scholarly journals Identification and genomic characterization of a novel human torque teno virus of 3.2 kb

2007 ◽  
Vol 88 (7) ◽  
pp. 1939-1944 ◽  
Author(s):  
Masashi Ninomiya ◽  
Tsutomu Nishizawa ◽  
Masaharu Takahashi ◽  
Felipe R. Lorenzo ◽  
Tooru Shimosegawa ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Torque Teno Virus ◽  
The Novel ◽  
Entire Genome ◽  
Human Sera ◽  
Genomic Characterization ◽  
Novel Virus ◽  
Entire Genomic Sequence ◽  
Genomic Length

In the process of searching for the recently described small anelloviruses 1 and 2 (SAVs) with the genomic DNA length of 2.2 or 2.6 kb in human sera, we isolated a novel virus with its genomic organization resembling those of torque teno virus (TTV) of 3.8–3.9 kb and torque teno mini virus (TTMV) of 2.8–2.9 kb. The entire genomic sequence of three isolates (MD1-032, MD1-073 and MD2-013), which comprised 3242–3253 bases and exhibited 76–99 % identities with the SAVs within the overlapping sequence, was determined. Although the MD1-032, MD1-073 and MD2-013 isolates differed by 10–28 % from each other over the entire genome, they segregated into the same cluster and were phylogenetically distinguishable from all reported TTVs and TTMVs. These results suggest that SAVs are deletion mutants of the novel virus with intermediate genomic length between those of TTV and TTMV and that the novel virus can be classified into a third group of the genus Anellovirus.

scholarly journals Genomic and evolutionary characterization of TT virus (TTV) in tupaias and comparison with species-specific TTVs in humans and non-human primates

2001 ◽  
Vol 82 (9) ◽  
pp. 2041-2050 ◽  
Author(s):  
Hiroaki Okamoto ◽  
Tsutomu Nishizawa ◽  
Masaharu Takahashi ◽  
Akio Tawara ◽  
Yihong Peng ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
Noncoding Regions ◽  
Tt Virus ◽  
C Terminus ◽  
Species Specific ◽  
Entire Genomic Sequence ◽  
Genomic Length ◽  
Reading Frames

TT virus (TTV) was recovered from the sera of tupaias (Tupaia belangeri chinensis) by PCR using primers derived from the noncoding region of the human TTV genome, and its entire genomic sequence was determined. One tupaia TTV isolate (Tbc-TTV14) consisted of only 2199 nucleotides (nt) and had three open reading frames (ORFs), spanning 1506 nt (ORF1), 177 nt (ORF2) and 642 nt (ORF3), which were in the same orientation as the ORFs of the human prototype TTV (TA278). ORF3 was presumed to arise from a splicing of TTV mRNA, similar to reported human TTVs whose spliced mRNAs have been identified, and encoded a joint protein of 214 amino acids with a Ser-, Lys- and Arg-rich sequence at the C terminus. Tbc-TTV14 was less than 50% similar to previously reported TTVs of 3·4–3·9 kb and TTV-like mini viruses (TLMVs) of 2·8–3·0 kb isolated from humans and non-human primates, and known animal circoviruses. Although Tbc-TTV14 has a genomic length similar to animal circoviruses (1·8–2·3 kb), Tbc-TTV14 resembled TTVs and TLMVs with regard to putative genomic organization and transcription profile. Conserved motifs were commonly observed in the coding and noncoding regions of the Tbc-TTV14 genome and in all TTV and TLMV genomes. Phylogenetic analysis revealed that Tbc-TTV14 is the closest to TLMVs, and is closer to TTVs isolated from tamarin and douroucouli than to TTVs isolated from humans and chimpanzees. These results indicate that tupaias are naturally infected with a new TTV species that has not been identified among primates.

scholarly journals Entire Genomic Sequence of Novel Canine Papillomavirus Type 13

