scholarly journals Characterization of Two Novel Polyomaviruses of Birds by Using Multiply Primed Rolling-Circle Amplification of Their Genomes

2006 ◽  
Vol 80 (7) ◽  
pp. 3523-3531 ◽  
Author(s):  
Reimar Johne ◽  
Walter Wittig ◽  
Daniel Fernández-de-Luco ◽  
Ursula Höfle ◽  
Hermann Müller
Keyword(s):  
Rolling Circle Amplification ◽  
Large Tumor ◽  
Rolling Circle ◽  
Reading Frame ◽  
Field Samples ◽  
Close Relationship ◽  
Avian Polyomavirus ◽  
Avian Group ◽  
Pyrrhula Pyrrhula

ABSTRACT Polyomaviruses are small nonenveloped particles with a circular double-stranded genome, approximately 5 kbp in size. The mammalian polyomaviruses mainly cause persistent subclinical infections in their natural nonimmunocompromised hosts. In contrast, the polyomaviruses of birds—avian polyomavirus (APV) and goose hemorrhagic polyomavirus (GHPV)—are the primary agents of acute and chronic disease with high mortality rates in young birds. Screening of field samples of diseased birds by consensus PCR revealed the presence of two novel polyomaviruses in the liver of an Eurasian bullfinch (Pyrrhula pyrrhula griseiventris) and in the spleen of a Eurasian jackdaw (Corvus monedula), tentatively designated as finch polyomavirus (FPyV) and crow polyomavirus (CPyV), respectively. The genomes of the viruses were amplified by using multiply primed rolling-circle amplification and cloned. Analysis of the FPyV and CPyV genome sequences revealed a close relationship to APV and GHPV, indicating the existence of a distinct avian group among the polyomaviruses. The main characteristics of this group are (i) involvement in fatal disease, (ii) the existence of an additional open reading frame in the 5′ region of the late mRNAs, and (iii) a different manner of DNA binding of the large tumor antigen compared to that of the mammalian polyomaviruses.

scholarly journals Circular genomes related to anelloviruses identified in human and animal samples by using a combined rolling-circle amplification/sequence-independent single primer amplification approach

2007 ◽  
Vol 88 (10) ◽  
pp. 2696-2701 ◽  
Author(s):  
Philippe Biagini ◽  
Rathviro Uch ◽  
Mourad Belhouchet ◽  
Houssam Attoui ◽  
Jean-François Cantaloube ◽  
...  
Keyword(s):  
Human Plasma ◽  
Genetic Divergence ◽  
Rolling Circle Amplification ◽  
Plasma Samples ◽  
Rolling Circle ◽  
Human Plasma Samples ◽  
Single Primer ◽  
Divergent Sequences

A combined rolling-circle amplification (RCA) and sequence-independent single primer amplification (SISPA) approach was applied to four samples of human plasma and one sample of saliva from a cat. This approach permitted the characterization of nine anelloviruses. Most of them were identified as highly divergent strains that were classified into species of the genus Anellovirus. The smallest anellovirus described so far in humans was characterized (2PoSMA, 2002 nt; ‘small anellovirus’ species). Two highly divergent sequences belonging to the species Torque Teno Mini Virus (LIL-y1, 2887 nt; LIL-y2, 2871 nt), which clustered into a new phylogenetic branch, were also identified in human plasma samples. Finally, two genomes that are separated by a genetic divergence of 46 % were characterized in the cat's saliva, one of these creating a distinct phylogenetic branch (PRA1, 2019 nt). These results highlight the potential of RCA–SISPA for detecting circular (or circularized) genomes.

scholarly journals Blueberry fruit drop-associated virus: A New Member of the Family Caulimoviridae Isolated From Blueberry Exhibiting Fruit-Drop Symptoms

Plant Disease ◽  
2016 ◽  
Vol 100 (11) ◽  
pp. 2211-2214 ◽  
Author(s):  
Alfredo Diaz-Lara ◽  
Robert R. Martin
Keyword(s):  
Rolling Circle Amplification ◽  
The United States ◽  
Washington State ◽  
Cloning And Sequencing ◽  
Rolling Circle ◽  
Reading Frame ◽  
Fruit Drop ◽  
Perfect Correlation ◽  
The Family ◽  
Single Field

