A Novel Virus Detected in Papillomas and Carcinomas of the Endangered Western Barred Bandicoot (Perameles bougainville) Exhibits Genomic Features of both the Papillomaviridae and Polyomaviridae

ABSTRACT Conservation efforts to prevent the extinction of the endangered western barred bandicoot (Perameles bougainville) are currently hindered by a progressively debilitating cutaneous and mucocutaneous papillomatosis and carcinomatosis syndrome observed in captive and wild populations. In this study, we detected a novel virus, designated the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1), in lesional tissue from affected western barred bandicoots using multiply primed rolling-circle amplification and PCR with the cutaneotropic papillomavirus primer pairs FAP59/FAP64 and AR-L1F8/AR-L1R9. Sequencing of the BPCV1 genome revealed a novel prototype virus exhibiting genomic properties of both the Papillomaviridae and the Polyomaviridae. Papillomaviral properties included a large genome size (∼7.3 kb) and the presence of open reading frames (ORFs) encoding canonical L1 and L2 structural proteins. The genomic organization in which structural and nonstructural proteins were encoded on different strands of the double-stranded genome and the presence of ORFs encoding the nonstructural proteins large T and small t antigens were, on the other hand, typical polyomaviral features. BPCV1 may represent the first member of a novel virus family, descended from a common ancestor of the papillomaviruses and polyomaviruses recognized today. Alternatively, it may represent the product of ancient recombination between members of these two virus families. The discovery of this virus could have implications for the current taxonomic classification of Papillomaviridae and Polyomaviridae and can provide further insight into the evolution of these ancient virus families.

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Isolation and cloning of a papillomavirus from a North American porcupine by using multiply primed rolling-circle amplification: the Erethizon dorsatum papillomavirus type 1

Virology ◽

10.1016/j.virol.2004.10.033 ◽

2005 ◽

Vol 331 (2) ◽

pp. 449-456 ◽

Cited By ~ 28

Author(s):

Annabel Rector ◽

Ruth Tachezy ◽

Koenraad Van Doorslaer ◽

Tracey MacNamara ◽

Robert D. Burk ◽

...

Keyword(s):

North American ◽

Rolling Circle Amplification ◽

Rolling Circle ◽

Erethizon Dorsatum

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Analysis of transcription of Porcine circovirus type 1

Journal of General Virology ◽

10.1099/0022-1317-83-11-2743 ◽

2002 ◽

Vol 83 (11) ◽

pp. 2743-2751 ◽

Cited By ~ 32

Author(s):

Annette Mankertz ◽

Bernd Hillenbrand

Keyword(s):

Infectious Clone ◽

Porcine Circovirus Type ◽

Open Reading Frames ◽

Porcine Circovirus ◽

Origin Of Replication ◽

Rolling Circle Replication ◽

Structural Protein ◽

Rolling Circle ◽

Rep Protein

Porcine circovirus type 1 (PCV1) contains two major open reading frames encoding the replication initiator proteins, Rep and Rep′, and the structural protein, Cap. The promoters of these two genes (P cap and P rep ) have been mapped. P cap is located within the rep open reading frame (nt 1328–1252). P rep has been mapped to the intergenic region immediately upstream of the rep gene (nt 640–796) and overlaps the origin of replication of PCV1. Although binding of both rep gene products to a fragment containing P rep and the overlapping origin of replication has been reported, only the full-length Rep protein repressed P rep , while the spliced isoform Rep′ did not. P rep repression is mediated by binding of the Rep protein to the two inner hexamers, H1 and H2, located in the origin of PCV1, whereas binding of Rep to hexamers H3 and H4 was not necessary. Use of Rep mutants indicated that the conserved rolling-circle replication domain II as well as the P loop are essential for repression of P rep . In contrast to P rep , transcription of P cap was not influenced by viral proteins. Additionally, the ratio of the rep and rep′ transcripts was analysed. Twelve hours after transfection of PK15 cells with an infectious clone of PCV1, similar amounts of both transcripts were detected, but later the amount of the two transcripts varied, indicating a balanced expression of the two rep transcripts.

