title: Determination of the complete genome sequence of infectious hematopoietic necrosis virus (IHNV) Ch20101008 and viral molecular evolution in China.
abstract: This study determined the complete genomic sequence of the infectious hematopoietic necrosis virus (IHNV) strain Ch20101008 isolated from farmed brook trout (Salvelinus fontinalis) that died from a disease caused by the virus in northeast China. The sequence was determined from 10 overlapping clones obtained through RT-PCR amplification. The whole genome length of Ch20101008 comprised 11,129 nucleotides (nt), and the overall organization was typical of that observed for all other IHNV strains. The phylogenetic analysis results of the 65 IHNV glycoprotein genes and 47 IHNV partial nucleoprotein genes presented five major genogroups (J, U, L, E and M). The J genogroup included the J Nagano and J Shizuoka subgroups. The IHNV Ch20101008 strain belonged to the J Nagano subgroup of the J genogroup and was significantly related to other Chinese IHNV strains. All Chinese IHNV isolates are monophyletic, with a recent common ancestor, except for the BjLL strain. The N, P, M, G, NV and L genes of Ch20101008 were compared with the available IHNV sequences in GenBank. The results indicated that 198 nt were substituted, 53 of which exhibited amino acid change in the Ch20101008 genome. An adenine nucleotide deletion was found at position 4959 of the 5' UTR of the L gene. In the G gene, specific nucleotides and amino acid variations of the Chinese IHNV strains were observed when compared with 23 isolates from other countries. Of the 15 nucleotide sites that changed, seven resulted in amino acid substitution. The data further demonstrated that the J genogroup IHNV was introduced to and evolved in salmon farm environments in China.
authors.affiliation: College of Animal Science and Veterinary Medicine, Jilin University, Jilin 130062, People's Republic of China; Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: ajack2012@hotmail.com.
authors.forename: Peng
authors.initials: P
authors.lastname: Jia
authors.affiliation: Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: 108914963@qq.com.
authors.forename: Xiao-Cong
authors.initials: XC
authors.lastname: Zheng
authors.affiliation: Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: sxiujie74@gmail.com.
authors.forename: Xiu-Jie
authors.initials: XJ
authors.lastname: Shi
authors.affiliation: Shenzhen Supervision and Testing Center for Quality and Safety of Agri-products, Shenzhen 518005, People's Republic of China. Electronic address: Kansf10@mails.jlu.edu.cn.
authors.forename: Shi-Fu
authors.initials: SF
authors.lastname: Kan
authors.affiliation: Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: w5213012@163.com.
authors.forename: Jin-Jin
authors.initials: JJ
authors.lastname: Wang
authors.affiliation: Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: 45578231@qq.com.
authors.forename: Jun-Qiang
authors.initials: JQ
authors.lastname: He
authors.affiliation: Jilin Academy of Fishery Science, Jilin 130033, People's Republic of China. Electronic address: zw0721@sohu.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: chrisyu0625@sina.com.
authors.forename: Li
authors.initials: L
authors.lastname: Yu
authors.affiliation: Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: 418389317@qq.com.
authors.forename: Wen-Sheng
authors.initials: WS
authors.lastname: Lan
authors.affiliation: Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: 984853934@qq.com.
authors.forename: Qun-Yi
authors.initials: QY
authors.lastname: Hua
authors.affiliation: Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen 518045, People's Republic of China. Electronic address: liuhong@szciq.gov.cn.
authors.forename: Hong
authors.initials: H
authors.lastname: Liu
authors.affiliation: College of Animal Science and Veterinary Medicine, Jilin University, Jilin 130062, People's Republic of China; Institute of Military Veterinary Medicine, Academy of Military Medical Sciences of PLA, Jilin 130117, People's Republic of China. Electronic address: grammar849@sohu.com.
authors.forename: Ning-Yi
authors.initials: NY
authors.lastname: Jin
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D001483:Base Sequence; D002681:China; D019143:Evolution, Molecular; D005393:Fish Diseases / Q000821:virology; D005814:Genes, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D029142:Infectious hematopoietic necrosis virus / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral; D018353:Rhabdoviridae Infections / Q000821:virology*; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral
keywords: Chinese isolate; Complete genomic sequence; IHNV; J genogroup; Phylogenetic analysis