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 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 Phylogenetic analysis of canine parvoviruses from Turkey

2020 ◽  
Vol 76 (01) ◽  
pp. 6334-2020
Author(s):  
ZEYNEP AKKUTAY-YOLDAR ◽  
TAYLAN KOÇ B.
Keyword(s):  
High Mortality ◽  
Phylogenetic Trees ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Canine Parvovirus ◽  
Mortality And Morbidity ◽  
Identity Match ◽  
Genomic Characterization

Canine parvovirus (CPV) type 2 is the causative agent of acute hemorrhagic enteritis and high mortality in the affected dogs. Numerous studies have been done to understand the origin of the virus and to exhibit new variants and circulating strains. This report describes the detection and genomic characterization of CPV strains from indoor and outdoor dogs in Ankara, Turkey. Samples were sent to our laboratory due to clinical symptoms in puppies. We tested blood and swab samples to determine the presence of canine parvovirus (CPV) in three puppies and two adult dogs by reverse transcription-polymerase chain reaction (RT-PCR) using VP2 (capsid protein) region primers of canine parvoviruses. Following that, to provide molecular characterization data Maximum Likelihood (ML) method was used for phylogenetic analyses. Constructed phylogenetic trees from the aligned nucleotide sequences revealed that our CPV strains demonstrated high genetic similarities, with 100% identity match on nucleotide alignments with each other and classified in CPV-2b genotypes.They have placed on a monophyletic clade as a sister branch with CPV VAC S quantum with 98.9% nucleotide homology. Our findings suggest that CPV-2b is actual and frequently seen variant in Turkey and shows high similarities with other CPV variants and a bit less with FPVs in Turkey and around the world. CPV causes high mortality and morbidity in dogs and to develop effective vaccines for protection of dogs in Turkey where there are few numbers of studies that have been done, field strains should be isolated and characterised.

scholarly journals African Basil (Ocimum gratissimum) Is a Reservoir of Divergent Begomoviruses in Uganda

Plant Disease ◽  
2020 ◽  
Vol 104 (3) ◽  
pp. 853-859
Author(s):  
Happyness G. Mollel ◽  
Joseph Ndunguru ◽  
Peter Sseruwagi ◽  
Titus Alicai ◽  
John Colvin ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Phylogenetic Analyses ◽  
Plant Viruses ◽  
Wild Plants ◽  
Bipartite Begomoviruses ◽  
Ocimum Gratissimum ◽  
Genomic Characterization ◽  
Open Access Article

Begomoviruses are plant viruses that cause major losses to many economically important crops. Although they are poorly understood, begomoviruses infecting wild plants may have an important role as reservoirs in the epidemiology of viral diseases. This study reports the discovery and genomic characterization of three novel bipartite begomoviruses from wild and cultivated African basil (Ocimum gratissimum) plants collected in Uganda, East Africa. Based on the symptoms shown by the infected plants, the names proposed for these viruses are Ocimum yellow vein virus (OcYVV), Ocimum mosaic virus (OcMV), and Ocimum golden mosaic virus (OcGMV). Genome and phylogenetic analyses suggest that DNA-A of OcGMV is mostly related to begomoviruses infecting tomato in Africa, whereas those of OcYVV and OcMV are closely related to one another and highly divergent within the Old World begomoviruses. The DNA-A of all characterized begomovirus isolates are of a recombinant nature, revealing the role of recombination in the evolution of these begomoviruses. The viruses characterized here are the first identified in O. gratissimum and the first in Ocimum spp. in the African continent and could have important epidemiological consequences for cultivated basils and other important crops. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

scholarly journals Identification and Characterization of Two Novel Geminiviruses Associated with Paper Mulberry (Broussonetia papyrifera) Leaf Curl Disease