This study describes the nucleotide sequence and genome organization of a new DNA virus isolated from ‘Bluecrop’ blueberry plants exhibiting fruit-drop symptoms and named Blueberry fruit drop-associated virus (BFDaV). Blueberry fruit drop disease was first detected in blueberry plants in British Columbia, Canada in the late 1990s, and in a single field in northern Washington state in the United States in 2012. Infected bushes abort nearly 100% of their fruit about three weeks prior to harvest, when the berries are about 3 to 5 mm in diameter. At harvest, the affected plants appear taller than healthy ones as there is no fruit weighing down the branches. The virus was amplified from diseased material using rolling circle amplification, followed by enzyme digestion, cloning, and sequencing. The full genome of BFDaV is 9,850 bp in length and contains a single open reading frame, encoding for a polyprotein, and a large noncoding region. Based on the genome size and organization and phylogenetics, BFDaV is proposed as a new and the largest member of family Caulimoviridae. Finally, in mapping part of a field with fruit-drop symptoms, there was a nearly perfect correlation between the presence of the virus and fruit-drop symptoms.

scholarly journals Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 202 ◽  
Author(s):  
Verónica A. Bornancini ◽  
José M. Irazoqui ◽  
Ceferino R. Flores ◽  
Carlos G. Vaghi Medina ◽  
Ariel F. Amadio ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Full Length ◽  
Yellow Spot ◽  
Streak Virus ◽  
Rolling Circle ◽  
Viral Particles ◽  
Bipartite Genome ◽  
First Time ◽  
Leaf Virus

In northwestern Argentina (NWA), pepper crops are threatened by the emergence of begomoviruses due to the spread of its vector, Bemisia tabaci (Gennadius). The genus Begomovirus includes pathogens that can have a monopartite or bipartite genome and are occasionally associated with sub-viral particles called satellites. This study characterized the diversity of begomovirus and alphasatellite species infecting pepper in NWA using a metagenomic approach. Using RCA-NGS (rolling circle amplification-next generation sequencing), 19 full-length begomovirus genomes (DNA-A and DNA-B) and one alphasatellite were assembled. This ecogenomic approach revealed six begomoviruses in single infections: soybean blistering mosaic virus (SbBMV), tomato yellow spot virus (ToYSV), tomato yellow vein streak virus (ToYVSV), tomato dwarf leaf virus (ToDfLV), sida golden mosaic Brazil virus (SiGMBRV), and a new proposed species, named pepper blistering leaf virus (PepBLV). SbBMV was the most frequently detected species, followed by ToYSV. Moreover, a new alphasatellite associated with ToYSV, named tomato yellow spot alphasatellite 2 (ToYSA-2), was reported for the first time in Argentina. For the Americas, this was the first report of an alphasatellite found in a crop (pepper) and in a weed (Leonurus japonicus). We also detected intra-species and inter-species recombination.

scholarly journals Characterization of Binding of Magnetic Nanoparticles to Rolling Circle Amplification Products by Turn-On Magnetic Assay

Biosensors ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 109 ◽  
Author(s):  
Sobhan Sepehri ◽  
Björn Agnarsson ◽  
Teresa Zardán Gómez de la Torre ◽  
Justin F. Schneiderman ◽  
Jakob Blomgren ◽  
...  
Keyword(s):  
Magnetic Nanoparticles ◽  
Specific Binding ◽  
Ac Susceptibility ◽  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
Low Concentrations ◽  
Assay Performance ◽  
Particle Ensemble ◽  
Kinetics Of

