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Characterization of a Novel Hepadnavirus in the White Sucker (Catostomus commersonii) from the Great Lakes Region of the United States.

Hahn CM, Iwanowicz LR, Cornman RS, Conway CM, Winton JR, Blazer VS - J. Virol. (2015)

Bottom Line: Phylogenetic analyses confirmed WSHBV as distinct from previously documented hepadnaviruses.These results are not sufficient to draw inferences regarding the association of WSHBV and carcinogenesis in white sucker.This may also offer another model system for mechanistic research.

View Article: PubMed Central - PubMed

Affiliation: West Virginia University, School of Natural Resources, Morgantown, West Virginia, USA U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, USA.

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Genome organization of the WSHBV. The complete genome consists of 3,542 nucleotides of double-stranded DNA that encode three partially or completely overlapping ORFs (RFs +1, +2, and +3). Open reading frames encoding the core, polymerase, and surface proteins are indicated in black. Conserved domains are indicated in gray.
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Figure 3: Genome organization of the WSHBV. The complete genome consists of 3,542 nucleotides of double-stranded DNA that encode three partially or completely overlapping ORFs (RFs +1, +2, and +3). Open reading frames encoding the core, polymerase, and surface proteins are indicated in black. Conserved domains are indicated in gray.

Mentions: The initial indication that a hepadnavirus was present in our pooled liver sample was based on blastx results of de novo-assembled RNA transcripts (Fig. 2). To avoid the inclusion of pgRNA or viral mRNA in the genome model, we isolated DNA from an ethanol-preserved liver. Resequencing was conducted on a single, PCR-positive fish collected from the Root River (white sucker hepatitis B virus [WSHBV] RR173). The DNA was extracted using a DNeasy kit (Qiagen, Valencia, CA) as per the manufacturer's protocols. Primers were designed to resequence the complete genome and confirm a circular architecture. We used Primer3, version 2.3.4 (27), to design these primers. Default parameters were modified to amplify 280- to 797-bp products (see Table S2 in the supplemental material). Sequence overlap ranged from 19 to 461 bp, with a mean overlap of 189 bp (see Fig. S1). PCR conditions are noted in Table S2 in the supplemental material. All PCR amplicons were purified using a QIAquick purification kit (Qiagen, Valencia, CA). Dideoxy sequencing was conducted using BigDye Terminator, version 3.1, chemistry and an ABI 3100 genetic analyzer (Applied Biosystems, Forster City, CA). The resulting sequences were assembled into a single circular sequence using Geneious (version R7; Biomatters) (Fig. 3).


Characterization of a Novel Hepadnavirus in the White Sucker (Catostomus commersonii) from the Great Lakes Region of the United States.

Hahn CM, Iwanowicz LR, Cornman RS, Conway CM, Winton JR, Blazer VS - J. Virol. (2015)

Genome organization of the WSHBV. The complete genome consists of 3,542 nucleotides of double-stranded DNA that encode three partially or completely overlapping ORFs (RFs +1, +2, and +3). Open reading frames encoding the core, polymerase, and surface proteins are indicated in black. Conserved domains are indicated in gray.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4645335&req=5

Figure 3: Genome organization of the WSHBV. The complete genome consists of 3,542 nucleotides of double-stranded DNA that encode three partially or completely overlapping ORFs (RFs +1, +2, and +3). Open reading frames encoding the core, polymerase, and surface proteins are indicated in black. Conserved domains are indicated in gray.
Mentions: The initial indication that a hepadnavirus was present in our pooled liver sample was based on blastx results of de novo-assembled RNA transcripts (Fig. 2). To avoid the inclusion of pgRNA or viral mRNA in the genome model, we isolated DNA from an ethanol-preserved liver. Resequencing was conducted on a single, PCR-positive fish collected from the Root River (white sucker hepatitis B virus [WSHBV] RR173). The DNA was extracted using a DNeasy kit (Qiagen, Valencia, CA) as per the manufacturer's protocols. Primers were designed to resequence the complete genome and confirm a circular architecture. We used Primer3, version 2.3.4 (27), to design these primers. Default parameters were modified to amplify 280- to 797-bp products (see Table S2 in the supplemental material). Sequence overlap ranged from 19 to 461 bp, with a mean overlap of 189 bp (see Fig. S1). PCR conditions are noted in Table S2 in the supplemental material. All PCR amplicons were purified using a QIAquick purification kit (Qiagen, Valencia, CA). Dideoxy sequencing was conducted using BigDye Terminator, version 3.1, chemistry and an ABI 3100 genetic analyzer (Applied Biosystems, Forster City, CA). The resulting sequences were assembled into a single circular sequence using Geneious (version R7; Biomatters) (Fig. 3).

Bottom Line: Phylogenetic analyses confirmed WSHBV as distinct from previously documented hepadnaviruses.These results are not sufficient to draw inferences regarding the association of WSHBV and carcinogenesis in white sucker.This may also offer another model system for mechanistic research.

View Article: PubMed Central - PubMed

Affiliation: West Virginia University, School of Natural Resources, Morgantown, West Virginia, USA U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, USA.

Show MeSH
Related in: MedlinePlus