The complete genome of Cyprinid herpesvirus 2, a new strain isolated from Allogynogenetic crucian carp

The haemorrhagic disease of the gill is caused by Cyprinid herpesvirus 2 (CyHV2) infection, which often results in the severe economic losses in the farm of Allogynogenetic crucian carp (ACC). In this study, the genome of CyHV2 strain CyHV2-SY (SY) collected from Sheyang County, Jiangsu Province, China was sequenced. The complete genome of SY is at length of 290,455 bp with 154 potential open reading frames (ORFs) and a terminal direct repeat (TR) of 15,353 bp. Many variations were found by comparison the sequenced CyHV2 genomes. The ORF10, ORF107, ORF156 of SY genome have insertions or deletions of repeat sequences compared with ST-J1 and SY-C1, which may be used as the marks of SY strains. Besides, the promoter sequence analysis showed that 13 of the 150 ORFs have TATA-box elements and 119 of the 150 ORFs have SP1 cis-acting elements in the promoter region (350 bp upstream sequence of the initiation codon ATG). Twenty-eight viral miRNAs candidates were predicted in the CyHV2 genome and expression of 24 virogenes may be regulated by viral miRNAs. Horizontal transfer analysis indicated that 16 and 2 genes in the CyHV2 genome may transfer from the host and bacteria, respectively. By the genome sequencing and sequence mining, our results provided more new clues to further understand CyHV2 genome.