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.

scholarly journals 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

2007 ◽  
Vol 81 (24) ◽  
pp. 13280-13290 ◽  
Author(s):  
Lucy Woolford ◽  
Annabel Rector ◽  
Marc Van Ranst ◽  
Andrea Ducki ◽  
Mark D. Bennett ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Open Reading Frames ◽  
Nonstructural Proteins ◽  
T Antigens ◽  
Virus Family ◽  
Rolling Circle ◽  
Large Genome Size ◽  
Novel Virus ◽  
L1 And L2

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.

scholarly journals Fundicoccus ignavus gen. nov., sp. nov., a novel genus of the family Aerococcaceae isolated from bulk tank milk

2020 ◽  
Vol 70 (8) ◽  
pp. 4774-4781 ◽  
Author(s):  
Annemarie Siebert ◽  
Christopher Huptas ◽  
Mareike Wenning ◽  
Siegfried Scherer ◽  
Etienne V. Doll
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Bulk Tank Milk ◽  
Novel Genus ◽  
Content Type ◽  
Link Type ◽  
A Genome ◽  
The Family ◽  
Bulk Tank

Three strains of a Gram-stain-positive, catalase-negative, facultative anaerobic, and coccoid species were isolated from German bulk tank milk. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that the three strains (WS4937T, WS4759 and WS5303) constitute an independent phylogenetic lineage within the family Aerococcaceae with Facklamia hominis CCUG 36813T (93.7–94.1 %) and Eremococcus coleocola M1831/95/2T (93.5 %) as most closely related type species. The unclassified strains demonstrated variable growth with 6.5 % (w/v) NaCl and tolerated pH 6.5–9.5. Growth was observed from 12 to 39 °C. Their cell-wall peptidoglycan belongs to the A1α type (l-Lys-direct) consisting of alanine, glutamic acid and lysine. The predominant fatty acids were C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c and in the polar lipids profile three glycolipids, a phospholipid, phosphatidylglycerol, phosphoglycolipid and diphosphatidylglycerol were found. The G+C content of strain WS4937T was 37.4 mol% with a genome size of ~3.0 Mb. Based on phylogenetic, phylogenomic and biochemical characterizations, the isolates can be demarcated from all other genera of the family Aerococcaceae and, therefore, the novel genus Fundicoccus gen. nov. is proposed. The type species of the novel genus is Fundicoccus ignavus gen. nov., sp. nov. WS4937T (=DSM 109652T=LMG 31441T).

Identification of Extrachromosomal Circular DNA in Hop via Rolling Circle Amplification

2016 ◽  
Vol 148 (2-3) ◽  
pp. 237-240 ◽  
Author(s):  
Alfredo Diaz-Lara ◽  
David H. Gent ◽  
Robert R. Martin
Keyword(s):  
Electron Microscopy ◽  
Sequence Analysis ◽  
Higher Plants ◽  
Rolling Circle Amplification ◽  
Small Region ◽  
Extrachromosomal Dna ◽  
Circular Dna ◽  
Rolling Circle ◽  
Dna Molecule ◽  
The Family

During a survey for new viruses affecting hop plants, a circular DNA molecule was identified via rolling circle amplification (RCA) and later characterized. A small region of the 5.7-kb long molecule aligned with a microsatellite region in the Humulus lupulus genome, and no coding sequence was identified. Sequence analysis and literature review suggest that the small DNA molecule is an extranuclear DNA element, specifically, an extrachromosomal circular DNA (eccDNA), and its presence was confirmed by electron microscopy. This work is the first report of eccDNAs in the family Cannabaceae. Additionally, this work highlights the advantages of using RCA to study extrachromosomal DNA in higher plants.

scholarly journals Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacifica corrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae

2020 ◽  
Vol 70 (3) ◽  
pp. 2147-2154 ◽  
Author(s):  
Guang-Da Feng ◽  
Xian-Jiao Zhang ◽  
Song-Zhen Yang ◽  
An-Zhang Li ◽  
Qing Yao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
New Genus ◽  
The Novel ◽  
New Combinations ◽  
Novel Genus ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Insight Into

During a phylogenetic analysis of Sphingorhabdus and its closely related genera in the family Sphingomonadaceae , we found that the genus Sphingorhabdus and the species Sphingopyxis baekryungensis might not be properly assigned in the taxonomy. Phylogenetic, phenotypic and chemotaxonomic characterizations clearly showed that the genus Sphingorhabdus should be reclassified into two genera (Clade I and Clade II), for which the original genus name, Sphingorhabdus , is proposed to be retained only for Clade I, and a new genus named as Parasphingorhabdus gen. nov. is proposed for Clade II with four new combinations: Parasphingorhabdus marina comb. nov., Parasphingorhabdus litoris comb. nov., Parasphingorhabdus flavimaris comb. nov. and Parasphingorhabdus pacifica comb. nov. Moreover, Sphingopyxis baekryungensis should represent a novel genus in the family Sphingomonadaceae , for which the name Novosphingopyxis gen. nov. is proposed, with a combination of Novosphingopyxis baekryungensis comb. nov. The study provides a new insight into the taxonomy of closely related genera in the family Sphingomonadaceae .

