101
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Brimer N, Drews CM, Vande Pol SB. Association of papillomavirus E6 proteins with either MAML1 or E6AP clusters E6 proteins by structure, function, and evolutionary relatedness. PLoS Pathog 2017; 13:e1006781. [PMID: 29281732 PMCID: PMC5760104 DOI: 10.1371/journal.ppat.1006781] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/09/2018] [Accepted: 11/29/2017] [Indexed: 01/11/2023] Open
Abstract
Papillomavirus E6 proteins bind to LXXLL peptide motifs displayed on targeted cellular proteins. Alpha genus HPV E6 proteins associate with the cellular ubiquitin ligase E6AP (UBE3A), by binding to an LXXLL peptide (ELTLQELLGEE) displayed by E6AP, thereby stimulating E6AP ubiquitin ligase activity. Beta, Gamma, and Delta genera E6 proteins bind a similar LXXLL peptide (WMSDLDDLLGS) on the cellular transcriptional co-activator MAML1 and thereby repress Notch signaling. We expressed 45 different animal and human E6 proteins from diverse papillomavirus genera to ascertain the overall preference of E6 proteins for E6AP or MAML1. E6 proteins from all HPV genera except Alpha preferentially interacted with MAML1 over E6AP. Among animal papillomaviruses, E6 proteins from certain ungulate (SsPV1 from pigs) and cetacean (porpoises and dolphins) hosts functionally resembled Alpha genus HPV by binding and targeting the degradation of E6AP. Beta genus HPV E6 proteins functionally clustered with Delta, Pi, Tau, Gamma, Chi, Mu, Lambda, Iota, Dyokappa, Rho, and Dyolambda E6 proteins to bind and repress MAML1. None of the tested E6 proteins physically and functionally interacted with both MAML1 and E6AP, indicating an evolutionary split. Further, interaction of an E6 protein was insufficient to activate degradation of E6AP, indicating that E6 proteins that target E6AP co-evolved to separately acquire both binding and triggering of ubiquitin ligase activation. E6 proteins with similar biological function clustered together in phylogenetic trees and shared structural features. This suggests that the divergence of E6 proteins from either MAML1 or E6AP binding preference is a major event in papillomavirus evolution.
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Affiliation(s)
- Nicole Brimer
- Department of Pathology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Camille M. Drews
- Department of Pathology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Scott B. Vande Pol
- Department of Pathology, University of Virginia, Charlottesville, Virginia, United States of America
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102
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Schmidt K, Butt J, Mauter P, Vogel K, Erles-Kemna A, Pawlita M, Nicklas W. Development of a multiplex serological assay reveals a worldwide distribution of murine astrovirus infections in laboratory mice. PLoS One 2017; 12:e0187174. [PMID: 29088279 PMCID: PMC5663422 DOI: 10.1371/journal.pone.0187174] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/14/2017] [Indexed: 12/22/2022] Open
Abstract
Laboratory mice play a tremendous role in biomedical research in studies on immunology, infection, cancer and therapy. In the course of standardization of mice used in animal experiments, health monitoring constitutes an important instrument towards microbiological standardization. Infections with murine astroviruses (MuAstV) were only recently discovered and are, therefore, still relatively unknown in laboratory animal science. In rodent health monitoring viral infections within a population are commonly assessed in terms of specific antibodies by serological testing, as active infection and excretion of virus is often temporary and can easily be missed. So far only ongoing infections with astroviruses can be detected by PCR. The objective of this work was the development of a sensitive and specific MuAstV multiplex serological assay with a high-throughput capability to be used in routine testing of laboratory mice. Four different MuAstV proteins were recombinantly expressed and used as antigens. The best reacting antigen, the capsid spike protein VP27, was selected and tested with a panel of 400 sera of mice from units with a known MuAstV status. Assay sensitivity and specificity resulted in 98.5% and 100%, respectively, compared to RT-PCR results. Eventually this assay was used to test 5529 serum samples in total, during routine diagnostics at the German Cancer Research Center (DKFZ) in Heidelberg between 2015 and 2017. High sero-prevalence rates of up to 98% were detected in units with open cages indicating that the virus is highly infectious and circulates within these populations virtually infecting all animals regardless of the mouse strain. In addition, data collected from 312 mice purchased from commercial breeders and from 661 mice from 58 research institutes in 15 countries worldwide allowed the conclusion that MuAstV is widespread in contemporary laboratory mouse populations.
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Affiliation(s)
- Katja Schmidt
- Microbiological Diagnostics, Center for Preclinical Research, German Cancer Research Center, Heidelberg, Germany
- * E-mail:
| | - Julia Butt
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center, Heidelberg, Germany
| | - Petra Mauter
- Microbiological Diagnostics, Center for Preclinical Research, German Cancer Research Center, Heidelberg, Germany
| | - Klaus Vogel
- Microbiological Diagnostics, Center for Preclinical Research, German Cancer Research Center, Heidelberg, Germany
| | - Andrea Erles-Kemna
- Microbiological Diagnostics, Center for Preclinical Research, German Cancer Research Center, Heidelberg, Germany
| | - Michael Pawlita
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center, Heidelberg, Germany
| | - Werner Nicklas
- Microbiological Diagnostics, Center for Preclinical Research, German Cancer Research Center, Heidelberg, Germany
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103
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PHYLOGENETIC ANALYSIS OF THE GENOME OF AN ENTERITIS-ASSOCIATED BOTTLENOSE DOLPHIN MASTADENOVIRUS SUPPORTS A CLADE INFECTING THE CETARTIODACTYLA. J Wildl Dis 2017; 54:112-121. [PMID: 29077545 DOI: 10.7589/2017-03-052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
: Adenoviruses are nonenveloped, double-stranded DNA viruses, known to infect members of all tetrapod classes, with a similarity between phylogenies of hosts and viruses observed. We characterized bottlenose dolphin adenovirus 2 (BdAdV-2) found in a bottlenose dolphin ( Tursiops truncatus) with enteritis. Virions were seen by negative staining electron microscopy of feces. Initial sequences obtained using conserved PCR primers were expanded using primer walking techniques, and the complete coding sequence was obtained. Phylogenetic analyses were consistent with coevolution of this virus and its bottlenose dolphin host, placing BdAdV-2 into a monophyletic group with other mastadenoviruses of Cetartiodactyla. When considering the low guanine/cytosine (G/C) content of BdAdV-2 with the phylogenetic data, this virus may represent a host-jumping event from another member of Cetartiodactyla. Analysis of partial polymerase indicated that bottlenose dolphin adenovirus 1, previously identified in Spain, and BdAdV-2 are sister taxa with harbor porpoise adenovirus 1, forming a cetacean clade. Bottlenose dolphin adenovirus 2 includes a highly divergent fiber gene. Two genes homologous to the dUTPase superfamily are also present which could play a role in enabling viral replication in nondividing cells. We used sequence data to develop a probe hybridization quantitative PCR assay specific to BdAdV-2 with a limit of detection of 10 copies.
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104
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Compton SR, Booth CJ, Macy JD. Lack of Effect of Murine Astrovirus Infection on Dextran Sulfate-induced Colitis in NLRP3-deficient Mice. Comp Med 2017; 67:400-406. [PMID: 28935001 PMCID: PMC5621567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/12/2017] [Accepted: 06/08/2017] [Indexed: 06/07/2023]
Abstract
Murine astrovirus (MuAstV) is a recently identified, widespread infection among laboratory mice. MuAstV is found predominantly in the gastrointestinal tract of mice. Human and turkey astroviruses have been shown to disrupt tight junctions in the intestinal epithelium. The potential of MuAstV to alter research results was tested in a well-established dextran sodium sulfate (DSS)-induced colitis model in Nod-like receptor 3 (NLRP3)-deficient mice. This model offers a direct approach to determine whether MuAstV, as a component of the mouse microbiome, contributes to the issue of poor reproducibility in murine inflammatory bowel disease research. In this model, defective inflammasome activation causes loss of epithelial integrity, resulting in leakage of intestinal bacteria and colitis. Our goal was to determine whether MuAstV, which also may affect intestinal permeability, altered the onset or severity of colitis. Male and female mice (age, 8 to 12 wk) homozygous or heterozygous for an NLRP3 mutation were inoculated orally with MuAstV or mock-inoculated with media 3 or 20 d prior to being exposed to 2% DSS in their drinking water for 9 d. MuAstV infection alone did not cause clinical signs or histopathologic changes in NLRP3-/- or NLRP3+/- mice. No significant difference was seen in weight loss, clinical disease, intestinal inflammation, edema, hyperplasia, or mucosal ulceration between MuAstV- infected and mock-infected mice that received 2% DSS for 9 d. Therefore, MuAstV does not appear to be a confounding variable in the DSS colitis model in NLRP3 mice.