The specific binding of oligonucleotide-tagged 100 nm magnetic nanoparticles (MNPs) to rolling circle products (RCPs) is investigated using our newly developed differential homogenous magnetic assay (DHMA). The DHMA measures ac magnetic susceptibility from a test and a control samples simultaneously and eliminates magnetic background signal. Therefore, the DHMA can reveal details of binding kinetics of magnetic nanoparticles at very low concentrations of RCPs. From the analysis of the imaginary part of the DHMA signal, we find that smaller MNPs in the particle ensemble bind first to the RCPs. When the RCP concentration increases, we observe the formation of agglomerates, which leads to lower number of MNPs per RCP at higher concentrations of RCPs. The results thus indicate that a full frequency range of ac susceptibility observation is necessary to detect low concentrations of target RCPs and a long amplification time is not required as it does not significantly increase the number of MNPs per RCP. The findings are critical for understanding the underlying microscopic binding process for improving the assay performance. They furthermore suggest DHMA is a powerful technique for dynamically characterizing the binding interactions between MNPs and biomolecules in fluid volumes.

scholarly journals Genomic characterization of ten novel cutaneous human papillomaviruses from keratotic lesions of immunosuppressed patients

2011 ◽  
Vol 92 (7) ◽  
pp. 1585-1594 ◽  
Author(s):  
Anja Köhler ◽  
Marc Gottschling ◽  
Kizzie Manning ◽  
Mandy D. Lehmann ◽  
Eric Schulz ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Rolling Circle Amplification ◽  
Organ Transplant ◽  
Human Papillomaviruses ◽  
Rolling Circle ◽  
Non Melanoma Skin Cancer ◽  
Immunosuppressed Patients ◽  
Genomic Characterization ◽  
Hpv Types

Viral warts from immunosuppressed organ transplant recipients (OTR) persist over years and may progress into non-melanoma skin cancer. The types of human papillomaviruses (HPV) in such lesions are different from that seen in the general population. A subset of these lesions is not infected with the classical wart-associated HPV types. In order to gain a better understanding of the HPV types in those lesions, we isolated ten novel HPVs from persisting keratotic lesions of immunosuppressed OTRs by rolling circle amplification and subsequent long-template PCR. Additionally, we sequenced and characterized the whole genome of the ten novel HPV types. Phylogenetic analyses revealed that nine HPV types belonged to the genus Gammapapillomavirus (γ-PV) and one to the genus Betapapillomavirus. In a phylogenetic analysis using L1 fragments of human and non-human PV types, primate papillomaviruses and our novel HPV types nested within the genus γ-PV in a highly polyphyletic pattern. This study significantly broadens the knowledge concerning the diversity and evolution of the poorly known γ-PV types.

scholarly journals Assessment and optimization of rolling circle amplification protocols for the detection and characterization of badnaviruses

Virology ◽  
2019 ◽  
Vol 529 ◽  
pp. 73-80 ◽  
Author(s):  
Amit C. Sukal ◽  
Dawit B. Kidanemariam ◽  
James L. Dale ◽  
Robert M. Harding ◽  
Anthony P. James
Keyword(s):  
Rolling Circle Amplification ◽  
Rolling Circle

scholarly journals Complete genome and phylogenetic position of bovine papillomavirus type 7

2007 ◽  
Vol 88 (7) ◽  
pp. 1934-1938 ◽  
Author(s):  
Tomoko Ogawa ◽  
Yoshimi Tomita ◽  
Mineyuki Okada ◽  
Hiroshi Shirasawa
Keyword(s):  
Complete Genome ◽  
Rolling Circle Amplification ◽  
Phylogenetic Position ◽  
Bovine Papillomavirus ◽  
Rolling Circle ◽  
Reading Frame ◽  
E6 And E7 ◽  
Lxcxe Motif ◽  
Zinc Binding Domain ◽  
L1 And L2

Six bovine papillomavirus (BPV) types and 16 putative BPV types have been reported previously. Here, the complete genome sequence of BAPV6, a novel putative BPV type isolated from cattle in Japan, was determined by using multiple-primed rolling-circle amplification. The genome consisted of 7412 bp (G+C content of 46 mol%) that encoded five early (E1, E2, E4, E6 and E7) and two late (L1 and L2) genes, but did not encode the E5 gene. The E6 protein contained a non-consensus CxxC(x)33CxxC and a consensus CxxC(x)29CxxC zinc-binding domain, and the E7 protein lacked the LxCxE motif. The nucleotide sequence of the L1 open reading frame (ORF) was related most closely (57–58 %) to the L1 ORF of member(s) of the genera Betapapillomavirus, Gammapapillomavirus and Pipapillomavirus. Phylogenetic analysis based on the complete L1 ORF suggests that BAPV6 should be classified in a novel genus in the family Papillomaviridae as BPV-7.