2012 ◽  
Vol 86 (18) ◽  
pp. 10226-10227 ◽  
Author(s):  
Christian E. Lange ◽  
Mathias Ackermann ◽  
Claude Favrot ◽  
Kurt Tobler
Keyword(s):  
Oral Cavity ◽  
Genomic Sequence ◽  
The Novel ◽  
Mucous Membranes ◽  
Novel Virus ◽  
Entire Genomic Sequence

Papillomaviruses are associated with benign and malignant neoplasias of the skin and mucous membranes. The sequence of a novel canine papillomavirus was determined from DNA detected in the oral cavity of a dog. The sequence of the novel virus canine papillomavirus type 13 (CPV13) shares the highest levels of similarity with the Tau papillomaviruses CPV2 and CPV7.

scholarly journals Complete Genome Sequence of an Avian Paramyxovirus Representative of Putative New Serotype 13

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Iryna Goraichuk ◽  
Poonam Sharma ◽  
Borys Stegniy ◽  
Denys Muzyka ◽  
Mary J. Pantin-Jackwood ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The Novel ◽  
Avian Paramyxovirus ◽  
Genomic Characterization

Here, we report the complete genome sequence of a virus of a putative new serotype of avian paramyxovirus (APMV). The virus was isolated from a white-fronted goose in Ukraine in 2011 and designated white-fronted goose/Ukraine/Askania-Nova/48-15-02/2011. The genomic characterization of the isolate suggests that it represents the novel avian paramyxovirus group APMV 13.

scholarly journals A New Flavivirus and a New Vector: Characterization of a Novel Flavivirus Isolated from Uranotaenia Mosquitoes from a Tropical Rain Forest

2009 ◽  
Vol 83 (9) ◽  
pp. 4462-4468 ◽  
Author(s):  
Sandra Junglen ◽  
Anne Kopp ◽  
Andreas Kurth ◽  
Georg Pauli ◽  
Heinz Ellerbrok ◽  
...  
Keyword(s):  
Rain Forest ◽  
Phylogenetic Analyses ◽  
Cell Culture Supernatant ◽  
The Novel ◽  
Glycosylation Sites ◽  
Ns3 Protein ◽  
Distinct Cluster ◽  
Infected Cells ◽  
Novel Virus

ABSTRACT A novel flavivirus was isolated from Uranotaenia mashonaensis, a mosquito genus not previously known to harbor flaviviruses. Mosquitoes were caught in the primary rain forest of the Taï National Park, Côte d'Ivoire. The novel virus, termed nounané virus (NOUV), seemed to grow only on C6/36 insect cells and not on vertebrate cells. Typical enveloped flavivirus-like particles of 60 to 65 nm in diameter were detected by electron microscopy in the cell culture supernatant of infected cells. The full genome was sequenced, and potential cleavage and glycosylation sites and cysteine residues were identified, suggesting that the processing of the NOUV polyprotein is similar to that of other flaviviruses. Phylogenetic analyses of the whole polyprotein and the NS3 protein showed that the virus forms a distinct cluster within the clade of mosquito-borne flaviviruses. Only a distant relationship to other known flaviviruses was found, indicating that NOUV is a novel lineage within the Flaviviridae.

scholarly journals Description of a Novel Monopartite Geminivirus and Its Defective Subviral Genome in Grapevine

2017 ◽  
Vol 107 (2) ◽  
pp. 240-251 ◽  
Author(s):  
Maher Al Rwahnih ◽  
Olufemi J. Alabi ◽  
Nathaniel M. Westrick ◽  
Deborah Golino ◽  
Adib Rowhani
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
The Novel ◽  
The Family ◽  
Circular Ssdna ◽  
Novel Virus ◽  
Full Length Genome ◽  
Nonanucleotide Sequence ◽  
Complementary Sense ◽  
Viral Genomic Sequence