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Affiliation(s)
- Susan R Compton
- Section of Comparative Medicine, Yale University, New Haven, Connecticut;,
| | - Carmen J Booth
- Section of Comparative Medicine, Yale University, New Haven, Connecticut
| | - James D Macy
- Section of Comparative Medicine, Animal Resources Center, Yale University, New Haven, Connecticut
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105
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Drewes S, Straková P, Drexler JF, Jacob J, Ulrich RG. Assessing the Diversity of Rodent-Borne Viruses: Exploring of High-Throughput Sequencing and Classical Amplification/Sequencing Approaches. Adv Virus Res 2017; 99:61-108. [PMID: 29029730 DOI: 10.1016/bs.aivir.2017.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research. In addition to rodent-specific viruses, rodent-borne viruses are causing a large number of zoonotic diseases. Most prominent examples are reemerging outbreaks of human hemorrhagic fever disease cases caused by arena- and hantaviruses. In addition, rodents are reservoirs for vector-borne pathogens, such as tick-borne encephalitis virus and Borrelia spp., and may carry human pathogenic agents, but likely are not involved in their transmission to human. In our days, next-generation sequencing or high-throughput sequencing (HTS) is revolutionizing the speed of the discovery of novel viruses, but other molecular approaches, such as generic RT-PCR/PCR and rolling circle amplification techniques, contribute significantly to the rapidly ongoing process. However, the current knowledge still represents only the tip of the iceberg, when comparing the known human viruses to those known for rodents, the mammalian taxon with the largest species number. The diagnostic potential of HTS-based metagenomic approaches is illustrated by their use in the discovery and complete genome determination of novel borna- and adenoviruses as causative disease agents in squirrels. In conclusion, HTS, in combination with conventional RT-PCR/PCR-based approaches, resulted in a drastically increased knowledge of the diversity of rodent viruses. Future improvements of the used workflows, including bioinformatics analysis, will further enhance our knowledge and preparedness in case of the emergence of novel viruses. Classical virological and additional molecular approaches are needed for genome annotation and functional characterization of novel viruses, discovered by these technologies, and evaluation of their zoonotic potential.
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Affiliation(s)
- Stephan Drewes
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Petra Straková
- Institute of Vertebrate Biology v.v.i., Academy of Sciences, Brno, Czech Republic
| | - Jan F Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Germany
| | - Jens Jacob
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Münster, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany; German Center for Infection Research (DZIF), Partner site Hamburg-Luebeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany.
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106
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Boujon CL, Koch MC, Seuberlich T. The Expanding Field of Mammalian Astroviruses: Opportunities and Challenges in Clinical Virology. Adv Virus Res 2017; 99:109-137. [PMID: 29029723 DOI: 10.1016/bs.aivir.2017.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Astroviruses are best known as being one of the leading causes of diarrhea in infants and were first described in this context in 1975. In its first years, astrovirus research was mainly restricted to electron microscopy and serology studies. The ability to culture some of these viruses in vitro allowed a first consequent step forward, especially at the molecular level. Since the emergence of more powerful genetic methods, though, the face of this research field has dramatically changed and evolved. From the exponential number of discoveries of new astrovirus strains in the most varied of animal species to their association with atypical diseases, these viruses revealed a lot of surprises, and many more are probably still waiting to be uncovered. This chapter summarizes the most important knowledge about astroviruses and discusses the implication of the latest findings in this area of research.
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107
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Detection of a new species of torque teno mini virus from the gingival epithelium of patients with periodontitis. Virus Genes 2017; 53:823-830. [PMID: 28866831 DOI: 10.1007/s11262-017-1505-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/16/2017] [Indexed: 12/12/2022]
Abstract
We describe a novel species of torque teno mini virus called TTMV-204, which was isolated from the gingival epithelium of patients with periodontitis and characterized using viral metagenomics. The sequence of the full genome is 2824 nt in length. Phylogenetic analysis and genetic analyses show classic Betatorquevirus species organization with less than 40% amino acid similarity in ORF1. The prevalence of TTMV-204 in the periodontitis patient population was 18.75% (15/80), which was higher than in periodontally healthy individuals (10.00%, 10/80). However, the difference of the TTMV-204 prevalence between two groups was not statistically significant (p = 0.115). Further investigation is required to determine whether this new virus is associated with inflammation.
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108
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Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea. J Virol 2017; 91:JVI.00952-17. [PMID: 28659484 DOI: 10.1128/jvi.00952-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, Adenoviridae, Astroviridae, Anelloviridae, Picobirnaviridae, and Parvoviridae, collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families Picornaviridae and Parvoviridae were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.
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109
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Walker D, Gregory WF, Turnbull D, Rocchi M, Meredith AL, Philbey AW, Sharp CP. Novel adenoviruses detected in British mustelids, including a unique Aviadenovirus in the tissues of pine martens ( Martes martes). J Med Microbiol 2017; 66:1177-1182. [PMID: 28749327 PMCID: PMC5817191 DOI: 10.1099/jmm.0.000546] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Several adenoviruses are known to cause severe disease in veterinary species. Recent evidence suggests that canine adenovirus type 1 (CAV-1) persists in the tissues of healthy red foxes (Vulpes vulpes), which may be a source of infection for susceptible species. It was hypothesized that mustelids native to the UK, including pine martens (Martes martes) and Eurasian otters (Lutra lutra), may also be persistently infected with adenoviruses. Based on high-throughput sequencing and additional Sanger sequencing, a novel Aviadenovirus, tentatively named marten adenovirus type 1 (MAdV-1), was detected in pine marten tissues. The detection of an Aviadenovirus in mammalian tissue has not been reported previously. Two mastadenoviruses, tentatively designated marten adenovirus type 2 (MAdV-2) and lutrine adenovirus type 1 (LAdV-1), were also detected in tissues of pine martens and Eurasian otters, respectively. Apparently healthy free-ranging animals may be infected with uncharacterized adenoviruses with possible implications for translocation of wildlife.
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Affiliation(s)
- David Walker
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
- *Correspondence: David Walker,
| | - William F. Gregory
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Dylan Turnbull
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh EH26 0PZ, UK
| | - Mara Rocchi
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh EH26 0PZ, UK
| | - Anna L. Meredith
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Adrian W. Philbey
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Colin P. Sharp
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
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110
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Abstract
Viruses rapidly evolve and can emerge in unpredictable ways. Transmission pathways by which foodborne viruses may enter human populations and evolutionary mechanisms by which viruses can become virulent are discussed in this chapter. A majority of viruses emerge from zoonotic animal reservoirs, often by adapting and infecting intermediate hosts, such as domestic animals and livestock. Viruses that are known foodborne threats include hepatitis E virus, tick-borne encephalitis virus, enteroviruses, adenovirus, and astroviruses, among others. Viruses may potentially evolve and emerge as a result of modern agricultural practices which can concentrate livestock and bring them into contact with wild animals. Examples of viruses that have emerged in this manner are influenza, coronaviruses such as severe acute respiratory syndrome and Middle East respiratory syndrome, and the Nipah virus. The role of bats, bush meat, rodents, pigs, cattle, and poultry as reservoirs from which infectious pathogenic viruses emerge are discussed.
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111
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Compton SR, Booth CJ, Macy JD. Murine Astrovirus Infection and Transmission in Neonatal CD1 Mice. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2017; 56:402-411. [PMID: 28724490 PMCID: PMC5517330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/07/2017] [Accepted: 04/20/2017] [Indexed: 06/07/2023]
Abstract
Murine astrovirus (MuAstV) is a recently identified, widespread infection among laboratory mice. Our goal was to determine the duration of MuAstV infection, susceptibility of pups, and efficacy of soiled-bedding sentinels and environmental monitoring. Eight CD1 dams and their litters of 3-d-old pups and 8 CD1 dams and their litters of 13-d-old mice were inoculated orally with MuAstV. Neither dams nor offspring demonstrated any clinical signs, and MuAstV had little to no effect on weight gain in pups. MuAstV RNA was detected in feces from 15 of the 16 dams through postnatal day (PND) 21, and 9 dams were still shedding MuAstV at PND 42. MuAstV RNA was highest in intestines of mice. Low levels of MuAstV RNA were sporadically detected in the spleen, liver, and kidney. MuAstV was detected in 97% of feces from 3- to 9-wk-old mice born to infected dams. Several weanlings became pregnant, and intestines from their pups were MuAstV-negative at PND 0 through 5. Weekly swabs of cages housing MuAstV-infected mice were MuAstV-positive through PND 42. Swabs of the rear exhaust manifold of the ventilated rack were MuAstV-positive at 21 through 56 d after inoculation. In addition, 98% of sentinels that received soiled bedding from dams and their litters and 83% of sentinels that received soiled bedding from weaned mice were MuAstV-positive. Feces from most sentinels exposed to soiled bedding that had been stored for 1, 2 or 3 wk before addition of the sentinels were MuAstV-positive.
