Analysis of the genome sequence of infectious hematopoietic necrosis virus HLJ-09 in China

Abstract

Infectious hematopoietic necrosis virus (IHNV) is a highly contagious disease of juvenile salmonid fish. Six genome target fragments of the complete genome sequence of IHNV HLJ-09 were amplified by RT-PCR, and the 3'-terminal and 5'-terminal region of the genomic RNA were amplified using the RACE method. The complete genome sequence of HLJ-09 comprises 11,132 nucleotides (nt) (Accession number JX649101) and is different from that of other IHNV strains published in GenBank. Homology comparison and phylogenetic analysis of six ORF sequences were carried out using HLJ-09 and other IHNV strains published in GenBank. From phylogenetic tree analysis, the N gene, M gene, and P gene had the closest genetic relationship to IHNV-PRT from Korea. Phylogenetic analysis for the full length of the G gene showed that the HLJ-09 strain exhibited very close homology to the ChYa07, RtNag96, RtUi02, and RtGu01 strains from Korea and Japan, indicating that the HLJ-09 strain belonged to the genotype JRt. Ultimately, the Chinese IHNV HLJ-09 strain may have originated in Korea and Japan.

Keywords: Complete genome; Infectious hematopoietic necrosis virus (IHNV); Phylogenetic tree; Sequence analysis.