scholarly journals Four New Members of The Family Cytophagaceae: Cryseosolum Histidinii gen. nov., sp. nov., Cryseosolum Indiensis gen. nov., sp. nov., Reichenbachia Cretensis, gen. nov., sp. nov., and Reichenbachia Soli, gen. nov., sp. nov. Isolated From Diverse Habitat

2022 ◽  
Author(s):  
Senlie Octaviana ◽  
Stefan Lorenczyk ◽  
Frederike Ackert ◽  
Joachim Wink
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
New Members ◽  
Novel Genus ◽  
Crete Island ◽  
The Family

Abstract Four strains isolated, PWU4T, PWU20T, PWU5T and PWU37T were from both of soil in Germany, India and a faces sheep collected in Crete Island, respectively. Cells were Gram-negative, strictly aerobic, rod shaped, grew optimally between 28oC and 34oC, pH between 7.0 and 8.0 without the addition of NaCl. Catalase and oxidase-negative and grew on most mono- and disaccharides, a few polysaccharides and organic acid. The predominant menaquinone was MK-7. Major fatty acid was c16:1 ω7c (PWU4T and PWU20T) and c16:1 ω5c (PWU5T and PWU37T). The DNA G+C content of them were 50.2 mol %; 51.6 mol %; 39.8 mol % and 53.8 mol %, respectively. The 16S rRNA gene sequence analysis revealed that the closest relatives of them are less than 93.8% compared to Ohtaekwangia koreensis 3B-2T and Ohtaekwangia kribbensis 10AOT. It classified in two groups, where PWU4T, PWU20T shared 93.0% and PWU5T, PWU37T shared 97.5% sequence similarity. However, in both groups represent different species on the low average nucleotide identity (ANI) of their genomes, 69.7% and 83.8%, respectively. We proposed that the four strains represent four novel species of two new genera in the family Cytophagaceae. The type species of the novel genus Cryseosolum are Cryseosolum histdinii gen. nov., sp. nov. strain PWU4T (=DSM 111594T=NCCB 100798T), Cryseosolum indiensis sp. nov. strain PWU20T (=DSM 111597T=NCCB 100800T). The type species of the novel genus Reichenbachia are Reichenbachia cretensis gen. nov., sp. nov. strain PWU5T (=DSM 111596T=NCCB 100799T), Reichenbachia soli sp. nov. strain PWU37T (=DSM 111595T=NCCB 100801T).

scholarly journals Causative Role of Grapevine Red Blotch Virus in Red Blotch Disease

2018 ◽  
Vol 108 (7) ◽  
pp. 902-909 ◽  
Author(s):  
Luz Marcela Yepes ◽  
Elizabeth Cieniewicz ◽  
Björn Krenz ◽  
Heather McLane ◽  
Jeremy R. Thompson ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Systemic Infection ◽  
Causative Role ◽  
Coding Region ◽  
Protein Coding ◽  
Rolling Circle ◽  
Reverse Transcription Pcr ◽  
Leaf Chlorosis ◽  
The Family

Grapevine red blotch virus (GRBV) has a monopartite single-stranded DNA genome and is the type species of the genus Grablovirus in the family Geminiviridae. To address the etiological role of GRBV in the recently recognized red blotch disease of grapevine, infectious GRBV clones were engineered from the genome of each of the two previously identified phylogenetic clades for Agrobacterium tumefaciens-mediated inoculations of tissue culture-grown Vitis spp. plants. Following agroinoculation and one or two dormancy cycles, systemic GRBV infection was detected by multiplex polymerase chain reaction (PCR) in Vitis vinifera exhibiting foliar disease symptoms but not in asymptomatic vines. Infected rootstock genotype SO4 (V. berlandieri × V. riparia) exhibited leaf chlorosis and cupping, while infection was asymptomatic in agroinoculated 110R (V. berlandieri × V. rupestris), 3309C (V. riparia × V. rupestris), and V. rupestris. Spliced GRBV transcripts of the replicase-associated protein coding region accumulated in leaves of agroinfected vines, as shown by reverse-transcription PCR; this was consistent with systemic infection resulting from virus replication. Additionally, a virus progeny identical in nucleotide sequence to the infectious GRBV clones was recovered from agroinfected vines by rolling circle amplification, cloning, and sequencing. Concomitantly, subjecting naturally infected grapevines to microshoot tip culture resulted in an asymptomatic plant progeny that tested negative for GRBV in multiplex PCR. Altogether, our agroinoculation and therapeutic experiments fulfilled Koch’s postulates and revealed the causative role of GRBV in red blotch disease.