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Affiliation(s)
- Susan R Compton
- Section of Comparative Medicine, School of Medicine, Yale University;,
| | - Carmen J Booth
- Section of Comparative Medicine, School of Medicine, Yale University
| | - James D Macy
- Section of Comparative Medicine, School of Medicine, Animal Resources Center, Yale University
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112
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Moreno PS, Wagner J, Mansfield CS, Stevens M, Gilkerson JR, Kirkwood CD. Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics. PLoS One 2017; 12:e0178433. [PMID: 28570584 PMCID: PMC5453527 DOI: 10.1371/journal.pone.0178433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/12/2017] [Indexed: 01/01/2023] Open
Abstract
The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted.
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Affiliation(s)
- Paloma S. Moreno
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | - Josef Wagner
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Caroline S. Mansfield
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Matthew Stevens
- Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - James R. Gilkerson
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Carl D. Kirkwood
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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113
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To KKW, Chan WM, Li KSM, Lam CSF, Chen Z, Tse H, Lau SKP, Woo PCY, Yuen KY. High prevalence of four novel astrovirus genotype species identified from rodents in China. J Gen Virol 2017; 98:1004-1015. [PMID: 28537544 DOI: 10.1099/jgv.0.000766] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Astroviruses cause gastrointestinal and neurological infections in humans and animals. Since astrovirus is genetically diverse and different astrovirus genotypes can be found in the same animal species, astrovirus is a potential zoonotic threat to humans. In this study, we screened for astroviruses in rodents from Hong Kong, Hunan and Guangxi. Astrovirus was detected in 11.9 % (67/562) of rectal swab specimens. Phylogenetic analysis of the ORF1b region, which encodes the RdRp, showed that there were four distinct clusters (clusters A, B, C and D). Whole genome sequencing was performed for 11 representative strains from each of these four clusters. The mean amino acid genetic distances (p-dist) of full-length ORF2 were >0.634 between clusters A, B, C and other known astroviruses. The p-dist between clusters A and B, A and C, and B and C were 0.371-0.375, 0.517-0.549 and 0.524-0.555, respectively. Within cluster C, the p-dist between HN-014 and GX-006 was 0.372. Since strains with p-dist of ≥0.368 in ORF2 are now considered to be of separate genotypes species, cluster A, cluster B, cluster C-HN-014 and cluster C-GX-006 can be classified as novel genotype species. Cluster D was most closely related to the rodent astrovirus previously identified in Hong Kong. Since rodents live in close proximity to humans, interspecies jumping of these novel astroviruses may represent a threat to human health.
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Affiliation(s)
- Kelvin K W To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China
| | - Wan-Mui Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kenneth S M Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China
| | - Carol S F Lam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China
| | - Zhiwei Chen
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China
| | - Herman Tse
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Susanna K P Lau
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China
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114
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Zhai SL, Zhang H, Lin T, Chen SN, Zhou X, Chen QL, Lv DH, Wen XH, Zhou XR, Jia CL, Wei WK. A novel porcine kobuvirus emerged in piglets with severe diarrhoea in China. Transbound Emerg Dis 2017; 64:1030-1036. [DOI: 10.1111/tbed.12663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Indexed: 11/29/2022]
Affiliation(s)
- S.-L. Zhai
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - H. Zhang
- College of Veterinary Medicine; South China Agricultural University; Guangzhou China
| | - T. Lin
- Department of Chemistry and Biochemistry; South Dakota State University; Brookings SD USA
| | - S.-N. Chen
- Department of Chemistry and Biochemistry; South Dakota State University; Brookings SD USA
| | - X. Zhou
- College of Veterinary Medicine; South China Agricultural University; Guangzhou China
| | - Q.-L. Chen
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - D.-H. Lv
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - X.-H. Wen
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - X.-R. Zhou
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - C.-L. Jia
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
| | - W.-K. Wei
- Guangdong Key Laboratory of Animal Disease Prevention; Animal Disease Diagnostic Center; Institute of Animal Health; Guangdong Academy of Agricultural Sciences; Guangzhou China
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115
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Lima DA, Cibulski SP, Finkler F, Teixeira TF, Varela APM, Cerva C, Loiko MR, Scheffer CM, Dos Santos HF, Mayer FQ, Roehe PM. Faecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular ssDNA viruses. J Gen Virol 2017; 98:690-703. [PMID: 28100302 DOI: 10.1099/jgv.0.000711] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This study is focused on the identification of the faecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with blastx revealed that 279 contigs (4 %) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes. In addition, a range of circular replication-associated protein encoding DNA viruses were also identified. The characterization of the faecal virome of healthy chickens described here not only provides a description of the viruses encountered in such niche but should also represent a baseline for future studies comparing viral populations in healthy and diseased chicken flocks. Moreover, it may also be relevant for human health, since chickens represent a significant proportion of the animal protein consumed worldwide.
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Affiliation(s)
- Diane A Lima
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Samuel P Cibulski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, Brazil
| | - Fabrine Finkler
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Thais F Teixeira
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Ana Paula M Varela
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Cristine Cerva
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Márcia R Loiko
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Camila M Scheffer
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Helton F Dos Santos
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
| | - Fabiana Q Mayer
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil
| | - Paulo M Roehe
- FEPAGRO Saúde Animal - Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Rio Grande do Sul, Brazil.,Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Brazil
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116
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Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae. Virol Sin 2017; 32:130-138. [PMID: 28466442 DOI: 10.1007/s12250-016-3896-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/22/2017] [Indexed: 12/27/2022] Open
Abstract
Recent studies have declared that members of the ssDNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease (CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD. Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.
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117
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Novel Single-Stranded DNA Virus Genomes Recovered from Chimpanzee Feces Sampled from the Mambilla Plateau in Nigeria. GENOME ANNOUNCEMENTS 2017; 5:5/9/e01715-16. [PMID: 28254982 PMCID: PMC5334589 DOI: 10.1128/genomea.01715-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Metagenomic approaches are rapidly expanding our knowledge of the diversity of viruses. In the fecal matter of Nigerian chimpanzees we recovered three gokushovirus genomes, one circular replication-associated protein encoding single-stranded DNA virus (CRESS), and a CRESS DNA molecule.
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118
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Chiappetta CM, Cibulski SP, Lima FES, Varela APM, Amorim DB, Tavares M, Roehe PM. Molecular Detection of Circovirus and Adenovirus in Feces of Fur Seals (Arctocephalus spp.). ECOHEALTH 2017; 14:69-77. [PMID: 27803979 PMCID: PMC7087719 DOI: 10.1007/s10393-016-1195-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/26/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
In some regions, little is known about exposure to viruses in coastal marine mammals. The present study aimed to detect viral RNA or DNA in 23 free-ranging fur seals on the northern coastline of Rio Grande do Sul State, Brazil. Polymerase chain reaction was used to detect nucleic acids of circoviruses, adenoviruses, morbilliviruses, vesiviruses, and coronaviruses in the feces from twenty-one South American fur seals (Arctocephalus australis) and two Subantarctic fur seals (A. tropicalis). Adenovirus DNA fragments were detected in two South American fur seals; nucleotide sequences of these fragments revealed a high degree of similarity to human adenovirus type C. Circovirus DNA fragments were detected in six animals of the same species. Two were phylogenetically similar to the Circovirus genus, whereas the other four nucleotide fragments showed no similarity to any of the known genera within the family Circoviridae. RNA fragments indicating the presence of coronavirus, vesivirus, and morbillivirus were not detected. These findings suggest that adenoviruses and circoviruses are circulating in fur seal populations found along the coast of Rio Grande do Sul State, Brazil.
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Affiliation(s)
- Catarina Marcon Chiappetta
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, (UFRGS), Rua Sarmento Leite 500, Porto Alegre, Rio Grande do Sul (RS), 90050-170, Brazil.
