Identification of a novel single-stranded, circular DNA virus from bovine stool

We report the identification of a novel single-stranded, circular DNA virus isolated from bovine stool. The virus, named bovine stool-associated circular DNA virus (BoSCV), has a genome comprising 2600 bases of circular ssDNA, with two putative ORFs encoding replicase and capsid proteins, arranged inversely. The stem–loop structure was located between the 3′ ends of the two putative ORFs, as in chimpanzee stool-associated circular virus (ChimpSCV) and unlike other circular DNA viruses, including members of the families Circoviridae, Nanoviridae and Geminiviridae. BoSCV was also genetically similar to ChimpSCV, with approximately 30 % identity in the replicase and capsid proteins. A phylogenetic analysis based on the replicase protein showed that BoSCV and ChimpSCV are in the same clade. A field survey using BoSCV-specific PCRs targeting ORF1 detected BoSCV and BoSCV-like sequences in bovine and porcine stool samples. BoSCV appears to belong to a new genus of circular DNA viruses.

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Feline Stool-Associated Circular DNA Virus (FeSCV) in Diarrheic Cats in China

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.694089 ◽

2021 ◽

Vol 8 ◽

Author(s):

Xiangqi Hao ◽

Yanchao Li ◽

Xinkai Hu ◽

Xueying Fu ◽

Jie Dong ◽

...

Keyword(s):

Pcr Amplification ◽

Epidemiological Studies ◽

Acid Sites ◽

Domestic Cats ◽

Dna Virus ◽

Stem Loop ◽

Circular Dna ◽

Additional Base ◽

The Impact ◽

Circular Dna Virus

Feline stool-associated circular DNA virus (FeSCV) is an unclassified circular replication-associated protein-encoding single-stranded (CRESS) DNA virus that was discovered in cats in Japan in 2018. Few studies on the genomic characteristics and prevalence of FeSCV have been conducted. To investigate whether FeSCV has been circulating in domestic cats in Guangdong, China, fecal samples were collected from cats with diarrhea in an animal hospital in 2018 to promote research on FeSCV. The FeSCV genome was obtained by PCR amplification and sequencing, and the detected virus was named PY4 (GenBank No. MT732515). The genome of PY4 was 2,034 nt in size, which was 12 nt smaller than the reported genome of Japanese FeSCV strains (KU7, KU8, KU9, KU14) (2,046 nt). The PY4 strain shared 95.1 ~ 95.5% homology with Japanese FeSCV strains. Notably, the Cap protein of PY4 was mutated at 15 amino acid sites, and the PY4 genome contained a unique open reading frame 3. In addition, there were two additional base insertions in the stem-loop structure of PY4, and the nucleotide homology of the spacer region was not high. A phylogenetic tree based on Rep proteins showed that PY4, Japanese FeSCVs and rodent stool-associated circular viruses (RodSCVs) clustered together, suggesting that they might share a similar origin in their phylogenetic evolution. In this study, samples collected in Guangzhou, China, in 2018 were subjected to an etiological investigation, and 20% (2/10) of the samples were positive for FeSCV. The ORFs, stem-loop structures, Cap proteins and intergenic region sequences of PY4 were significantly different from those reported in Japan. This is the first report of FeSCV in domestic cats with diarrhea in China, and further epidemiological studies are urgently needed to assess the impact of the virus on cats.

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Novel circular DNA virus identified in Opuntia discolor (Cactaceae) that codes for proteins with similarity to those of geminiviruses

Journal of General Virology ◽

10.1099/jgv.0.001671 ◽

2021 ◽

Vol 102 (11) ◽

Author(s):

Rafaela S. Fontenele ◽

Matias Köhler ◽

Lucas C. Majure ◽

Jesús A. Avalos-Calleros ◽

Gerardo R. Argüello-Astorga ◽

...