scholarly journals Identification of a Novel Geminivirus in Fraxinus rhynchophylla in Korea

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2385
Author(s):  
Aamir Lal ◽  
Yong-Ho Kim ◽  
Thuy Thi Bich Vo ◽  
I Gusti Ngurah Prabu Wira Sanjaya ◽  
Phuong Thi Ho ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Indian Subcontinent ◽  
Chemical Constituents ◽  
Rolling Circle Amplification ◽  
Open Reading Frames ◽  
Stem Loop ◽  
Rolling Circle ◽  
Reading Frame ◽  
Infectious Clones ◽  
Ash Trees

Fraxinus rhynchophylla, common name ash, belongs to the family Oleaceae and is found in China, Korea, North America, the Indian subcontinent, and eastern Russia. It has been used as a traditional herbal medicine in Korea and various parts of the world due to its chemical constituents. During a field survey in March 2019, mild vein thickening (almost negligible) was observed in a few ash trees. High-throughput sequencing of libraries of total DNA from ash trees, rolling-circle amplification (RCA), and polymerase chain reaction (PCR) allowed the identification of a Fraxinus symptomless virus. This virus has five confirmed open reading frames along with a possible sixth open reading frame that encodes the movement protein and is almost 2.7 kb in size, with a nonanucleotide and stem loop structure identical to begomoviruses. In terms of its size and structure, this virus strongly resembles begomoviruses, but does not show any significant sequence identity with them. To confirm movement of the virus within the trees, different parts of infected trees were examined, and viral movement was successfully observed. No satellite molecules or DNA B were identified. Two-step PCR confirmed the virion and complementary strands during replication in both freshly collected infected samples of ash tree and Nicotiana benthamiana samples agro-inoculated with infectious clones. This taxon is so distantly grouped from other known geminiviruses that it likely represents a new geminivirus genus.

Characterization of putative circular plasmids in sponge‐associated bacterial communities using a selective multiply‐primed rolling circle amplification

2020 ◽  
Vol 21 (1) ◽  
pp. 110-121
Author(s):  
Vanessa Oliveira ◽  
Ana R. M. Polónia ◽  
Daniel F. R. Cleary ◽  
Yusheng M. Huang ◽  
Nicole J. Voogd ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rolling Circle Amplification ◽  
Rolling Circle

scholarly journals Characterization of a Novel Close-to-Root Papillomavirus from a Florida Manatee by Using Multiply Primed Rolling-Circle Amplification: Trichechus manatus latirostris Papillomavirus Type 1

2004 ◽  
Vol 78 (22) ◽  
pp. 12698-12702 ◽  
Author(s):  
Annabel Rector ◽  
Gregory D. Bossart ◽  
Shin-Je Ghim ◽  
John P. Sundberg ◽  
A. Bennett Jenson ◽  
...  
Keyword(s):  
Marine Mammals ◽  
Rolling Circle Amplification ◽  
Phylogenetic Position ◽  
Florida Manatee ◽  
Trichechus Manatus ◽  
Trichechus Manatus Latirostris ◽  
Rolling Circle ◽  
Amplification Protocol

ABSTRACT By using an isothermal multiply primed rolling-circle amplification protocol, the complete genomic DNA of a novel papillomavirus was amplified from a skin lesion biopsy of a Florida manatee (Trichechus manatus latirostris), one of the most endangered marine mammals in United States coastal waters. The nucleotide sequence, genome organization, and phylogenetic position of the Trichechus manatus latirostris papillomavirus type 1 (TmPV-1) were determined. TmPV-1 is the first virus isolated from the order of Sirenia. A phylogenetic analysis shows that TmPV-1 is only distantly related to other papillomavirus sequences, and it appears in our phylogenetic tree as a novel close-to-root papillomavirus genus.

Sign in / Sign up

Export Citation Format

Share Document