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves 9090, Porto Alegre, Rio Grande do Sul (RS), 9154-000, Brazil.
| | - Samuel Paulo Cibulski
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves 9090, Porto Alegre, Rio Grande do Sul (RS), 9154-000, Brazil
| | - Francisco Esmaile Sales Lima
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, (UFRGS), Rua Sarmento Leite 500, Porto Alegre, Rio Grande do Sul (RS), 90050-170, Brazil
| | - Ana Paula Muterle Varela
- Instituto de Pesquisas Veterinárias "Desidério Finamor" (IPVDF), Estrada do Conde 6000, Eldorado do Sul, Rio Grande do Sul (RS), 92990-000, Brazil
| | - Derek Blaese Amorim
- Centro de Estudos Costeiros, Limnológicos e Marinhos, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Tramandaí 976, Imbé, Rio Grande do Sul (RS), 95625-000, Brazil
| | - Maurício Tavares
- Centro de Estudos Costeiros, Limnológicos e Marinhos, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Tramandaí 976, Imbé, Rio Grande do Sul (RS), 95625-000, Brazil
| | - Paulo Michel Roehe
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, (UFRGS), Rua Sarmento Leite 500, Porto Alegre, Rio Grande do Sul (RS), 90050-170, Brazil
- Instituto de Pesquisas Veterinárias "Desidério Finamor" (IPVDF), Estrada do Conde 6000, Eldorado do Sul, Rio Grande do Sul (RS), 92990-000, Brazil
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119
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Moreira ASD, Raabis SM, Graham ME, Dreyfus JM, Sibley SD, Godhardt-Cooper JA, Toohey-Kurth KL, Goldberg TL, Peek SF. Identification by next-generation sequencing of Aichivirus B in a calf with enterocolitis and neurologic signs. J Vet Diagn Invest 2017; 29:208-211. [PMID: 28176615 DOI: 10.1177/1040638716685597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An 11-d-old Holstein bull calf was presented to the Veterinary Medical Teaching Hospital at the University of Wisconsin-Madison because of a 4-d history of diarrhea and persistent low-grade fever. Initial diagnosis was enteritis caused by Cryptosporidium and rotavirus. During hospitalization, the calf became stuporous and was only responsive to noxious stimuli, with hypotonia of all 4 limbs, tail, head, and neck. A cerebrospinal fluid analysis revealed xanthochromia, with marked lymphocytic pleocytosis, which was suggestive of viral meningitis and/or encephalitis. Aichivirus B, which belongs to the Kobuvirus genus, was tentatively identified in spinal fluid by next-generation DNA sequencing. This virus can affect a multitude of species, including humans and cattle, and has been isolated from both healthy and diarrheic individuals. However, to date, a possible connection with neurologic disease has not been described, to our knowledge.
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Affiliation(s)
- Ana S D Moreira
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Sarah M Raabis
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Melissa E Graham
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer M Dreyfus
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Samuel D Sibley
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer A Godhardt-Cooper
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Kathy L Toohey-Kurth
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Tony L Goldberg
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Simon F Peek
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
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120
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Janowski AB, Krishnamurthy SR, Lim ES, Zhao G, Brenchley JM, Barouch DH, Thakwalakwa C, Manary MJ, Holtz LR, Wang D. Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals. Virology 2017; 504:36-44. [PMID: 28152382 PMCID: PMC5515247 DOI: 10.1016/j.virol.2017.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/13/2017] [Accepted: 01/17/2017] [Indexed: 01/21/2023]
Abstract
Next-generation sequencing has expanded our understanding of the viral populations that constitute the mammalian virome. We describe a novel taxon of viruses named Statoviruses, for Stool associated Tombus-like viruses, present in multiple metagenomic datasets. These viruses define a novel clade that is phylogenetically related to the RNA virus families Tombusviridae and Flaviviridae. Five distinct statovirus types were identified in human, macaque, mouse, and cow gastrointestinal tract samples. The prototype genome, statovirus A, was frequently identified in macaque stool samples from multiple geographically distinct cohorts. Another genome, statovirus C1, was discovered in a stool sample from a human child with fever, cough, and rash. Further experimental data will clarify whether these viruses are infectious to mammals or if they originate from another source present in the mammalian gastrointestinal tract.
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Affiliation(s)
- Andrew B Janowski
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Siddharth R Krishnamurthy
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Efrem S Lim
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Guoyan Zhao
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jason M Brenchley
- Lab of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center, Boston, MA, USA; Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
| | - Chrissie Thakwalakwa
- Department of Community Health, College of Medicine, University of Malawi, Blantyre 3, Malawi
| | - Mark J Manary
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - David Wang
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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121
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Molecular detection of kobuviruses in livestock in Northern Ireland and the Republic of Ireland. Arch Virol 2017; 162:1275-1279. [DOI: 10.1007/s00705-017-3223-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
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122
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Pérot P, Lecuit M, Eloit M. Astrovirus Diagnostics. Viruses 2017; 9:v9010010. [PMID: 28085120 PMCID: PMC5294979 DOI: 10.3390/v9010010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 01/25/2023] Open
Abstract
Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.
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Affiliation(s)
- Philippe Pérot
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Institut Pasteur, Centre d'innovation et de Recherche Technologique (Citech), 75015 Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Paris Descartes University, Sorbonne Paris Cité, 75005, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, 75015 Paris, France.
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Ecole Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France.
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123
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An optimistic protein assembly from sequence reads salvaged an uncharacterized segment of mouse picobirnavirus. Sci Rep 2017; 7:40447. [PMID: 28071766 PMCID: PMC5223137 DOI: 10.1038/srep40447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/07/2016] [Indexed: 11/16/2022] Open
Abstract
Advances in Next Generation Sequencing technologies have enabled the generation of millions of sequences from microorganisms. However, distinguishing the sequence of a novel species from sequencing errors remains a technical challenge when the novel species is highly divergent from the closest known species. To solve such a problem, we developed a new method called Optimistic Protein Assembly from Reads (OPAR). This method is based on the assumption that protein sequences could be more conserved than the nucleotide sequences encoding them. By taking advantage of metagenomics, bioinformatics and conventional Sanger sequencing, our method successfully identified all coding regions of the mouse picobirnavirus for the first time. The salvaged sequences indicated that segment 1 of this virus was more divergent from its homologues in other Picobirnaviridae species than segment 2. For this reason, only segment 2 of mouse picobirnavirus has been detected in previous studies. OPAR web tool is available at http://bioinformatics.czc.hokudai.ac.jp/opar/.
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124
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Abstract
Taxonomical classification of newly discovered viruses and reclassification of previously discovered viruses provide an important foundation for detailing biological differences of scientific and clinical interest. The development of molecular analytical methods has enabled finer levels and more precise levels of classification. Periodically, there is need to refresh the literature and common understanding of current taxonomic classification, which we attempt to do here in addressing changes in human and animal viruses of medical significance between 2012 and 2015.
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125
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Kong N, Zuo Y, Wang Z, Yu H, Zhou EM, Shan T, Tong G. Molecular characterization of new described kobuvirus in dogs with diarrhea in China. SPRINGERPLUS 2016; 5:2047. [PMID: 27995024 PMCID: PMC5130936 DOI: 10.1186/s40064-016-3738-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022]
Abstract
Canine kobuvirus (CaKVs) was a newly described virus detected in dogs in the US and Italy. To learn more about CaKVs, 5 of 106 fecal samples from diarrhea dogs were positive with CaKVs in China, and the full genome of CaKVs strain CH-1 isolated from dog with diarrhea was sequenced. The genome consists of 8186 nucleotides, excluding the 3′ poly (A) tail, and an open reading frame that maps between nucleotide positions 601 and 7943 which encodes a 2446 amino acid polyprotein. Based on the complete amino acid sequence of polyprotein, phylogenetic analysis showed that CH-1 was grouped along with other canine kobuvirus strains detected in the USA (US-PC0082, AN211D).
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Affiliation(s)
- Ning Kong
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 China ; Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Yewen Zuo
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Zhongze Wang
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Hai Yu
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 China
| | - Guangzhi Tong
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China ; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 China
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Lau SKP, Yeung HC, Li KSM, Lam CSF, Cai JP, Yuen MC, Wang M, Zheng BJ, Woo PCY, Yuen KY. Identification and genomic characterization of a novel rat bocavirus from brown rats in China. INFECTION GENETICS AND EVOLUTION 2016; 47:68-76. [PMID: 27871815 DOI: 10.1016/j.meegid.2016.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/15/2016] [Accepted: 11/14/2016] [Indexed: 01/19/2023]
Abstract
Despite recent discoveries of novel animal bocaparvoviruses, current understandings on the diversity and evolution of bocaparvoviruses are still limited. We report the identification and genome characterization of a novel bocaparvovirus, rat bocaparvovirus (RBoV), in brown rats (Rattus norvegicus) in China. RBoV was detected in 11.5%, 2.4%, 16.2% and 0.3% of alimentary, respiratory, spleen and kidney samples respectively, of 636 brown rats by PCR, but not in samples of other rodent species, suggesting that brown rats are the primary reservoir of RBoV. Six RBoV genomes sequenced from three brown rats revealed the presence of three ORFs, characteristic of bocaparvoviruses. Phylogenetic analysis showed that RBoV was distantly related to other bocaparvoviruses, forming a distinct cluster within the genus, with ≤55.5% nucleotide identities to the genome of ungulate bocaparvovirus 3, supporting its classification as a novel bocaparvovirus species. RBoV possessed a putative second exon encoding the C-terminal region of NS1 and conserved RNA splicing signals, similar to human bocaparvoviruses and canine bocaparvovirus. In contrast to human, feline and canine bocaparvoviruses which demonstrates inter/intra-host viral diversity, partial VP1/VP2 sequences of 49 RBoV strains demonstrated little inter-host genetic diversity, suggesting a single genetic group. Although the pathogenicity of RBoV remains to be determined, its presence in different host tissues suggests wide tissue tropism. RBoV represents the first bocaparvovirus in rodents with genome sequenced, which extends our knowledge on the host range of bocaparvoviruses. Further studies are required to better understand the epidemiology, genetic diversity and pathogenicity of bocaparvoviruses in different rodent populations.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Hazel C Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kenneth S M Li
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Carol S F Lam
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jian-Piao Cai
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ming-Chi Yuen
- Food and Environmental Hygiene Department, The Government of the Hong Kong Special Administrative Region, Hong Kong, China
| | - Ming Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Bo-Jian Zheng
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China.
