scholarly journals Development of a Novel Rolling-Circle Amplification Technique to Detect Banana streak virus that also Discriminates Between Integrated and Episomal Virus Sequences

Plant Disease ◽  
2011 ◽  
Vol 95 (1) ◽  
pp. 57-62 ◽  
Author(s):  
A. P. James ◽  
R. J. Geijskes ◽  
J. L. Dale ◽  
R. M. Harding
Keyword(s):  
Rolling Circle Amplification ◽  
Cauliflower Mosaic Virus ◽  
Diagnostic Methods ◽  
Streak Virus ◽  
Banana Streak Virus ◽  
Rolling Circle ◽  
Sugarcane Bacilliform Virus ◽  
Amplification Technique ◽  
Banana Streak Ol Virus

Banana plants are hosts to a large number of Banana streak virus (BSV) species. However, diagnostic methods for BSV are inadequate because of the considerable genetic and serological diversity among BSV isolates and the presence of integrated BSV sequences in some banana cultivars which leads to false positives. In this study, a sequence-nonspecific, rolling-circle amplification (RCA) technique was developed and shown to overcome these limitations for the detection and subsequent characterization of BSV isolates infecting banana. This technique was shown to discriminate between integrated and episomal BSV DNA, specifically detecting the latter in several banana cultivars known to contain episomal or integrated sequences of Banana streak Mysore virus (BSMyV), Banana streak OL virus (BSOLV), and Banana streak GF virus (BSGFV). Using RCA, the presence of BSMyV and BSOLV was confirmed in Australia, while BSOLV, BSGFV, Banana streak Uganda I virus (BSUgIV), Banana streak Uganda L virus (BSUgLV), and Banana streak Uganda M virus (BSUgMV) were detected in Uganda. This is the first confirmed report of episomally-derived BSUglV, BSUgLV, and BSUgMV in Uganda. As well as its ability to detect BSV, RCA was shown to detect two other pararetroviruses, Sugarcane bacilliform virus in sugarcane and Cauliflower mosaic virus in turnip.

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 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 Molecular characterization of Banana streak virus isolate from Musa Acuminata in China

2011 ◽  
Vol 26 (6) ◽  
pp. 393-402 ◽  
Author(s):  
Jun Zhuang ◽  
Jian-hua Wang ◽  
Xin Zhang ◽  
Zhi-xin Liu
Keyword(s):  
Molecular Characterization ◽  
Virus Isolate ◽  
Musa Acuminata ◽  
Streak Virus ◽  
Banana Streak Virus

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.

A netlike rolling circle nucleic acid amplification technique

The Analyst ◽  
2015 ◽  
Vol 140 (1) ◽  
pp. 74-78 ◽  
Author(s):  
Xiaoli Zhu ◽  
Chang Feng ◽  
Bin Zhang ◽  
Hui Tong ◽  
Tao Gao ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Rolling Circle Amplification ◽  
Nucleic Acid Amplification ◽  
Amplification Efficiency ◽  
Rolling Circle ◽  
Isothermal Nucleic Acid Amplification ◽  
Amplification Technique ◽  
Nucleic Acid Amplification Technique ◽  
Network Morphology

An isothermal nucleic acid amplification technique termed as netlike rolling circle amplification is proposed. Dense and uniform network morphology of amplified products is first observed, suggesting the ultrahigh amplification efficiency.

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.

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