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Molecular characterization of the virulent infectious hematopoietic necrosis virus (IHNV) strain 220-90.

Ammayappan A, LaPatra SE, Vakharia VN - Virol. J. (2010)

Bottom Line: An additional uracil nucleotide was found at the end of the 5'-trailer region, which was not reported before in other IHNV strains.Comparison of the virulent 220-90 genomic sequences with less virulent WRAC isolate shows more than 300 nucleotides changes in the genome, which doesn't allow one to speculate putative residues involved in the virulence of IHNV.We have molecularly characterized one of the well studied IHNV isolates, 220-90 of genogroup M, which is virulent for rainbow trout, and compared phylogenetic relationship with North American and other strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202-3101, USA.

ABSTRACT

Background: Infectious hematopoietic necrosis virus (IHNV) is the type species of the genus Novirhabdovirus, within the family Rhabdoviridae, infecting several species of wild and hatchery reared salmonids. Similar to other rhabdoviruses, IHNV has a linear single-stranded, negative-sense RNA genome of approximately 11,000 nucleotides. The IHNV genome encodes six genes; the nucleocapsid, phosphoprotein, matrix protein, glycoprotein, non-virion protein and polymerase protein genes, respectively. This study describes molecular characterization of the virulent IHNV strain 220-90, belonging to the M genogroup, and its phylogenetic relationships with available sequences of IHNV isolates worldwide.

Results: The complete genomic sequence of IHNV strain 220-90 was determined from the DNA of six overlapping clones obtained by RT-PCR amplification of genomic RNA. The complete genome sequence of 220-90 comprises 11,133 nucleotides (GenBank GQ413939) with the gene order of 3'-N-P-M-G-NV-L-5'. These genes are separated by conserved gene junctions, with di-nucleotide gene spacers. An additional uracil nucleotide was found at the end of the 5'-trailer region, which was not reported before in other IHNV strains. The first 15 of the 16 nucleotides at the 3'- and 5'-termini of the genome are complementary, and the first 4 nucleotides at 3'-ends of the IHNV are identical to other novirhadoviruses. Sequence homology and phylogenetic analysis of the glycoprotein genes show that 220-90 strain is 97% identical to most of the IHNV strains. Comparison of the virulent 220-90 genomic sequences with less virulent WRAC isolate shows more than 300 nucleotides changes in the genome, which doesn't allow one to speculate putative residues involved in the virulence of IHNV.

Conclusion: We have molecularly characterized one of the well studied IHNV isolates, 220-90 of genogroup M, which is virulent for rainbow trout, and compared phylogenetic relationship with North American and other strains. Determination of the complete nucleotide sequence is essential for future studies on pathogenesis of IHNV using a reverse genetics approach and developing efficient control strategies.

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Phylogenetic tree analysis of sequences of nucleocapsid (N), matrix (M), phosphoprotein (P), and non-virion protein (NV) of various IHNV strains. Information about the IHNV strains used in this analysis is described in additional file 1. IHNV 220-90 strain is marked with blue diamond. Phylogenetic tree analysis was conducted by neighbor-joining method using 1000 bootstrap replications. The scale at the bottom indicates the number of substitution events and bootstrap confidence values are shown at branch nodes.
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Figure 3: Phylogenetic tree analysis of sequences of nucleocapsid (N), matrix (M), phosphoprotein (P), and non-virion protein (NV) of various IHNV strains. Information about the IHNV strains used in this analysis is described in additional file 1. IHNV 220-90 strain is marked with blue diamond. Phylogenetic tree analysis was conducted by neighbor-joining method using 1000 bootstrap replications. The scale at the bottom indicates the number of substitution events and bootstrap confidence values are shown at branch nodes.

Mentions: The phylogenetic tree analysis of sequences of nucleocapsid (N), matrix (M), phosphoprotein (P), and non-virion protein (NV) of various IHNV strains are shown in Fig. 3. Phylogenetic analysis of the N gene shows clustering of 220-90 with HO-7, 193-110 and LR-80 and maintains 98% identity with those strains. Among the available sequences, WRAC strain exhibits very close identity (98%) with 220-90 for both P and M genes. All the strains display 98% identity with the 220-90 M gene, which demonstrates the highly conserved nature of M gene. When the NV genes were compared, 220-90 strain shows 95-97% identity with other IHNV strains. Previously, the North American IHNV isolates were genogrouped as U, M and L based on glycoprotein sequences [10]. Phylogenetic tree of the G genes displays that 220-90 strain belongs to the M genogroup (Fig. 4).