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China.
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127
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Deep sequencing for discovery and evolutionary analysis of plant viruses. Virus Res 2016; 239:82-86. [PMID: 27876625 DOI: 10.1016/j.virusres.2016.11.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/18/2016] [Indexed: 11/21/2022]
Abstract
The advent of next generation sequencing (NGS), or deep sequencing, has allowed great advances to be made in discovery, diagnostics, and evolutionary studies in plant viruses. Various methods have been used for enrichment for virus-specific nucleic acids, each of which have some drawbacks. Many novel viruses have been discovered in plants by NGS technologies, and there is a good deal of promise for more comprehensive studies in virus evolution. However, each aspect of using NGS has its caveats that need to be considered, and there is still a need for better tools of analysis, as well as method for validation of sequence variation.
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128
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Pearson VM, Caudle SB, Rokyta DR. Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant. PeerJ 2016; 4:e2585. [PMID: 27781171 PMCID: PMC5075696 DOI: 10.7717/peerj.2585] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/19/2016] [Indexed: 12/26/2022] Open
Abstract
Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group.
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Affiliation(s)
- Victoria M Pearson
- Department of Biological Science, Florida State University , Tallahassee , FL , USA
| | - S Brian Caudle
- Division of Food Safety, Florida Department of Agriculture and Consumer Services , Tallahassee , FL , USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University , Tallahassee , FL , USA
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129
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Lau SKP, Woo PCY, Li KSM, Zhang HJ, Fan RYY, Zhang AJX, Chan BCC, Lam CSF, Yip CCY, Yuen MC, Chan KH, Chen ZW, Yuen KY. Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model. PLoS Pathog 2016; 12:e1005911. [PMID: 27737017 PMCID: PMC5063349 DOI: 10.1371/journal.ppat.1005911] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/02/2016] [Indexed: 01/14/2023] Open
Abstract
While novel picornaviruses are being discovered in rodents, their host range and pathogenicity are largely unknown. We identified two novel picornaviruses, rosavirus B from the street rat, Norway rat, and rosavirus C from five different wild rat species (chestnut spiny rat, greater bandicoot rat, Indochinese forest rat, roof rat and Coxing's white-bellied rat) in China. Analysis of 13 complete genome sequences showed that “Rosavirus B” and “Rosavirus C” represent two potentially novel picornavirus species infecting different rodents. Though being most closely related to rosavirus A, rosavirus B and C possessed distinct protease cleavage sites and variations in Yn-Xm-AUG sequence in 5’UTR and myristylation site in VP4. Anti-rosavirus B VP1 antibodies were detected in Norway rats, whereas anti-rosavirus C VP1 and neutralizing antibodies were detected in Indochinese forest rats and Coxing's white-bellied rats. While the highest prevalence was observed in Coxing's white-bellied rats by RT-PCR, the detection of rosavirus C from different rat species suggests potential interspecies transmission. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with high viral loads and positive viral antigen expression in organs of infected mice after oral or intracerebral inoculation. Histological examination revealed alveolar fluid exudation, interstitial infiltration, alveolar fluid exudate and wall thickening in lungs, and hepatocyte degeneration and lymphocytic/monocytic inflammatory infiltrates with giant cell formation in liver sections of sacrificed mice. Since rosavirus A2 has been detected in fecal samples of children, further studies should elucidate the pathogenicity and emergence potential of different rosaviruses. We identified two novel picornaviruses, rosavirus B and C, infecting street and wild rats respectively in China. While rosavirus B was detected from Norway rats, rosavirus C was detected from five different wild rat species (chestnut spiny rat, greater bandicoot rat, Indochinese forest rat, roof rat and Coxing's white-bellied rat) by RT-PCR. Anti-rosavirus B antibodies were detected in Norway rats, whereas anti-rosavirus C antibodies were detected in Indochinese forest rats and Coxing's white-bellied rats, supporting potential interspecies transmission of rosavirus C. Genome analysis supported the classification of rosavirus B and C as two novel picornavirus species, with genome features distinct from rosavirus A. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with viruses and pathologies detected in various organs of infected mice after oral or intracerebral inoculation. Our results extend our knowledge on the host range and pathogenicity of rodent picornaviruses.
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Affiliation(s)
- Susanna K. P. Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Patrick C. Y. Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kenneth S. M. Li
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Hao-Ji Zhang
- Department of Veterinary Medicine, Foshan University, Foshan, China
| | - Rachel Y. Y. Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Anna J. X. Zhang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Brandon C. C. Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Carol S. F. Lam
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Cyril C. Y. Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ming-Chi Yuen
- Food and Environmental Hygiene Department, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Zhi-Wei Chen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- * E-mail:
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130
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Distribution and characteristics of rodent picornaviruses in China. Sci Rep 2016; 6:34381. [PMID: 27682620 PMCID: PMC5041129 DOI: 10.1038/srep34381] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/12/2016] [Indexed: 01/13/2023] Open
Abstract
Rodents are important reservoir hosts of many important zoonotic viruses. The family Picornaviridae contains clinically important pathogens that infect humans and animals, and increasing numbers of rodent picornaviruses have recently been associated with zoonoses. We collected 574 pharyngeal and anal swab specimens from 287 rodents of 10 different species from eight representative regions of China from October 2013 to July 2015. Seven representative sequences identified from six rodent species were amplified as full genomes and classified into four lineages. Three lineage 1 viruses belonged to a novel genus of picornaviruses and was more closely related to Hepatovirus than to others genera of picornaviruses based on aa homology. Lineage 2, lineage 3, and lineage 4 viruses belonged to the genera Rosavirus, Hunnivirus, and Enterovirus, respectively, representing new species. According to both phylogenetic and identity analyses, Lineage 2 viruses had a close relationship with rosavirus 2 which was recovered from the feces of a child in Gambia and Lineage 3 viruses had a close relationship with domestic animal Hunnivirus. Lineage 4 viruses provide the first evidence of these enteroviruses and their evolution in rodent hosts in China.
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131
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Candido M, Batinga MCA, Alencar ALF, de Almeida-Queiroz SR, da Glória Buzinaro M, Livonesi MC, Fernandes AM, de Sousa RLM. Molecular characterization and genetic diversity of bovine Kobuvirus, Brazil. Virus Genes 2016; 53:105-110. [PMID: 27623839 DOI: 10.1007/s11262-016-1391-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/06/2016] [Indexed: 12/01/2022]
Abstract
It is suggested that Bovine kobuvirus (BKV) is involved in the etiology of gastroenteric diseases especially among calves; however, this association remains unknown. This study evaluated 216 fecal samples from cattle with and without diarrhea symptoms obtained from different regions of Brazil. A 216 bp fragment of the BKV 3D gene was amplified by RT-PCR in 14.4 % (31/216) of the studied samples, and 17 samples were subjected to nucleotide sequencing. All positive samples were obtained from animals aged less than 5 months, and most of animals presented diarrhea (p < 0.05). Phylogenetic analyses showed that the obtained sequences were grouped within the genogroup 2 of BKV forming subclades specific for each Brazilian municipality sampled. In addition, the alignment of the sequences revealed differences of nucleotides between sequences from different locations. Our results indicate for the first time that there is a regional genotypic differentiation of BKV in Brazil.
