Efficient generation of recombinant adenoviruses using adenovirus DNA-terminal protein complex and a cosmid bearing the full-length virus genome.

African swine fever (ASF) is an infectious transboundary disease of domestic pigs and wild swine and is currently the most serious constraint to piggery in Uganda. The causative agent of ASF is a large double-stranded linear DNA virus with a complex structure. There are twenty-four ASFV genotypes described to date; however, in Uganda, only genotypes IX and X have been previously described. Inadequate ASF outbreak investigation has contributed to the delayed establishment of effective interventions to aid the control of ASF. Continuous virus characterization enhances the understanding of ASF epidemiology in terms of viral genome variations, extent, severity, and the potential source of the viruses responsible for outbreaks. We collected samples from pigs that had died of a hemorrhagic disease indicative of ASF. DNA was extracted from all samples and screened with the OIE recommended diagnostic PCR for ASF. Partial B646L (p72), full-length E183L (p54) genes, and CVR region of the P72 gene were amplified, purified, and sequenced. Web-based BLAST and MEGA X software were used for sequence analysis. ASF was confirmed in 10 of the 15 suspected pig samples. Phylogenetic analysis confirmed circulation of genotype IX by both full-length E183 (p54) and partial B646L (p72) gene sequencing. Intragenotypic resolution of the CVR region revealed major deletions in the virus genome, in some isolates of this study. The marked reduction in the number of tetrameric tandem repeats in some isolates of this study could potentially play a role in influencing the virulence of this particular genotype IX in Uganda.

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Analysis of full-length hepatitis A virus genome in sera from patients with fulminant and self-limited acute type A hepatitis

Journal of Hepatology ◽

10.1016/s0168-8278(01)00074-5 ◽

2001 ◽

Vol 35 (1) ◽

pp. 112-119 ◽

Cited By ~ 66

Author(s):

Keiichi Fujiwara ◽

Osamu Yokosuka ◽

Kenichi Fukai ◽

Fumio Imazeki ◽

Hiromitsu Saisho ◽

...

Keyword(s):

Hepatitis A ◽

Hepatitis A Virus ◽

Type A ◽

Virus Genome ◽

Full Length ◽

Acute Type

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Block to the Production of Full-Length B19 Virus Transcripts by Internal Polyadenylation Is Overcome by Replication of the Viral Genome

Journal of Virology ◽

10.1128/jvi.01162-08 ◽

2008 ◽

Vol 82 (20) ◽

pp. 9951-9963 ◽

Cited By ~ 49

Author(s):

Wuxiang Guan ◽

Fang Cheng ◽

Yuko Yoto ◽

Steve Kleiboeker ◽

Susan Wong ◽

...

Keyword(s):

Nonstructural Protein ◽

Infectious Clone ◽

Alternative Polyadenylation ◽

Virus Genome ◽

Full Length ◽

Genome Replication ◽

Limiting Step ◽

Replication Systems ◽

Viral Capsid Proteins ◽

Distal Site

ABSTRACT The pre-mRNA processing strategy of the B19 virus is unique among parvoviruses. B19 virus-generated pre-mRNAs are transcribed from a single promoter and are extensively processed by alternative splicing and alternative polyadenylation to generate 12 transcripts. Blockage of the production of full-length B19 virus transcripts at the internal polyadenylation site [(pA)p] was previously reported to be a limiting step in B19 virus permissiveness. We show here that in the absence of genome replication, internal polyadenylation of B19 virus RNAs at (pA)p is favored in cells which are both permissive and nonpermissive for B19 viral replication. Replication of the B19 virus genome, however, introduced either by viral infection or by transfection of an infectious clone into permissive cells or forced by heterologous replication systems in nonpermissive cells, enhanced readthrough of (pA)p and the polyadenylation of B19 virus transcripts at the distal site [(pA)d]. Therefore, replication of the genome facilitates the generation of sufficient full-length transcripts that encode the viral capsid proteins and the essential 11-kDa nonstructural protein. Furthermore, we show that polyadenylation of B19 viral RNA at (pA)p likely competes with splicing at the second intron. Thus, we conclude that replication of the B19 virus genome is the primary limiting step governing B19 virus tropism.

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Virion-like structures in HeLa G cells transfected with the full-length sequence of the hepatitis C virus genome

European Journal of Gastroenterology & Hepatology ◽

10.1097/00042737-199604000-00028 ◽

1996 ◽

Vol 8 (4) ◽

pp. 410

Author(s):

M. Mizuno ◽

G. Yamada ◽

T. Tanaka ◽

K. Shimotohno ◽

M. Takatani ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Virus Genome ◽

Full Length ◽

G Cells ◽

Full Length Sequence

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Signals in the φ29 DNA-terminal protein template for the initiation of phage φ29 DNA replication

Virology ◽

10.1016/0042-6822(86)90209-6 ◽

1986 ◽

Vol 155 (2) ◽

pp. 474-483 ◽

Cited By ~ 26

Author(s):

Julio Gutiérrez ◽

Javier Vinós ◽

Ignacio Prieto ◽

Enrique Méndez ◽

Jose M. Hermoso ◽

...

Keyword(s):

Dna Replication ◽

Terminal Protein ◽

Dna Terminal Protein

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A new full-length virus genome sequencing method reveals that antiviral RNAi changes geminivirus populations in field-grown cassava

10.1101/168724 ◽

2017 ◽

Cited By ~ 1

Author(s):

Devang Mehta ◽

Matthias Hirsch-Hoffmann ◽

Mariam Were ◽

Andrea Patrignani ◽

Hassan Were ◽

...

Keyword(s):

Single Molecule ◽

Deep Sequencing ◽

Cost Effective ◽

Virus Genome ◽

Full Length ◽

Dna Viruses ◽

Circular Dna ◽

Sequencing Technologies ◽

Virus Genomes ◽

And Control

ABSTRACTDeep-sequencing of virus isolates using short-read sequencing technologies is problematic since viruses are often present in complexes sharing a high-degree of sequence identity. The full-length genomes of such highly-similar viruses cannot be assembled accurately from short sequencing reads. We present a new method, CIDER-Seq (Circular DNA Enrichment Sequencing) which successfully generates accurate full-length virus genomes from individual sequencing reads with no sequence assembly required. CIDER-Seq operates by combining a PCR-free, circular DNA enrichment protocol with Single Molecule Real Time sequencing and a new sequence deconcatenation algorithm. We apply our technique to produce more than 1,200 full-length, highly accurate geminivirus genomes from RNAi-transgenic and control plants in a field trial in Kenya. Using CIDER-Seq we can demonstrate for the first time that the expression of antiviral doublestranded RNA (dsRNA) in transgenic plants causes a consistent shift in virus populations towards species sharing low homology to the transgene derived dsRNA. Our results show that CIDER-seq is a powerful, cost-effective tool for accurately sequencing circular DNA viruses, with future applications in deep-sequencing other forms of circular DNA such as transposons and plasmids.

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