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      Detection of a novel circovirus PCV3 in pigs with cardiac and multi-systemic inflammation

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          Abstract

          Background

          Porcine circovirus 2 causes different clinical syndromes resulting in a significant economic loss in the pork industry. Three pigs with unexplained cardiac and multi-organ inflammation that tested negative for PCV2 and other known porcine pathogens were further analyzed.

          Methods

          Histology was used to identify microscopic lesions in multiple tissues. Metagenomics was used to detect viral sequences in tissue homogenates. In situ hybridization was used to detect viral RNA expression in cardiac tissue.

          Results

          In all three cases we characterized the genome of a new circovirus we called PCV3 with a replicase and capsid proteins showing 55 and 35 % identities to the genetically-closest proteins from a bat-feces associated circovirus and were even more distant to those of porcine circovirus 1 and 2. Common microscopic lesions included non-suppurative myocarditis and/or cardiac arteriolitis. Viral mRNA was detected intralesionally in cardiac cells. Deep sequencing in tissues also revealed the presence of porcine astrovirus 4 in all three animals as well as rotavirus A, porcine cytomegalovirus and porcine hemagglutinating encephalomyelitis virus in individual cases.

          Conclusion

          The pathogenicity and molecular epidemiology of this new circovirus, alone or in the context of co-infections, warrants further investigations.

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          Most cited references26

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          A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.

          Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.
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            Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces.

            Circoviruses are known to infect birds and pigs and can cause a wide range of severe symptoms with significant economic impact. Using viral metagenomics, we identified circovirus-like DNA sequences and characterized 15 circular viral DNA genomes in stool samples from humans in Pakistan, Nigeria, Tunisia, and the United States and from wild chimpanzees. Distinct genomic features and phylogenetic analysis indicate that some viral genomes were part of a previously unrecognized genus in the Circoviridae family we tentatively named "Cyclovirus" whose genetic diversity is comparable to that of all the known species in the Circovirus genus. Circoviridae detection in the stools of U.S. adults was limited to porcine circoviruses which were also found in most U.S. pork products. To determine whether the divergent cycloviruses found in non-U.S. human stools were of dietary origin, we genetically compared them to the cycloviruses in muscle tissue samples of commonly eaten farm animals in Pakistan and Nigeria. Limited genetic overlap between cycloviruses in human stool samples and local cow, goat, sheep, camel, and chicken meat samples indicated that the majority of the 25 Cyclovirus species identified might be human viruses. We show that the genetic diversity of small circular DNA viral genomes in various mammals, including humans, is significantly larger than previously recognized, and frequent exposure through meat consumption and contact with animal or human feces provides ample opportunities for cyclovirus transmission. Determining the role of cycloviruses, found in 7 to 17% of non-U.S. human stools and 3 to 55% of non-U.S. meat samples tested, in both human and animal diseases is now facilitated by knowledge of their genomes.
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              Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery

              Highlights • The effect of simple virus enrichment methods were tested on a metagenomics dataset. • Centrifugation, filtration or nuclease-treatment was evaluated. • A multi-step enrichment method increased the proportion of virus sequences. • This evaluation guides researchers in their choice of enrichment methodology.
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                Author and article information

                Contributors
                415-923-5763 , delwarte@medicine.ucsf.edu
                Journal
                Virol J
                Virol. J
                Virology Journal
                BioMed Central (London )
                1743-422X
                11 November 2016
                11 November 2016
                2016
                : 13
                : 184
                Affiliations
                [1 ]Blood Systems Research Institute, San Francisco, CA 94118 USA
                [2 ]Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118 USA
                [3 ]Veterinary Diagnostic Laboratory, University of Minnesota, Saint Paul, MN 55108 USA
                [4 ]Instituto Nacional de Investigación Agropecuaria, La Estanzuela, Colonia, 70000 Uruguay
                Article
                642
                10.1186/s12985-016-0642-z
                5105309
                27835942
                91ca85ad-ba1b-4383-a6cc-8d32153332a7
                © The Author(s). 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 2 September 2016
                : 3 November 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000050, National Heart, Lung, and Blood Institute;
                Award ID: R01 HL105770
                Award Recipient :
                Categories
                Short Report
                Custom metadata
                © The Author(s) 2016

                Microbiology & Virology
                arteriolitis,circovirus,myocarditis,pig,vasculitis,metagenomics
                Microbiology & Virology
                arteriolitis, circovirus, myocarditis, pig, vasculitis, metagenomics

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