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Affiliation(s)
- Marcelo Candido
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil.
| | - Maria Cryskely Agra Batinga
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Anna Luiza Farias Alencar
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Sabrina Ribeiro de Almeida-Queiroz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Maria da Glória Buzinaro
- Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellani, Rural, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Márcia Cristina Livonesi
- Department of Clinical Analysis, Alfenas Federal University (UNIFAL), Rua Gabriel Monteiro da Silva, 700, Centro, Alfenas, Minas Gerais, 37130-000, Brazil
| | - Andrezza Maria Fernandes
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Ricardo Luiz Moro de Sousa
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
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132
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First molecular evidence of kobuviruses in goats in Italy. Arch Virol 2016; 161:3245-8. [DOI: 10.1007/s00705-016-3017-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
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133
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Hansen TA, Mollerup S, Nguyen NP, White NE, Coghlan M, Alquezar-Planas DE, Joshi T, Jensen RH, Fridholm H, Kjartansdóttir KR, Mourier T, Warnow T, Belsham GJ, Bunce M, Willerslev E, Nielsen LP, Vinner L, Hansen AJ. High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerg Microbes Infect 2016; 5:e90. [PMID: 27530749 PMCID: PMC5034103 DOI: 10.1038/emi.2016.90] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/30/2016] [Accepted: 06/13/2016] [Indexed: 12/02/2022]
Abstract
Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.
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Affiliation(s)
- Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Nam-Phuong Nguyen
- Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA
| | - Nicole E White
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - Megan Coghlan
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tejal Joshi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800 Kongens Lyngby, Denmark
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.,Virus Research and Development, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tandy Warnow
- Departments of Bioengineering and Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA
| | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Michael Bunce
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
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134
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Phan TG, Messacar K, Dominguez SR, da Costa AC, Deng X, Delwart E. A new densovirus in cerebrospinal fluid from a case of anti-NMDA-receptor encephalitis. Arch Virol 2016; 161:3231-5. [PMID: 27522586 DOI: 10.1007/s00705-016-3002-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/26/2016] [Indexed: 01/16/2023]
Abstract
We characterized the genome of a densovirus, tentatively called human CSF-associated densovirus 1 (HuCSFDV1), in cerebrospinal fluid (CSF) from a human case of encephalitis with antibodies against the N-methyl D-aspartate receptor. The presence of the viral genome in CSF was independently confirmed. This virus, which is proposed to be a member of a new species in the genus Iteradensovirus of the subfamily Densovirinae, showed the typical two ORFs encoding nonstructural and structural proteins with low-level identities of 22 and 16 % to the closest known densovirus relative. No other eukaryotic viral sequences were detected using deep sequencing. The replication and pathogenicity in humans of this virus, which belongs to a viral subfamily whose members are only known to replicate in invertebrates, remain to be demonstrated. Alternative explanations for the detection of densovirus DNA in CSF are discussed.
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Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Kevin Messacar
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Samuel R Dominguez
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Antonio Charlys da Costa
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
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135
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Reperant LA, Brown IH, Haenen OL, de Jong MD, Osterhaus ADME, Papa A, Rimstad E, Valarcher JF, Kuiken T. Companion Animals as a Source of Viruses for Human Beings and Food Production Animals. J Comp Pathol 2016; 155:S41-53. [PMID: 27522300 DOI: 10.1016/j.jcpa.2016.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 01/12/2023]
Abstract
Companion animals comprise a wide variety of species, including dogs, cats, horses, ferrets, guinea pigs, reptiles, birds and ornamental fish, as well as food production animal species, such as domestic pigs, kept as companion animals. Despite their prominent place in human society, little is known about the role of companion animals as sources of viruses for people and food production animals. Therefore, we reviewed the literature for accounts of infections of companion animals by zoonotic viruses and viruses of food production animals, and prioritized these viruses in terms of human health and economic importance. In total, 138 virus species reportedly capable of infecting companion animals were of concern for human and food production animal health: 59 of these viruses were infectious for human beings, 135 were infectious for food production mammals and birds, and 22 were infectious for food production fishes. Viruses of highest concern for human health included hantaviruses, Tahyna virus, rabies virus, West Nile virus, tick-borne encephalitis virus, Crimean-Congo haemorrhagic fever virus, Aichi virus, European bat lyssavirus, hepatitis E virus, cowpox virus, G5 rotavirus, influenza A virus and lymphocytic choriomeningitis virus. Viruses of highest concern for food production mammals and birds included bluetongue virus, African swine fever virus, foot-and-mouth disease virus, lumpy skin disease virus, Rift Valley fever virus, porcine circovirus, classical swine fever virus, equine herpesvirus 9, peste des petits ruminants virus and equine infectious anaemia virus. Viruses of highest concern for food production fishes included cyprinid herpesvirus 3 (koi herpesvirus), viral haemorrhagic septicaemia virus and infectious pancreatic necrosis virus. Of particular concern as sources of zoonotic or food production animal viruses were domestic carnivores, rodents and food production animals kept as companion animals. The current list of viruses provides an objective basis for more in-depth analysis of the risk of companion animals as sources of viruses for human and food production animal health.
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Affiliation(s)
- L A Reperant
- Department of Viroscience, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - I H Brown
- Animal and Plant Health Agency Weybridge, New Haw, Addlestone, Surrey, UK
| | - O L Haenen
- National Reference Laboratory for Fish, Shellfish and Crustacean Diseases, Central Veterinary Institute of Wageningen UR, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - M D de Jong
- Department of Medical Microbiology, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - A D M E Osterhaus
- Department of Viroscience, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - A Papa
- Department of Microbiology, Medical School Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - E Rimstad
- Department of Food Safety and Infection Biology, University of Life Sciences, Oslo, Norway
| | - J-F Valarcher
- Department of Virology, Immunology, and Parasitology, National Veterinary Institute, Uppsala, Sweden
| | - T Kuiken
- Department of Viroscience, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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Vandegrift KJ, Critchlow JT, Kapoor A, Friedman DA, Hudson PJ. Peromyscus as a model system for human hepatitis C: An opportunity to advance our understanding of a complex host parasite system. Semin Cell Dev Biol 2016; 61:123-130. [PMID: 27498234 DOI: 10.1016/j.semcdb.2016.07.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023]
Abstract
Worldwide, there are 185 million people infected with hepatitis C virus and approximately 350,000 people die each year from hepatitis C associated liver diseases. Human hepatitis C research has been hampered by the lack of an appropriate in vivo model system. Most of the in vivo research has been conducted on chimpanzees, which is complicated by ethical concerns, small sample sizes, high costs, and genetic heterogeneity. The house mouse system has led to greater understanding of a wide variety of human pathogens, but it is unreasonable to expect Mus musculus to be a good model system for every human pathogen. Alternative animal models can be developed in these cases. Ferrets (influenza), cotton rats (human respiratory virus), and woodchucks (hepatitis B) are all alternative models that have led to a greater understanding of human pathogens. Rodent models are tractable, genetically amenable and inbred and outbred strains can provide homogeneity in results. Recently, a rodent homolog of hepatitis C was discovered and isolated from the liver of a Peromyscus maniculatus. This represents the first small mammal (mouse) model system for human hepatitis C and it offers great potential to contribute to our understanding and ultimately aid in our efforts to combat this serious public health concern. Peromyscus are available commercially and can be used to inform questions about the origin, transmission, persistence, pathology, and rational treatment of hepatitis C. Here, we provide a disease ecologist's overview of this new virus and some suggestions for useful future experiments.
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Affiliation(s)
- Kurt J Vandegrift
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Justin T Critchlow
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, United States
| | - Amit Kapoor
- Center for Vaccines and Immunity, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, United States
| | - David A Friedman
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, United States
| | - Peter J Hudson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, United States
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137
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Chuchaona W, Khamrin P, Yodmeeklin A, Kumthip K, Saikruang W, Thongprachum A, Okitsu S, Ushijima H, Maneekarn N. Detection and characterization of Aichi virus 1 in pediatric patients with diarrhea in Thailand. J Med Virol 2016; 89:234-238. [PMID: 27420653 DOI: 10.1002/jmv.24630] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2016] [Indexed: 11/06/2022]
Abstract
Kobuvirus is a newly discovered virus that belongs to the Kobuvirus genus in Picornaviridae family, which comprised of three species including Aichivirus A, Aichivirus B, and Aichivirus C. The kobuvirus isolated from human has been classified as Aichi virus 1 and belongs to Aichivirus A species. The present study aimed to assess the epidemiology and to perform molecular characterization of Aichi virus 1 in children admitted to hospitals with acute gastroenteritis in Chiang Mai, Thailand. A total of 923 fecal specimens collected from January, 2011 to December, 2013 were screened for the presence of Aichi virus 1 by RT semi-nested PCR. Out of 923 fecal specimens tested, Aichi virus 1 was detected with the prevalence of 2.6% (24/923). Of these, 0.3% (3/923) was genotype A and 2.3% (21/923) were genotype B. It is interesting to note that the genotype A showed the nucleotide sequence closely related to the Aichi virus reference strain isolated from sewage in Tunisia, while genotype B was most closely related to other human Aichi virus B reference strains. The results suggest that Aichi virus 1 of both genotypes A and B are circulating in pediatric patients in Thailand. J. Med. Virol. 89:234-238, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Watchaporn Chuchaona
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Wilaiporn Saikruang
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Aksara Thongprachum
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shoko Okitsu
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
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138
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Fawaz M, Vijayakumar P, Mishra A, Gandhale PN, Dutta R, Kamble NM, Sudhakar SB, Roychoudhary P, Kumar H, Kulkarni DD, Raut AA. Duck gut viral metagenome analysis captures snapshot of viral diversity. Gut Pathog 2016; 8:30. [PMID: 27284287 PMCID: PMC4899906 DOI: 10.1186/s13099-016-0113-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/30/2016] [Indexed: 11/18/2022] Open
Abstract
Background Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential. Methods To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds. Result In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx E score, <10−3) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. Further, several duck virome sequences had homologous with the insect viruses of the Poxviridae, Alphatetraviridae, Baculoviridae, Densovirinae, Iflaviridae and Dicistroviridae families; and plant viruses of the Secoviridae, Virgaviridae, Tombusviridae and Partitiviridae families, which reflects the diet and habitation of ducks. Conclusion This study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.
