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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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Kozak sequence context of each gene of IHNV 220-90. Sequences shown here are positive-sense anti-genome. * Conserved adenosine (A) at position -3. ** Start codon (ATG)
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Figure 5: Kozak sequence context of each gene of IHNV 220-90. Sequences shown here are positive-sense anti-genome. * Conserved adenosine (A) at position -3. ** Start codon (ATG)

Mentions: All the genes of VHSV start with a conserved gene start sequence (-CGUG-) like other novirhabdoviruses, followed by an ORF and conserved gene-end sequence (A/GUCUAU/ACU7). All the genes end with 7 uracil (U) residues, which are polyadenylation signal for polymerase when it transcribes a gene. Polymerase adds poly (A) by stuttering mechanism [23]. After this poly (A) signal, there are two conserved intergenic di-nucleotides (G/AC), which are untranscribed and act as spacers between two genes. Polymerase skips these two nucleotides to next gene start sequence and starts transcribing next gene [23]. Transcription of rhabdovirus mRNAs is regulated by cis-acting signals located within the 3' leader region and untranslated region between each gene ORF [23-26]. In case of NV, the stop codon of NV gene is merged with gene-end sequences (Fig. 2A). Transcription of rhabdovirus mRNAs is regulated by cis-acting signals located within the 3' leader region and untranslated region between each gene ORF [23-26]. The Kozak context for each gene was compared, as shown in Fig. 5. At position -3, all the genes have adenosine (A) nucleotide, except the ORF of N gene.


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

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

Kozak sequence context of each gene of IHNV 220-90. Sequences shown here are positive-sense anti-genome. * Conserved adenosine (A) at position -3. ** Start codon (ATG)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Kozak sequence context of each gene of IHNV 220-90. Sequences shown here are positive-sense anti-genome. * Conserved adenosine (A) at position -3. ** Start codon (ATG)
Mentions: All the genes of VHSV start with a conserved gene start sequence (-CGUG-) like other novirhabdoviruses, followed by an ORF and conserved gene-end sequence (A/GUCUAU/ACU7). All the genes end with 7 uracil (U) residues, which are polyadenylation signal for polymerase when it transcribes a gene. Polymerase adds poly (A) by stuttering mechanism [23]. After this poly (A) signal, there are two conserved intergenic di-nucleotides (G/AC), which are untranscribed and act as spacers between two genes. Polymerase skips these two nucleotides to next gene start sequence and starts transcribing next gene [23]. Transcription of rhabdovirus mRNAs is regulated by cis-acting signals located within the 3' leader region and untranslated region between each gene ORF [23-26]. In case of NV, the stop codon of NV gene is merged with gene-end sequences (Fig. 2A). Transcription of rhabdovirus mRNAs is regulated by cis-acting signals located within the 3' leader region and untranslated region between each gene ORF [23-26]. The Kozak context for each gene was compared, as shown in Fig. 5. At position -3, all the genes have adenosine (A) nucleotide, except the ORF of N gene.

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