Plant Disease ◽  
2020 ◽  
Vol 104 (11) ◽  
pp. 3010-3018 ◽  
Author(s):  
Yuanjian Qiu ◽  
Song Zhang ◽  
Haodong Yu ◽  
Zhiyou Xuan ◽  
Liu Yang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Close Association ◽  
Phylogenetic Analyses ◽  
Rolling Circle Amplification ◽  
Field Investigation ◽  
Broussonetia Papyrifera ◽  
New Members ◽  
Rolling Circle ◽  
Mulberry Leaf ◽  
Leaf Curl

Paper mulberry (Broussonetia papyrifera) is a perennial woody plant used as source material for Cai Lun paper making, in traditional Chinese medicine, and as livestock feed. To identify the presence of viruses in paper mulberry plants affected by a disease with leaf curl symptoms, high-throughput sequencing of total RNA was performed. Analysis of transcriptome libraries allowed the reconstruction of two geminivirus-like genomes. Rolling-circle amplification and PCR with back-to-back primers confirmed the presence of two geminiviruses with monopartite genomes in these plants, with the names paper mulberry leaf curl virus 1 and 2 (PMLCV-1 and PMLCV-2) proposed. The genomes of PMLCV-1 (3,056 nt) and PMLCV-2 (3,757 to 3,763 nt) encode six proteins, with the V4 protein of PMLCV-1 and the V3 proteins of both viruses having low similarities to any known protein in databases. Alternative splicing of an intron, akin to that of mastre-, becurto-, capula-, and grabloviruses, was identified by small RNA (sRNA)-seq and RNA-seq reads mapping to PMLCV-1 and PMLCV-2 antisense transcripts. Phylogenetic analyses and pairwise comparisons showed that PMLCV-1 and PMLCV-2 are most closely related to, but distinct from, two unassigned geminiviruses, citrus chlorotic dwarf associated virus and mulberry mosaic dwarf associated virus, suggesting that they are two new members of the family Geminiviridae. Field investigation confirmed the close association of the two viruses with leaf curl symptoms in paper mulberry plants and that coinfection can aggravate the symptoms.

scholarly journals Human papillomavirus type 38 E6 and E7 act as tumour promoters during chemically induced skin carcinogenesis

2013 ◽  
Vol 94 (4) ◽  
pp. 749-752 ◽  
Author(s):  
Daniele Viarisio ◽  
Karin Müller Decker ◽  
Birgit Aengeneyndt ◽  
Christa Flechtenmacher ◽  
Lutz Gissmann ◽  
...  
Keyword(s):  
Skin Lesions ◽  
Human Papillomaviruses ◽  
Skin Carcinogenesis ◽  
Non Melanoma Skin Cancer ◽  
Multi Stage ◽  
Chemically Induced ◽  
Contrast Exposure ◽  
Tumour Promoters ◽  
Hpv Types ◽  
E6 And E7

Many findings support a possible involvement of a subgroup of human papillomaviruses (HPVs), called cutaneous beta HPV types, in the development of non-melanoma skin cancer. The skin of transgenic (Tg) mice expressing viral oncoproteins E6 and E7 from different cutaneous beta HPV types, including HPV38, showed an increased susceptibility to UV-induced and/or chemically induced skin carcinogenesis compared with wild-type animals. In this study, we show that beta HPV38 E6 and E7 oncoproteins act as promoter and progression factors in multi-stage skin carcinogenesis, strongly cooperating with the initiator and DNA damage agent 7,12-dimethylbenz[a]anthracene. In contrast, exposure of HPV38 E6/E7 Tg mice to the promoter 12-O-tetradecanoylphorbol-13-acetate did not significantly result in the development of skin lesions. These findings further support the role of beta HPV types in skin carcinogenesis, providing additional insight into their precise contribution to the multi-step process.