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Affiliation(s)
- Mohammed Fawaz
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Periyasamy Vijayakumar
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Anamika Mishra
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Pradeep N Gandhale
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Rupam Dutta
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Nitin M Kamble
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Shashi B Sudhakar
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Parimal Roychoudhary
- College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Aizawl, Mizoram India
| | - Himanshu Kumar
- Laboratory of Immunology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
| | - Diwakar D Kulkarni
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Ashwin Ashok Raut
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
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139
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Springer YP, Hoekman D, Johnson PTJ, Duffy PA, Hufft RA, Barnett DT, Allan BF, Amman BR, Barker CM, Barrera R, Beard CB, Beati L, Begon M, Blackmore MS, Bradshaw WE, Brisson D, Calisher CH, Childs JE, Diuk‐Wasser M, Douglass RJ, Eisen RJ, Foley DH, Foley JE, Gaff HD, Gardner SL, Ginsberg HS, Glass GE, Hamer SA, Hayden MH, Hjelle B, Holzapfel CM, Juliano SA, Kramer LD, Kuenzi AJ, LaDeau SL, Livdahl TP, Mills JN, Moore CG, Morand S, Nasci RS, Ogden NH, Ostfeld RS, Parmenter RR, Piesman J, Reisen WK, Savage HM, Sonenshine DE, Swei A, Yabsley MJ. Tick‐, mosquito‐, and rodent‐borne parasite sampling designs for the National Ecological Observatory Network. Ecosphere 2016. [DOI: 10.1002/ecs2.1271] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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140
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A novel species of torque teno mini virus (TTMV) in gingival tissue from chronic periodontitis patients. Sci Rep 2016; 6:26739. [PMID: 27221159 PMCID: PMC4879676 DOI: 10.1038/srep26739] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/06/2016] [Indexed: 11/20/2022] Open
Abstract
A new species of torque teno mini virus, named TTMV-222, was detected in gingival tissue from periodontitis patients using a viral metagenomics method. The 2803-nucleotide genome of TTMV-222 is closely related to TTMV1-CBD279, with 62.6% overall nucleotide similarity. Genetic analyses of the new virus genome revealed a classic genomic organization but a weak identity with known sequences. The prevalence of TTMV-222 in the periodontitis group (n = 150) was significantly higher than that in the healthy group (n = 150) (p = 0.032), suggesting that the new virus may be associated with inflammation in chronic periodontitis patients. However, this finding requires further investigation.
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141
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Discovery and complete genome sequence of a novel circovirus-like virus in the endangered rowi kiwi, Apteryx rowi. Virus Genes 2016; 52:727-31. [PMID: 27115421 DOI: 10.1007/s11262-016-1342-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
Abstract
Circoviruses are circular, non-enveloped, single-stranded DNA viruses around 2000 nucleotides (nt) in length and include the pathogenic species, Porcine circovirus 1 and Beak and feather disease virus, capable of causing significant morbidity and mortality. This group of viruses may be robust to degradation by external environments, and avian circoviruses are known to move between closely related hosts. Using a de novo metagenomic approach, followed by confirmatory PCR, we identify for the first time a circular Rep-encoding single-stranded (CRESS) DNA virus in New Zealand kiwi, Apteryx spp., derived from faecal matter of the rowi kiwi (A. rowi) showing signs of verminous dermatitis. The entire 2085 nt genome was cloned and sequenced and contains both capsid and replicase genes, as well as a conserved 9 nt motif. Phylogenetic analyses place it within Circoviridae, adjacent to other environmental CRESS-DNA viruses, and most closely related to badger circovirus-like virus (Meles meles circovirus-like virus). As the rowi is the most critically endangered kiwi, it is vital to understand the role of rowi kiwi circovirus-like virus as a possible pathogen and also any potential cross-species transmission.
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142
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Enteric Viruses Ameliorate Gut Inflammation via Toll-like Receptor 3 and Toll-like Receptor 7-Mediated Interferon-β Production. Immunity 2016; 44:889-900. [DOI: 10.1016/j.immuni.2016.03.009] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/14/2015] [Accepted: 12/29/2015] [Indexed: 12/19/2022]
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143
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Tsoleridis T, Onianwa O, Horncastle E, Dayman E, Zhu M, Danjittrong T, Wachtl M, Behnke JM, Chapman S, Strong V, Dobbs P, Ball JK, Tarlinton RE, McClure CP. Discovery of Novel Alphacoronaviruses in European Rodents and Shrews. Viruses 2016; 8:84. [PMID: 27102167 PMCID: PMC4810274 DOI: 10.3390/v8030084] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/29/2016] [Accepted: 03/11/2016] [Indexed: 12/04/2022] Open
Abstract
Eight hundred and thirteen European rodents and shrews encompassing seven different species were screened for alphacoronaviruses using PCR detection. Novel alphacoronaviruses were detected in the species Rattus norvegicus, Microtus agrestis, Sorex araneus and Myodes glareolus. These, together with the recently described Lucheng virus found in China, form a distinct rodent/shrew-specific clade within the coronavirus phylogeny. Across a highly conserved region of the viral polymerase gene, the new members of this clade were up to 22% dissimilar at the nucleotide level to the previously described Lucheng virus. As such they might represent distinct species of alphacoronaviruses. These data greatly extend our knowledge of wildlife reservoirs of alphacoronaviruses.
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Affiliation(s)
| | - Okechukwu Onianwa
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Emma Horncastle
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Emma Dayman
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Miaoran Zhu
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | | | - Marta Wachtl
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Jerzy M Behnke
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Sarah Chapman
- Twycross Zoo, Burton Road, Atherstone, Warwickshire CV9 3PX, UK.
| | - Victoria Strong
- Twycross Zoo, Burton Road, Atherstone, Warwickshire CV9 3PX, UK.
| | - Phillipa Dobbs
- Twycross Zoo, Burton Road, Atherstone, Warwickshire CV9 3PX, UK.
| | - Jonathan K Ball
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Rachael E Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
| | - C Patrick McClure
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
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144
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Viral metagenomics applied to blood donors and recipients at high risk for blood-borne infections. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2016; 14:400-7. [PMID: 27136432 DOI: 10.2450/2016.0160-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/18/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Characterisation of human-associated viral communities is essential for epidemiological surveillance and to be able to anticipate new potential threats for blood transfusion safety. In high-resource countries, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) is currently considered to be under control. However, other unknown or unsuspected viruses may be transmitted to recipients by blood-derived products. To investigate this, the virome of plasma from individuals at high risk for parenterally and sexually transmitted infections was analysed by high throughput sequencing (HTS). MATERIALS AND METHODS Purified nucleic acids from two pools of 50 samples from recipients of multiple transfusions, and three pools containing seven plasma samples from either HBV-, HCV- or HIV-infected blood donors, were submitted to HTS. RESULTS Sequences from resident anelloviruses and HPgV were evidenced in all pools. HBV and HCV sequences were detected in pools containing 3.8×10(3) IU/mL of HBV-DNA and 1.7×10(5) IU/mL of HCV-RNA, respectively, whereas no HIV sequence was found in a pool of 150 copies/mL of HIV-RNA. This suggests a lack of sensitivity in HTS performance in detecting low levels of virus. In addition, this study identified other issues, including laboratory contaminants and the uncertainty of taxonomic assignment of short sequence. No sequence suggestive of a new viral species was identified. DISCUSSION This study did not identify any new blood-borne virus in high-risk individuals. However, rare and/or viruses present at very low titre could have escaped our protocol. Our results demonstrate the positive contribution of HTS in the detection of viral sequences in blood donations.
