 2085, an avian herpesvirus (GenBank ID: JF999965). The nucleotide sequence was derived from the 2085 genome cloned as an infectious bacterial artificial chromosome (BAC) clone. The DEV 2085 genome is 160,649-bp in length and encodes 78 predicted open reading frames (ORFs), a number identical to that identified for the attenuated DEV VAC strain (GenBank ID: EU082088.2). Comparison of the genome sequences DEV 2085 and VAC with partial sequences of the virulent CHv strain and the attenuated strain Clone-03 was carried out to identify nucleotide or amino acid polymorphisms that potentially contribute to DEV virulence. No amino acid changes were identified in 24 of the 78 ORFs, a result indicating high conservation in DEV independently of strain origin or virulence. In addition, 39 ORFs contain non-synonymous nucleotide substitutions, while 15 ORFs had nucleotide insertions or deletions, frame-shift mutations and/or non-synonymous nucleotide substitutions with an effect on ORF initiation or termination. In 7 of the 15 ORFs with high and 27 of the 39 ORFs with low variability, polymorphisms were exclusively found in DEV 2085, a finding that likely is a result of a different origin of 2085 (Europe) or VAC, Clone-03 and CHv (Eastern Asia). Five ORFs (UL2, UL12, US10, UL47 and UL41) with polymorphisms were identical between the virulent DEV 2085 and CHv but different from VAC or Clone-03. They, individually or in combination, may therefore represent DEV virulence factors. Our comparative analysis of four DEV sequences provides a comprehensive overview of DEV genome structure and identifies ORFs that are changed during serial virus passage.