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 Pseudovirion-binding and neutralizing antibodies to cutaneous human papillomaviruses (HPV) correlated with the presence of HPV DNA in skin

2013 ◽  
Vol 94 (5) ◽  
pp. 1096-1103 ◽  
Author(s):  
Helena Faust ◽  
Kristin Andersson ◽  
Ola Forslund ◽  
Joakim Dillner
Keyword(s):  
Antibody Response ◽  
Cell Carcinoma ◽  
Neutralizing Antibodies ◽  
Skin Lesions ◽  
Human Papillomaviruses ◽  
Serum Samples ◽  
Specific Antibody Response ◽  
Hpv Dna ◽  
Immunosuppressed Patients ◽  
Hpv Types

Whereas the antibody response to the anogenital human papillomaviruses (HPVs) is known to be mainly type-specific, correlated with the presence of viral DNA and mainly directed to conformational epitopes of the virion, it is not known if this applies also to the antibody response to cutaneous HPVs. For 434 non-immunosuppressed patients with skin lesions (squamous cell carcinoma and basal cell carcinoma of the skin, actinic keratosis and benign skin lesions), we compared HPV DNA status with seroreactivity to HPV pseudovirions (PsV) and to GST-L1 fusion proteins from HPV types -5, -6, -15, -16, -32 and -38. Biopsies from the skin lesions were tested for the presence of HPV DNA using three different PCR methods, with typing by sequencing. Serum samples from subjects with HPV DNA-positive biopsies and randomly selected serum samples from subjects with HPV DNA-negative biopsies were also tested with neutralization assays with HPV5, -38 and -76 PsV. Agreement of the three serological methods varied from poor to moderate. Type-specific seroprevalences among patients positive for the same type of HPV DNA (sensitivity of serology) was improved with the PsV-based method (mean of 40 %, maximum 63 %) compared with the GST-L1 method (mean of 20 %, maximum of 25 %). Neutralization was the most sensitive assay for HPV38 (50 %). In summary, cutaneous HPVs also appear to induce a type-specific antibody response that correlates with the presence of HPV DNA and that can be detected with improved sensitivity using PsV-based serology.

scholarly journals Cloning, Structural Characterization, and Phylogenetic Analysis of Flower MADS-Box Genes from Crocus (Crocus sativusL.)

2007 ◽  
Vol 7 ◽  
pp. 1047-1062 ◽  
Author(s):  
Athanasios S. Tsaftaris ◽  
Alexios N. Polidoros ◽  
Konstantinos Pasentsis ◽  
Apostolos Kalivas
Keyword(s):  
Molecular Mechanisms ◽  
Phylogenetic Analyses ◽  
Rolling Circle Amplification ◽  
Crocus Sativus ◽  
Flower Formation ◽  
Mads Box ◽  
Crop Species ◽  
Rolling Circle ◽  
Cdna Sequences ◽  
Single Compound

Crocus (Crocus sativusL.) is a crop species cultivated for its flowers and, more specifically, for its red stigmas. The flower of crocus is bisexual and sterile, since crocus is a triploid species. Its perianth consists of six petaloid tepals: three tepals in whorl 1 (outer tepals) and three tepals in whorl 2 (inner tepals). The androecium consists of three distinct stamens and the gynoecium consists of a single compound pistil with three carpels, a single three-branched style, and an inferior ovary. The dry form of the stigmas constitutes the commercial saffron used as a food additive, in the coloring industry, and in medicine. In order to uncover and understand the molecular mechanisms controlling flower development in cultivated crocus and its relative wild progenitor species, and characterize a number of crocus flower mutants, we have cloned and characterized different, full-length, cDNA sequences encoding MADS-box transcription factor proteins involved in flower formation.Here we review the different methods followed or developed for obtaining these sequences involving conventional 5' 3' RACE, as well as newly developed methods from our group, named Rolling Circle Amplification – RACE (RCA-RACE) and its modification named familyRCA-RACE (famRCA-RACE). Furthermore, the characteristics of the protein structure and their common and specific domains for each type of MADS-box transcription factors in this lower nongrass monocot belonging to the Iridaceae family are described. Finally, a phylogenetic tree of all the MADS-box sequences available in our lab is presented and discussed in relation to other data from studies of species of the Iridaceae group and closely related families from an evolutionary perspective. The structural and phylogenetic analyses are based on both published and unpublished data.

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

2006 ◽  
Vol 87 (12) ◽  
pp. 3551-3557 ◽  
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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