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145
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Amimo JO, El Zowalaty ME, Githae D, Wamalwa M, Djikeng A, Nasrallah GK. Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa. Arch Virol 2016; 161:887-97. [PMID: 26965436 DOI: 10.1007/s00705-016-2819-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/03/2016] [Indexed: 01/01/2023]
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.
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Affiliation(s)
- Joshua O Amimo
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, P.O Box 29053, Nairobi, 00625, Kenya. .,Bioscieces of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, P.O Box 30709, Nairobi, 00100, Kenya.
| | | | - Dedan Githae
- Bioscieces of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, P.O Box 30709, Nairobi, 00100, Kenya
| | - Mark Wamalwa
- Bioscieces of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, P.O Box 30709, Nairobi, 00100, Kenya
| | - Apollinaire Djikeng
- Bioscieces of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI), Hub, Nairobi, P.O Box 30709, Nairobi, 00100, Kenya
| | - Gheyath K Nasrallah
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar. .,Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, 2713, Qatar.
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146
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Wang Y, Zhu N, Li Y, Lu R, Wang H, Liu G, Zou X, Xie Z, Tan W. Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China. Clin Microbiol Infect 2016; 22:458.e1-9. [PMID: 26802214 PMCID: PMC7172101 DOI: 10.1016/j.cmi.2016.01.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/21/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory infection (SARI) in children is thought to be mainly caused by infection with various viruses, some of which have been well characterized; however, analyses of respiratory tract viromes among children with SARI versus those without are limited. In this study, nasopharyngeal swabs from children with and without SARI (135 versus 15) were collected in China between 2008 and 2010 and subjected to multiplex metagenomic analyses using a next-generation sequencing platform. The results show that members of the Paramyxoviridae, Coronaviridae, Parvoviridae, Orthomyxoviridae, Picornaviridae, Anelloviridae and Adenoviridae families represented the most abundant species identified (>50% genome coverage) in the respiratory tracts of children with SARI. The viral population found in the respiratory tracts of children without SARI was less diverse and mainly dominated by the Anelloviridae family with only a small proportion of common epidemic respiratory viruses. Several almost complete viral genomes were assembled, and the genetic diversity was determined among several samples based on next-generation sequencing. This research provides comprehensive mapping of the viromes of children with SARI and indicates high heterogeneity of known viruses present in the childhood respiratory tract, which may benefit the detection and prevention of respiratory disease.
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Affiliation(s)
- Y Wang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - N Zhu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - Y Li
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - R Lu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - H Wang
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - G Liu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - X Zou
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - Z Xie
- Key Laboratory of Major Diseases in Children and National Key Discipline of Paediatrics Capital Medical University, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - W Tan
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China.
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147
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Pfeiffer JK, Virgin HW. Viral immunity. Transkingdom control of viral infection and immunity in the mammalian intestine. Science 2016; 351:aad5872. [PMID: 26816384 PMCID: PMC4751997 DOI: 10.1126/science.aad5872] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viruses that infect the intestine include major human pathogens (retroviruses, noroviruses, rotaviruses, astroviruses, picornaviruses, adenoviruses, herpesviruses) that constitute a serious public health problem worldwide. These viral pathogens are members of a large, complex viral community inhabiting the intestine termed "the enteric virome." Enteric viruses have intimate functional and genetic relationships with both the host and other microbial constituents that inhabit the intestine, such as the bacterial microbiota, their associated phages, helminthes, and fungi, which together constitute the microbiome. Emerging data indicate that enteric viruses regulate, and are in turn regulated by, these other microbes through a series of processes termed "transkingdom interactions." This represents a changing paradigm in intestinal immunity to viral infection. Here we review recent advances in the field and propose new ways in which to conceptualize this important area.
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Affiliation(s)
- Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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148
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Abstract
The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.
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Affiliation(s)
- V Sauvage
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence des hépatites virales B et C et du VIH en transfusion, 75015 Paris, France.
| | - M Eloit
- PathoQuest, bâtiment François-Jacob, 25, rue du Dr-Roux, 75015 Paris, France; Inserm U1117, Biology of Infection Unit, Laboratory of Pathogen Discovery, Institut Pasteur, 28, rue du Docteur-Roux, 75724 Paris, France
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149
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Broecker F, Klumpp J, Schuppler M, Russo G, Biedermann L, Hombach M, Rogler G, Moelling K. Long-term changes of bacterial and viral compositions in the intestine of a recovered Clostridium difficile patient after fecal microbiota transplantation. Cold Spring Harb Mol Case Stud 2016; 2:a000448. [PMID: 27148577 PMCID: PMC4849847 DOI: 10.1101/mcs.a000448] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/27/2015] [Indexed: 12/12/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infections (RCDIs). However, long-term effects on the patients' gut microbiota and the role of viruses remain to be elucidated. Here, we characterized bacterial and viral microbiota in the feces of a cured RCDI patient at various time points until 4.5 yr post-FMT compared with the stool donor. Feces were subjected to DNA sequencing to characterize bacteria and double-stranded DNA (dsDNA) viruses including phages. The patient's microbial communities varied over time and showed little overall similarity to the donor until 7 mo post-FMT, indicating ongoing gut microbiota adaption in this time period. After 4.5 yr, the patient's bacteria attained donor-like compositions at phylum, class, and order levels with similar bacterial diversity. Differences in the bacterial communities between donor and patient after 4.5 yr were seen at lower taxonomic levels. C. difficile remained undetectable throughout the entire timespan. This demonstrated sustainable donor feces engraftment and verified long-term therapeutic success of FMT on the molecular level. Full engraftment apparently required longer than previously acknowledged, suggesting the implementation of year-long patient follow-up periods into clinical practice. The identified dsDNA viruses were mainly Caudovirales phages. Unexpectedly, sequences related to giant algae-infecting Chlorella viruses were also detected. Our findings indicate that intestinal viruses may be implicated in the establishment of gut microbiota. Therefore, virome analyses should be included in gut microbiota studies to determine the roles of phages and other viruses-such as Chlorella viruses-in human health and disease, particularly during RCDI.
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Affiliation(s)
- Felix Broecker
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland;; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, 8096 Zurich, Switzerland
| | - Markus Schuppler
- Institute of Food, Nutrition and Health, ETH Zurich, 8096 Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
| | - Luc Biedermann
- Division of Gastroenterology and Hepatology, University Hospital Zurich, 8006 Zurich, Switzerland
| | - Michael Hombach
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Gerhard Rogler
- Division of Gastroenterology and Hepatology, University Hospital Zurich, 8006 Zurich, Switzerland
| | - Karin Moelling
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland;; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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Pankovics P, Boros Á, Bíró H, Horváth KB, Phan TG, Delwart E, Reuter G. Novel picornavirus in domestic rabbits (Oryctolagus cuniculus var. domestica). INFECTION GENETICS AND EVOLUTION 2015; 37:117-22. [PMID: 26588888 PMCID: PMC7172602 DOI: 10.1016/j.meegid.2015.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/20/2015] [Accepted: 11/14/2015] [Indexed: 12/12/2022]
Abstract
Picornaviruses (family Picornaviridae) are small, non-enveloped viruses with positive sense, single-stranded RNA genomes. The numbers of the novel picornavirus species and genera are continuously increasing. Picornaviruses infect numerous vertebrate species from fish to mammals, but have not been identified in a member of the Lagomorpha order (pikas, hares and rabbits). In this study, a novel picornavirus was identified in 16 (28.6%) out of 56 faecal samples collected from clinically healthy rabbits (Oryctolagus cuniculus var. domestica) in two (one commercial and one family farms) of four rabbit farms in Hungary. The 8364 nucleotide (2486 amino acid) long complete genome sequence of strain Rabbit01/2013/HUN (KT325852) has typical picornavirus genome organization with type-V IRES at the 5'UTR, encodes a leader (L) and a single 2A(H-box/NC) proteins, contains a hepatitis-A-virus-like cis-acting replication element (CRE) in the 2A, but it does not contain the sequence forming a "barbell-like" secondary structure in the 3'UTR. Rabbit01/2013/HUN has 52.9%, 52% and 57.2% amino acid identity to corresponding proteins of species Aichivirus A (genus Kobuvirus): to murine Kobuvirus (JF755427) in P1, to canine Kobuvirus (JN387133) in P2 and to feline Kobuvirus (KF831027) in P3, respectively. The sequence and phylogenetic analysis indicated that Rabbit01/2013/HUN represents a novel picornavirus species possibly in genus Kobuvirus. This is the first report of detection of picornavirus in rabbit. Further study is needed to clarify whether this novel picornavirus plays a part in any diseases in domestic or wild rabbits.
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Affiliation(s)
- Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | | | - Katalin Barbara Horváth
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.
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