Molecular characterization of the virulent infectious hematopoietic necrosis virus (IHNV) strain 220-90.

Ammayappan A, LaPatra SE, Vakharia VN - Virol. J. (2010)

Phylogenetic tree analysis of sequences of nucleocapsid (N), matrix (M), phosphoprotein (P), and non-virion protein (NV) of various IHNV strains. Information about the IHNV strains used in this analysis is described in additional file 1. IHNV 220-90 strain is marked with blue diamond. Phylogenetic tree analysis was conducted by neighbor-joining method using 1000 bootstrap replications. The scale at the bottom indicates the number of substitution events and bootstrap confidence values are shown at branch nodes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2820013&req=5

Figure 3: Phylogenetic tree analysis of sequences of nucleocapsid (N), matrix (M), phosphoprotein (P), and non-virion protein (NV) of various IHNV strains. Information about the IHNV strains used in this analysis is described in additional file 1. IHNV 220-90 strain is marked with blue diamond. Phylogenetic tree analysis was conducted by neighbor-joining method using 1000 bootstrap replications. The scale at the bottom indicates the number of substitution events and bootstrap confidence values are shown at branch nodes.
Mentions: The phylogenetic tree analysis of sequences of nucleocapsid (N), matrix (M), phosphoprotein (P), and non-virion protein (NV) of various IHNV strains are shown in Fig. 3. Phylogenetic analysis of the N gene shows clustering of 220-90 with HO-7, 193-110 and LR-80 and maintains 98% identity with those strains. Among the available sequences, WRAC strain exhibits very close identity (98%) with 220-90 for both P and M genes. All the strains display 98% identity with the 220-90 M gene, which demonstrates the highly conserved nature of M gene. When the NV genes were compared, 220-90 strain shows 95-97% identity with other IHNV strains. Previously, the North American IHNV isolates were genogrouped as U, M and L based on glycoprotein sequences [10]. Phylogenetic tree of the G genes displays that 220-90 strain belongs to the M genogroup (Fig. 4).

Bottom Line: An additional uracil nucleotide was found at the end of the 5'-trailer region, which was not reported before in other IHNV strains.Comparison of the virulent 220-90 genomic sequences with less virulent WRAC isolate shows more than 300 nucleotides changes in the genome, which doesn't allow one to speculate putative residues involved in the virulence of IHNV.We have molecularly characterized one of the well studied IHNV isolates, 220-90 of genogroup M, which is virulent for rainbow trout, and compared phylogenetic relationship with North American and other strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202-3101, USA.

ABSTRACT

Background: Infectious hematopoietic necrosis virus (IHNV) is the type species of the genus Novirhabdovirus, within the family Rhabdoviridae, infecting several species of wild and hatchery reared salmonids. Similar to other rhabdoviruses, IHNV has a linear single-stranded, negative-sense RNA genome of approximately 11,000 nucleotides. The IHNV genome encodes six genes; the nucleocapsid, phosphoprotein, matrix protein, glycoprotein, non-virion protein and polymerase protein genes, respectively. This study describes molecular characterization of the virulent IHNV strain 220-90, belonging to the M genogroup, and its phylogenetic relationships with available sequences of IHNV isolates worldwide.

Results: The complete genomic sequence of IHNV strain 220-90 was determined from the DNA of six overlapping clones obtained by RT-PCR amplification of genomic RNA. The complete genome sequence of 220-90 comprises 11,133 nucleotides (GenBank GQ413939) with the gene order of 3'-N-P-M-G-NV-L-5'. These genes are separated by conserved gene junctions, with di-nucleotide gene spacers. An additional uracil nucleotide was found at the end of the 5'-trailer region, which was not reported before in other IHNV strains. The first 15 of the 16 nucleotides at the 3'- and 5'-termini of the genome are complementary, and the first 4 nucleotides at 3'-ends of the IHNV are identical to other novirhadoviruses. Sequence homology and phylogenetic analysis of the glycoprotein genes show that 220-90 strain is 97% identical to most of the IHNV strains. Comparison of the virulent 220-90 genomic sequences with less virulent WRAC isolate shows more than 300 nucleotides changes in the genome, which doesn't allow one to speculate putative residues involved in the virulence of IHNV.

Conclusion: We have molecularly characterized one of the well studied IHNV isolates, 220-90 of genogroup M, which is virulent for rainbow trout, and compared phylogenetic relationship with North American and other strains. Determination of the complete nucleotide sequence is essential for future studies on pathogenesis of IHNV using a reverse genetics approach and developing efficient control strategies.

Show MeSH
Related in: MedlinePlus