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Detection of the prototype of a potential novel genus in the family Papillomaviridae in association with canine epidermodysplasia verruciformis

Journal of General Virology ◽

10.1099/vir.0.82305-0 ◽

2006 ◽

Vol 87 (12) ◽

pp. 3551-3557 ◽

Cited By ~ 36

Author(s):

Kurt Tobler ◽

Claude Favrot ◽

Gilles Nespeca ◽

Mathias Ackermann

Keyword(s):

Rolling Circle Amplification ◽

Malignant Lesion ◽

Human Papillomaviruses ◽

Epidermodysplasia Verruciformis ◽

The Novel ◽

Novel Genus ◽

Rolling Circle ◽

The Family ◽

L1 And L2 ◽

Flat Warts

Epidermodysplasia verruciformis (EV) is a rare human genetic predisposition to develop flat warts, some of which subsequently undergo cancer transformation. Some human papillomaviruses (HPVs), i.e. HPV 5 and 8, have been associated with cancer development as a sequela of EV. As similar diseases have been observed in dogs, it was hypothesized that unknown canine papillomaviruses (CPVs) may exist and that they may be present in cases of canine EV. Consequently, DNA was extracted from a malignant lesion of a dog with EV and circular DNA was amplified by multiple-primed rolling-circle amplification (RCA). Indeed, sequence determination and analysis of the RCA-amplified and cloned DNA from a malignant canine EV lesion resulted in the detection and primary description of a third CPV (CPV3). Typical papillomavirus genes were identified, with deduced amino acid similarities ranging from 20 to 57 % for E1, E2, E6, E7, L1 and L2, respectively. According to the sequence of the L1 gene, which is used for papillomavirus classification, the new isolate meets the majority of criteria needed to declare detection of a novel genus among the papillomaviruses. Thus, CPV3 may represent the prototype of this novel genus. As the novel virus was found in a dog in association with lesions reminiscent of human EV, it should be interesting to test in the future whether this condition can be reproduced in experimental animals. If such were the case, a new model for EV could be established.

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Genome of a novel circovirus of starlings, amplified by multiply primed rolling-circle amplification

Journal of General Virology ◽

10.1099/vir.0.81561-0 ◽

2006 ◽

Vol 87 (5) ◽

pp. 1189-1195 ◽

Cited By ~ 59

Author(s):

Reimar Johne ◽

Daniel Fernández-de-Luco ◽

Ursula Höfle ◽

Hermann Müller

Keyword(s):

Rolling Circle Amplification ◽

Open Reading Frames ◽

Degenerate Primers ◽

Rolling Circle ◽

Specific Pcr ◽

Sturnus Unicolor ◽

Evolutionarily Conserved ◽

Degree Of Similarity ◽

Reading Frames ◽

Apparently Healthy

The genus Circovirus comprises small non-enveloped viruses with a circular single-stranded DNA genome. By using PCR with degenerate primers, a novel circovirus (starling circovirus, StCV) was detected in spleen samples of wild starlings (Sturnus vulgaris and Sturnus unicolor) found dead during an epidemic outbreak of septicaemic salmonellosis in northeastern Spain. Using a specific PCR, StCV was also detected in apparently healthy birds from the same population. The genome was amplified using multiply primed rolling-circle amplification and cloned. Open reading frames (ORFs) with similarities to the replication-associated protein and the capsid protein of circoviruses as well as an additional ORF encoding a protein of 106 aa were evident from the sequence. Phylogenetic analysis of circovirus genomes revealed the highest degree of similarity (67·1 %) between StCV and canary circovirus. A similar analysis of the evolutionarily conserved cytochrome b gene of the circovirus host species revealed a strict co-evolution of circoviruses with their hosts; however, the circoviruses showed about a threefold higher genetic divergence than their hosts.

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Herpes Simplex Virus Type 1 Co-Infection Leads to the Formation of Rolling Circle Amplification-Like Adeno-Associated Virus DNA Replication Products

10.1101/2020.12.23.424160 ◽

2020 ◽

Author(s):

Anita F. Meier ◽

Kurt Tobler ◽

Remo Leisi ◽

Anouk Lkharrazi ◽

Carlos Ros ◽

...

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Rolling Circle Amplification ◽

Helper Virus ◽

Genome Replication ◽

Adeno Associated Virus ◽

Rolling Circle ◽

Simplex Virus ◽

Hsv 1

ABSTRACTAdeno-associated virus (AAV) genome replication only occurs in the presence of a co-infecting helper virus such as adenovirus type 5 (AdV5) or herpes simplex virus type 1 (HSV-1). AdV5-supported replication of the AAV genome has been described to occur in a strand-displacement rolling hairpin mechanism initiated at the AAV 3’ inverted terminal repeat (ITR) end. It has been assumed that the same mechanism applies to HSV-1-supported AAV genome replication. We demonstrate the formation of double-stranded head-to-tail concatemers of AAV genomes in presence of HSV-1, and thus provide evidence for an unequivocal rolling circle amplification (RCA) mechanism. This study reveals the ability of AAV to modify the canonical rolling hairpin replication mechanism and to mimic the replication strategy of a co-infecting herpesvirus. This stands in contrast to the textbook model of AAV genome replication when HSV-1 is the helper virus. Furthermore, we introduce nanopore sequencing as a novel, high-throughput approach to study viral genome replication in unprecedented detail.