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 Neodendryphiella, a novel genus of the Dictyosporiaceae (Pleosporales)

MycoKeys ◽  
2018 ◽  
Vol 37 ◽  
pp. 19-38 ◽  
Author(s):  
Isabel Iturrieta-González ◽  
Josepa Gené ◽  
Josep Guarro ◽  
Rafael F. Castañeda-Ruiz ◽  
Dania García
Keyword(s):  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
The Other ◽  
The Novel ◽  
Novel Genus ◽  
Monophyletic Lineage ◽  
The Family ◽  
Three New Species ◽  
Branched Chains ◽  
Reference Strains

In a survey of soil and herbivore dung microfungi in Mexico and Spain, several dendryphiella-like species were found. Phylogenetic analyses based on ITS and LSU sequences showed that these fungi belonged to the family Dictyosporiaceae (Pleosporales) and represent an undescribed monophyletic lineage distant fromDendryphiella. Therefore, the genusNeodendryphiellais proposed to accommodate three new species,N.mali,N.michoacanensisandN.tarraconensis. The novel genus shares morphological features withDendryphiellasuch as differentiated conidiophores and polytretic integrated conidiogenous cells, that produce acropetal branched chains of conidia.Neodendryphielladiffers in the absence of nodulose conidiophores bearing conidiogenous cells with pores surrounded by a thickened and darkened wall, typical features in the conidiogenous apparatus ofDendryphiella. In addition, the phylogenetic and morphological analysis of several reference strains of differentDendryphiellaspecies, available for comparison, support the proposal ofD.variabilissp. nov., which mainly differs from the other species of the genus by having conidia up to 7 septa and highlight thatD.vinosaandD.infuscansare obscure species that require further taxonomic review.

scholarly journals Krokinobacter gen. nov., with three novel species, in the family Flavobacteriaceae

2006 ◽  
Vol 56 (2) ◽  
pp. 323-328 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Tween 80 ◽  
Distinct Species ◽  
Sequence Difference ◽  
Rrna Gene ◽  
The Novel ◽  
Novel Genus ◽  
The Pacific ◽  
The Family

Five strains belonging to the family Flavobacteriaceae were isolated from marine-sediment samples collected in Sagami and Tokyo bays on the Pacific coastline of Japan. The five isolates formed a coherent and novel genus-level lineage within the family Flavobacteriaceae. The most closely related species with a validly published name was Cellulophaga lytica. The five isolates were rod-shaped, Gram-negative, aerobic, catalase- and oxidase-positive, flexirubin-negative and yellow-pigmented. The dominant fatty acids were branched or hydroxy acids, i.e. i-C15 : 0, i-C15 : 1 and i-C17 : 0 3-OH. These strains degraded gelatin, casein, DNA and Tween 80. The G+C content of their DNAs ranged between 33 and 39 mol%. Although analysis of the 16S rRNA gene sequence similarity divided these strains into two subgroups with a 2·3 % sequence difference, the results of DNA–DNA hybridization indicated the grouping of these strains into three distinct species. On the basis of phenotypic and genotypic analyses, the novel genus Krokinobacter is proposed, with Krokinobacter genikus sp. nov., containing three of the strains, as the type species. The type strain is Cos-13T (=NBRC 100811T=CIP 108744T). The names Krokinobacter eikastus sp. nov. (type strain PMA-26T=NBRC 100814T=CIP 108743T) and Krokinobacter diaphorus sp. nov. (type strain MSKK-32T=NBRC 100817T=CIP 108745T) are proposed for the other two isolates.

scholarly journals Revolution in Evolution of Human “Anellome”

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 50
Author(s):  
Joanna Kaczorowska ◽  
Mila Sparreboom ◽  
Martin Deijs ◽  
Maarten F. Jebbink ◽  
Lia van der Hoek
Keyword(s):  
Genome Sequencing ◽  
Sanger Sequencing ◽  
Rolling Circle Amplification ◽  
Serum Samples ◽  
Rolling Circle ◽  
The Family ◽  
Full Length Genome ◽  
Viral Sequences ◽  
Hiv 1 ◽  
Repeating Patterns

Torque teno viruses (TTVs), the most well-known members of the family Anelloviridae, are not associated with any disease. They are one of the most abundant and divergent entities in the viral world; however, the cause of their variability is not currently known. In this study, a set of longitudinally collected serum samples from two HIV-1 infected and two non-infected persons was analyzed for the presence of TTVs and other Anelloviridae using a genera-specific quantitative PCR. The samples positive for TTVs were selected for the quantitative heteroduplex tracking assay (QHTA), which showed repeating patterns of TTV genotypes. Sanger sequencing of the partial viral sequences revealed that the same strains of TTVs are most probably disappearing and returning in different stages of life, with scarcely any new introductions. The partial sequences were grouped into phylogenetic genogroups, and samples representing each of these genogroups were selected for full-length genome sequencing using an in-house optimized rolling circle amplification (RCA)–Illumina protocol.

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