Keyword(s):

South America ◽

Rolling Circle Replication ◽

Dna Virus ◽

Single Stranded Dna ◽

Dna Viruses ◽

Circular Dna ◽

Rolling Circle ◽

Rep Protein ◽

Molecular Features ◽

Viral Components

Viral metagenomic studies have enabled the discovery of many unknown viruses and revealed that viral communities are much more diverse and ubiquitous than previously thought. Some viruses have multiple genome components that are encapsidated either in separate virions (multipartite viruses) or in the same virion (segmented viruses). In this study, we identify what is possibly a novel bipartite plant-associated circular single-stranded DNA virus in a wild prickly pear cactus, Opuntia discolor, that is endemic to the Chaco ecoregion in South America. Two ~1.8 kb virus-like circular DNA components were recovered, one encoding a replication-associated protein (Rep) and the other a capsid protein (CP). Both of the inferred protein sequences of the Rep and CP are homologous to those encoded by members of the family Geminiviridae. These two putatively cognate components each have a nonanucleotide sequence within a likely hairpin structure that is homologous to the origins of rolling-circle replication (RCR), found in diverse circular single-stranded DNA viruses. In addition, the two components share similar putative replication-associated iterative sequences (iterons), which in circular single-stranded DNA viruses are important for Rep binding during the initiation of RCR. Such molecular features provide support for the possible bipartite nature of this virus, which we named utkilio virus (common name of the Opuntia discolor in South America) components A and B. In the infectivity assays conducted in Nicotiana benthamiana plants, only the A component of utkilio virus, which encodes the Rep protein, was found to move and replicate systemically in N. benthamiana. This was not true for component B, for which we did not detect replication, which may have been due to this being a defective molecule or because of the model plants (N. benthamiana) used for the infection assays. Future experiments need to be conducted with other plants, including O. discolor, to understand more about the biology of these viral components.

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Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China

Virologica Sinica ◽

10.1007/s12250-020-00232-3 ◽

2020 ◽

Author(s):

Zhibin Shi ◽

Chunguo Liu ◽

Huanliang Yang ◽

Yan Chen ◽

Hua Liu ◽

...

Keyword(s):

Dna Virus ◽

Circular Dna ◽

Fur Seal ◽

Circular Dna Virus

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Multiple Controls Regulate the Expression of mobE, an HNH Homing Endonuclease Gene Embedded within a Ribonucleotide Reductase Gene of Phage Aeh1

Journal of Bacteriology ◽

10.1128/jb.00321-07 ◽

2007 ◽

Vol 189 (13) ◽

pp. 4648-4661 ◽

Cited By ~ 17

Author(s):

Ewan A. Gibb ◽

David R. Edgell

Keyword(s):

Ribonucleotide Reductase ◽

Large Subunit ◽

Homing Endonuclease ◽

Insertion Site ◽

Gene Organization ◽

Rnase E ◽

Stem Loop ◽

Stem Loop Structure ◽

Expression Of Genes ◽

A Genome

ABSTRACT Mobile genetic elements have the potential to influence the expression of genes surrounding their insertion site upon invasion of a genome. Here, we examine the transcriptional organization of a ribonucleotide reductase operon (nrd) that has been invaded by an HNH family homing endonuclease, mobE. In Aeromonas hydrophila phage Aeh1, mobE has inserted into the large-subunit gene (nrdA) of aerobic ribonucleotide reductase (RNR), splitting it into two smaller genes, nrdA-a and nrdA-b. This gene organization differs from that in phages T4, T6, RB2, RB3, RB15, and LZ7, where mobE is inserted in the nrdA-nrdB intergenic region. We present evidence that the expression of Aeh1 mobE is regulated by transcriptional, posttranscriptional, and translational controls. An Aeh1-specific late promoter drives expression of mobE, but strikingly the mobE transcript is processed internally at an RNase E-like site. We also identified a putative stem-loop structure upstream of mobE that sequesters the mobE ribosome binding site, presumably acting to down regulate MobE translation. Moreover, our transcriptional analyses indicate that the surrounding nrd genes of phage Aeh1 are expressed by a different strategy than are the corresponding phage T4 genes and that transcriptional readthrough is the only mechanism by which the promoterless Aeh1 nrdB gene is expressed. We suggest that the occurrence of multiple layers of control to limit the expression of mobE to late in the Aeh1 infection cycle is an adaptation of Aeh1 to reduce any effects on expression of the surrounding nrd genes early in phage infection when RNR function is critical.