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Complete genome and phylogenetic position of bovine papillomavirus type 7

Journal of General Virology ◽

10.1099/vir.0.82794-0 ◽

2007 ◽

Vol 88 (7) ◽

pp. 1934-1938 ◽

Cited By ~ 41

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.

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Identification of a Novel Geminivirus in Fraxinus rhynchophylla in Korea

Viruses ◽

10.3390/v13122385 ◽

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.

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Isolation and cloning of two variant papillomaviruses from domestic pigs: Sus scrofa papillomaviruses type 1 variants a and b

Journal of General Virology ◽

10.1099/vir.0.2008/003186-0 ◽

2008 ◽

Vol 89 (10) ◽

pp. 2475-2481 ◽

Cited By ~ 18

Author(s):

Hans Stevens ◽

Annabel Rector ◽

Kees Van Der Kroght ◽

Marc Van Ranst

Keyword(s):

Sus Scrofa ◽

Open Reading Frames ◽

Domestic Pigs ◽

Transposon Insertion ◽

Insertion Method ◽

Nucleotide Sequence Alignment ◽

L1 And L2 ◽

Similarity Searches ◽

Sus Scrofa Domestica

The healthy skin of two female domestic pigs (Sus scrofa domestica) was sampled with cotton-tipped swabs. Total genomic DNA was extracted from the samples and subjected to PCR with degenerate papillomavirus (PV)-specific primers. Similarity searches performed with blastn showed that partial E1 and L1 sequences of two novel PVs were amplified. Subsequently, the complete genomes of these Sus scrofa papillomaviruses (SsPVs) were amplified by long-template PCR, cloned and sequenced using a transposon insertion method. They contained the typical PV open reading frames (ORFs) E1, E2, E4, E6, L1 and L2, but the E7 ORF was absent in both viruses. Pairwise nucleotide sequence alignment of the L1 ORFs of the SsPVs showed 98.5 % similarity, classifying these viruses as SsPV type 1 ‘variants’ (SsPV-1a and -1b). Based on a concatenated alignment of the E1, E2, L1 and L2 ORFs of SsPV-1 variants a and b, and 81 other human and animal PV type species, a neighbour-joining phylogenetic tree was constructed. This phylogenetic analysis showed that the SsPV-1a and -1b variants did not cluster with the other PVs of artiodactyls (cloven-hoofed) host species, but clustered on the edge of the genus Alphapapillomavirus, very near to the root of this genus.

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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

Journal of Virology ◽

10.1128/jvi.78.22.12698-12702.2004 ◽

2004 ◽

Vol 78 (22) ◽

pp. 12698-12702 ◽

Cited By ~ 61

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.

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Ferromagnetic Resonance Biosensor for Homogeneous and Volumetric Detection of DNA

10.26434/chemrxiv.5662315.v1 ◽

2017 ◽

Author(s):

Bo Tian ◽

Peter Svedlindh ◽

Mattias Strömberg ◽

Erik Wetterskog

Keyword(s):

Magnetic Nanoparticles ◽

Ferromagnetic Resonance ◽

Limit Of Detection ◽

Point Of Care ◽

Rolling Circle Amplification ◽

Resonance Field ◽

Isothermal Amplification ◽

Detection Sensitivity ◽

Serum Samples ◽

Rolling Circle

In this work, we demonstrate for the first time, a ferromagnetic resonance (FMR) based homogeneous and volumetric biosensor for magnetic label detection. Two different isothermal amplification methods, i.e., rolling circle amplification (RCA) and loop-mediated isothermal amplification (LAMP) are adopted and combined with a standard electron paramagnetic resonance (EPR) spectrometer for FMR biosensing. For RCA-based FMR biosensor, binding of RCA products of a synthetic Vibrio cholerae target DNA sequence gives rise to the formation of aggregates of magnetic nanoparticles. Immobilization of nanoparticles within the aggregates leads to a decrease of the net anisotropy of the system and a concomitant increase of the resonance field. A limit of detection of 1 pM is obtained with an average coefficient of variation of 0.16%, which is superior to the performance of other reported RCA-based magnetic biosensors. For LAMP-based sensing, a synthetic Zika virus target oligonucleotide is amplified and detected in 20% serum samples. Immobilization of magnetic nanoparticles is induced by their co-precipitation with Mg2P2O7 (a by-product of LAMP) and provides a detection sensitivity of 100 aM. The fast measurement, high sensitivity and miniaturization potential of the proposed FMR biosensing technology makes it a promising candidate for designing future point-of-care devices.

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