A novel virus was detected in grapevines by Illumina sequencing during the screening of two table grape (Vitis vinifera) accessions, cultivars Black Beet and Nagano Purple, from South Korea. The monopartite circular ssDNA genome sequence was subsequently confirmed by rolling cycle amplification, cloning and Sanger sequencing. The complete viral genomic sequence from both accessions ranged from 2,903 to 2,907 nucleotides in length and contained the conserved nonanucleotide sequence TAATATT↓AC and other sequence features typical of the family Geminiviridae, including two predicted sense and four complementary-sense open reading frames. Phylogenetic analysis placed the novel virus in a unique taxon within the family Geminiviridae. A naturally occurring defective subviral DNA was also discovered. This defective DNA molecule carried a deletion of approximately 46% of the full-length genome. Both the genomic and defective DNA molecules were graft-transmissible although no disease is yet correlated with their occurrence in Vitis spp. The tentative names Grapevine geminivirus A (GGVA) and GGVA defective DNA (GGVA D-DNA) are proposed. PCR assays developed using primers designed in the coat protein gene led to the detection of GGVA in 1.74% of 1,262 vines derived from 15 grapevine cultivars from six countries across three continents.

scholarly journals Genomic characterization of a novel virus found in papillomatous lesions from a southern brown bandicoot (Isoodon obesulus) in Western Australia

Virology ◽  
2008 ◽  
Vol 376 (1) ◽  
pp. 173-182 ◽  
Author(s):  
Mark D. Bennett ◽  
Lucy Woolford ◽  
Hans Stevens ◽  
Marc Van Ranst ◽  
Timothy Oldfield ◽  
...  
Keyword(s):  
Western Australia ◽  
Genomic Characterization ◽  
Novel Virus

scholarly journals Genomic characterization of grapevine virus J, a novel virus identified in grapevine

2018 ◽  
Vol 163 (7) ◽  
pp. 1965-1967 ◽  
Author(s):  
Alfredo Diaz-Lara ◽  
Deborah Golino ◽  
Maher Al Rwahnih
Keyword(s):  
Grapevine Virus ◽  
Genomic Characterization ◽  
Novel Virus

scholarly journals Genomic Characterization of a Novel Virus of the Family Tymoviridae Isolated from Mosquitoes

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e39845 ◽  
Author(s):  
Lihua Wang ◽  
Xinjun Lv ◽  
Yougang Zhai ◽  
Shihong Fu ◽  
David Wang ◽  
...  
Keyword(s):  
The Family ◽  
Genomic Characterization ◽  
Novel Virus

scholarly journals Genomic Characterization of Mycobacteriophage Giles: Evidence for Phage Acquisition of Host DNA by Illegitimate Recombination

2008 ◽  
Vol 190 (6) ◽  
pp. 2172-2182 ◽  
Author(s):  
Peter Morris ◽  
Laura J. Marinelli ◽  
Deborah Jacobs-Sera ◽  
Roger W. Hendrix ◽  
Graham F. Hatfull
Keyword(s):  
Illegitimate Recombination ◽  
Recombination Analysis ◽  
The Novel ◽  
Individual Genome ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Current Perspective ◽  
Recombination Processes ◽  
Genomic Characterization

ABSTRACT A characteristic feature of bacteriophage genomes is that they are architecturally mosaic, with each individual genome representing a unique assemblage of individual exchangeable modules. Plausible mechanisms for generating mosaicism include homologous recombination at shared boundary sequences of module junctions, illegitimate recombination in a non-sequence-directed process, and site-specific recombination. Analysis of the novel mycobacteriophage Giles genome not only extends our current perspective on bacteriophage genetic diversity, with more than 60% of the genes unrelated to other mycobacteriophages, but offers novel insights into how mosaic genomes are created. In one example, the integration/excision cassette is atypically situated within the structural gene operon and could have moved there either by illegitimate recombination or more plausibly via integrase-mediated site-specific recombination. In a second example, a DNA segment has been recently acquired from the host bacterial chromosome by illegitimate recombination, providing further evidence that phage genomic mosaicism is generated by nontargeted recombination processes.

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