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

ArticleinArchives of Virology 158(10) · April 2013with19 Reads
Impact Factor: 2.39 · DOI: 10.1007/s00705-013-1701-z · Source: PubMed
Abstract

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.

    • "Pigs are known to have a high incidence of picobirnavirus infections464748; however, in this study, picobirnavirus constituted to less than 1 % of all viral sequence contigs. Various metagenomic studies on the swine fecal virome have also shown that picobirnavirus constitute 0-7 % of total mammalian viruses [10, 49, 50]. Picornaviridae is a large family of non-enveloped viruses with a positive-sense ssRNA genome encoding a single polyprotein. "
    [Show abstract] [Hide abstract] ABSTRACT: Pigs harbor a variety of viruses that are closely related to human viruses and are suspected to have zoonotic potential. Little is known about the presence of viruses in smallholder farms where pigs are in close contact with humans and wildlife. This study provides insight into viral communities and the prevalence and characteristics of enteric viral co-infections in smallholder pigs in East Africa. Sequence-independent amplification and high-throughput sequencing were applied to the metagenomics analysis of viruses in feces collected from asymptomatic pigs. A total of 47,213 de novo-assembled contigs were constructed and compared with sequences from the GenBank database. Blastx search results revealed that 1039 contigs (>200 nt) were related to viral sequences in the GenBank database. Of the 1039 contigs, 612 were not assigned to any viral taxa because they had little similarity to known viral genomic or protein sequences, while 427 contigs had a high level of sequence similarity to known viruses and were assigned to viral taxa. The most frequent contigs related to mammalian viruses resembling members of the viral genera Astrovirus, Rotavirus, Bocavirus, Circovirus, and Kobuvirus. Other less abundant contigs were related to members of the genera Sapelovirus, Pasivirus, Posavirus, Teschovirus and Picobirnavirus. This is the first report on the diversity of the fecal virome of pig populations in East Africa. The findings of the present study help to elucidate the etiology of diarrheal diseases in pigs and identify potential zoonotic and emerging viruses in the region. Further investigations are required to compare the incidence of these viruses in healthy and diseased pigs in order to better elucidate their pathogenic role.
    Full-text · Article · Mar 2016 · Archives of Virology
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    • "This virus belongs to the single-stranded circular DNA viruses. The members of this family show extensive genetic diversity [20]. TheFigure 4 Taxonomic classification using the LCA with BLASTN viruses. "
    [Show abstract] [Hide abstract] ABSTRACT: Background Emerging viral diseases, most of which are caused by the transmission of viruses from animals to humans, pose a threat to public health. Discovering pathogenic viruses through surveillance is the key to preparedness for this potential threat. Next generation sequencing (NGS) helps us to identify viruses without the design of a specific PCR primer. The major task in NGS data analysis is taxonomic identification for vast numbers of sequences. However, taxonomic identification via a BLAST search against all the known sequences is a computational bottleneck. Description Here we propose an enhanced lowest-common-ancestor based method (ELM) to effectively identify viruses from massive sequence data. To reduce the computational cost, ELM uses a customized database composed only of viral sequences for the BLAST search. At the same time, ELM adopts a novel criterion to suppress the rise in false positive assignments caused by the small database. As a result, identification by ELM is more than 1,000 times faster than the conventional methods without loss of accuracy. Conclusions We anticipate that ELM will contribute to direct diagnosis of viral infections. The web server and the customized viral database are freely available at http://bioinformatics.czc.hokudai.ac.jp/ELM/. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-254) contains supplementary material, which is available to authorized users.
    Full-text · Article · Jul 2014 · BMC Bioinformatics
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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). Thus, the understanding and surveillance of viruses in piglets provides epidemiological baseline information about potential future pathogens. "
    [Show abstract] [Hide abstract] 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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