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Complete Genome Sequence of a New Circular DNA Virus from Grapevine

Journal of Virology ◽

10.1128/jvi.00943-12 ◽

2012 ◽

Vol 86 (14) ◽

pp. 7715-7715 ◽

Cited By ~ 79

Author(s):

B. Krenz ◽

J. R. Thompson ◽

M. Fuchs ◽

K. L. Perry

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Dna Virus ◽

Circular Dna ◽

Circular Dna Virus

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Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi

Archives of Virology ◽

10.1007/s00705-015-2503-2 ◽

2015 ◽

Vol 160 (9) ◽

pp. 2349-2351 ◽

Cited By ~ 21

Author(s):

Elizabeth Fahsbender ◽

Ian Hewson ◽

Karyna Rosario ◽

Allison D. Tuttle ◽

Arvind Varsani ◽

...

Keyword(s):

Sea Star ◽

Dna Virus ◽

Circular Dna ◽

Asterias Forbesi ◽

Circular Dna Virus

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Identification of Two Virus Integration Sites in the Brown Alga Feldmannia Chromosome

Journal of Virology ◽

10.1128/jvi.01983-07 ◽

2007 ◽

Vol 82 (3) ◽

pp. 1407-1413 ◽

Cited By ~ 12

Author(s):

Russel H. Meints ◽

Richard G. Ivey ◽

Amy M. Lee ◽

Tae-Jin Choi

Keyword(s):

Vegetative Cells ◽

Stem Loop ◽

Dna Viruses ◽

Viral Genomes ◽

Virus Particles ◽

Double Stranded Dna ◽

Stem Loop Structure ◽

Integration Sites ◽

Virus Integration ◽

Cg Dinucleotide

ABSTRACT Two similar, large double-stranded DNA viruses, Feldmannia species virus 158 (FsV-158) and FsV-178, replicate only in the unilocular reproductive cells (sporangia) of a brown filamentous alga in the genus Feldmannia. Virus particles are not present in vegetative cells but they are produced in the sporangia formed on vegetative filaments that have been transferred newly into culture. Thus, we proposed that these viruses exist in the vegetative cells in a latent form (R. G. Ivey, E. C. Henry, A. M. Lee, L. Klepper, S. K. Krueger, and R. H. Meints, Virology 220:267-273, 1996). In this article we present evidence that the two FsV genomes are integrated into the host genome during vegetative growth. The FsV genome integration sites were identified by cloning the regions where the FsV genome is linked to the host DNA. FsV-158 and FsV-178 are integrated into two distinct locations in the algal genome. In contrast, the integration sites in the two viral genomes are identical. Notably, the integration sites in the host and viruses contain GC and CG dinucleotide sequences, respectively, from which the GC sequences are recovered at both host-virus junctions. The splice sites in the two FsV genomes are predicted to form a stem-loop structure with the CG dinucleotide in the loop portion.

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A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs

Journal of General Virology ◽

10.1099/jgv.0.001706 ◽

2021 ◽

Vol 102 (12) ◽

Author(s):

Caroline Tochetto ◽

Samuel Paulo Cibulski ◽

Ana Paula Muterle Varela ◽

Cristine Cerva ◽

Diane Alves de Lima ◽

...

Keyword(s):

Potential Role ◽

Clinical Signs ◽

Viral Metagenomics ◽

Dna Viruses ◽

Circular Dna ◽

Viral Genomes ◽

The Family ◽

Circular Ssdna ◽

Ssdna Viruses ◽

Targeted Approach

Over the last decade, viral metagenomics has been established as a non-targeted approach for identifying viruses in stock animals, including pigs. This has led to the identification of a vast diversity of small circular ssDNA viruses. The present study focuses on the investigation of eukaryotic circular Rep-encoding single-stranded (CRESS) DNA viral genomes present in serum of commercially reared pigs from southern Brazil. Several CRESS DNA viral genomes were detected, including representatives of the families Smacoviridae (n=5), Genomoviridae (n=3), Redondoviridae (n=1), Nenyaviridae (n=1) and other yet unclassified genomes (n=9), plus a circular DNA molecule, which probably belongs to the phylum Cressdnaviricota. A novel genus within the family Smacoviridae, tentatively named ‘Suismacovirus’, comprising 21 potential new species, is proposed. Although the reported genomes were recovered from pigs with clinical signs of respiratory disease, further studies should examine their potential role as pathogens. Nonetheless, these findings highlight the diversity of circular ssDNA viruses in serum of domestic pigs, expand the knowledge on CRESS DNA viruses’ genetic diversity and distribution and contribute to the global picture of the virome of commercially reared pigs.

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