A divergent clade of circular single-stranded DNA viruses from pig feces

Virus and Prion Diseases, Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, PO Box 70, Ames, IA, 50010, USA, .
Archives of Virology (Impact Factor: 2.39). 04/2013; 158(10). DOI: 10.1007/s00705-013-1701-z
Source: PubMed


Using metagenomics and molecular cloning methods, we characterized five novel small, circular viral genomes from pig feces that are distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). Phylogenetic analysis placed these viruses into a highly divergent clade of this rapidly growing new viral family. This new clade of viruses, provisionally named porcine stool-associated circular virus 2 and 3 (PoSCV2 and PoSCV3), encodes a stem-loop structure (presumably the origin of DNA replication) in the small intergenic region and a replication initiator protein commonly found in other biological systems that replicate their genomes via the rolling-circle mechanism. Furthermore, these viruses also exhibit three additional overlapping open reading frames in the large intergenic region between the capsid and replication initiator protein genes.

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    • "Recently, novel viruses associated with diarrhoea have emerged in outbreaks on piglet farms (Meng, 2012), such as bocavirus (Shan et al., 2011a), kobuvirus (Reuter et al., 2008), sapovirus (Liu et al., 2012), sepelovirus (Chen et al., 2012) and astrovirus (Shan et al., 2012). Novel viruses continue to emerge from studies of piglet diarrhoeic faeces (Cheung et al., 2013; Sikorski et al., 2013; Yu et al., 2013). "
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    ABSTRACT: To investigate the diversity of viral flora, we used metagenomics to study the viral communities in a pooled fecal sample of 27 diarrheic piglets from intensive commercial farms in China. The 15 distinct mammalian viruses identified in the pooled diarrheic sample were, in order of abundance of nucleic acids sequence, porcine epidemic diarrhea virus (PEDV), sapovirus, porcine bocavirus-4 (PBoV-4), sapelovirus, torovirus, coronavirus, PBoV-2, stool-associated single-stranded DNA virus (poSCV), astrovirus (AstV), kobuvirus, posavirus-1, porcine enterovirus-9 (PEV-9), porcine circovirus-like (po-circo-like) virus, picobirnavirus (PBV) and torque teno sus virus 2 (TTSuV-2). The every virus prevalence rate was verified from diarrheic and healthy piglets by PCR assay. An average of 5.5 different viruses was shed in diarrheic piglet, and one piglet was in fact co-infected with 11 different viruses. In contrary, healthy piglets shed an average of 3.2 different viruses. Compared to healthy piglets, the co-infection of PEDV and PBoV had a high prevalence rate in diarrhea samples, suggesting a correlation to the appearance of diarrhea in piglets. Furthermore, several recently described viruses were here reported for the first time in China, and novel genotypes were identified. Therefore, our investigation results provided an unbiased survey of viral communities and prevalence in fecal sample of piglets.
    Full-text · Article · Apr 2014 · Journal of General Virology
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    ABSTRACT: The pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. Only little is known about factors influencing its general composition. Here, the effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. In average, 14% of the reads showed significant sequence identities to known viruses. The percentage of detected mammalian virus sequences was highest (55-77%) in the samples of the youngest piglets and lowest (8-10%) in the samples of the sows. In contrast, the percentage of bacteriophage sequences increased from 22-44% in the youngest piglets to approximately 90% in the sows. The dominating mammalian viruses differed remarkably among 12 day-old piglets (kobuvirus), 54 day-old piglets (boca-, dependo- and pig stool-associated small circular DNA virus [PigSCV]) and the sows (PigSCV, circovirus and "circovirus-like" viruses CB-A and RW-A). In addition, the Shannon index, which reflects the diversity of sequences present in a sample, was generally higher for the sows as compared to the piglets. No consistent differences in the virome composition could be identified between the viromes of the probiotic bacterium-treated group and the control group. The analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method.
    Full-text · Article · Feb 2014 · PLoS ONE
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    ABSTRACT: Recently, a novel group of unclassified single-stranded (ss) circular small DNA viruses (called stool-associated circular virus; SCV) were identified in fecal samples of three mammalian species, namely, chimpanzee (ChiSCV), pig (PoSCV) and cattle (BoSCV). In this study, a novel genomic relative of stool-associated circular virus (TuSCV, KF880727) was detected in faeces of an avian species, namely, domestic turkey (Meleagris gallopavo). The complete TuSCV genome is 2479 nt long and has two open reading frames (ORF), which are bidirectionally transcribed and separated by intergenic regions. The ORF1 (replicase) and ORF2 (capsid) proteins have 77 % and 48 % aa sequence identity to different porcine-origin SCVs.
    No preview · Article · Feb 2014 · Archives of Virology
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