151
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Focosi D, Antonelli G, Pistello M, Maggi F. Torquetenovirus: the human virome from bench to bedside. Clin Microbiol Infect 2016; 22:589-93. [PMID: 27093875 DOI: 10.1016/j.cmi.2016.04.007] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/04/2016] [Accepted: 04/10/2016] [Indexed: 12/15/2022]
Abstract
Torquetenovirus (TTV) is the most abundant component of human virome. Virologists have long ignored this orphan and highly divergent virus, in part because TTV cannot be cultured and because it lacks serology reagents and animal models. Nevertheless, it is almost endemic worldwide and is insensitive to current antiviral drugs, so its monitoring is useful in various conditions. To date, TTV as a marker has proved useful in at least two circumstances: to identify anthropogenic pollution and to assess functional immune competence in immunosuppressed individuals. This review summarizes recent findings about TTV and discusses the main hurdles in translating them into clinical diagnostics.
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Affiliation(s)
- D Focosi
- North-Western Tuscany Blood Bank, Italy
| | - G Antonelli
- Laboratory of Virology, Department of Molecular Medicine, and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - M Pistello
- Virology Unit and Retrovirus Centre, Pisa University Hospital, Italy; Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - F Maggi
- Virology Unit and Retrovirus Centre, Pisa University Hospital, Italy.
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152
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Aguirre de Cárcer D, López-Bueno A, Alonso-Lobo JM, Quesada A, Alcamí A. Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula. FEMS Microbiol Ecol 2016; 92:fiw074. [PMID: 27059864 DOI: 10.1093/femsec/fiw074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 01/21/2023] Open
Abstract
Environmental viruses constitute the most abundant biological entities on earth, and harbor an enormous genetic diversity. While their strong influence on the ecosystem is widely acknowledged, current knowledge about their diversity and distribution remains limited. Here we present the metagenomic study of viral communities from freshwater bodies located along a transect of the Antarctic Peninsula. These ecosystems were chosen on the basis of environmental and biogeographical variation. The results obtained indicate that the virus assemblages were diverse, and that the larger fraction represented viruses with no close relatives in the databases. Comparisons to existing metaviromes showed that the communities studied were dissimilar to other freshwater viromes including those from the Arctic. Finally, we observed no indication of there being a reduction in either viral richness or diversity estimates with increasing latitude along the studied transect, further adding to the controversy regarding the possible existence of latitudinal gradients of diversity in the microbial world.
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Affiliation(s)
- Daniel Aguirre de Cárcer
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan M Alonso-Lobo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Antonio Quesada
- Departamento de Biología, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain
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153
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Bernardo P, Muhire B, François S, Deshoux M, Hartnady P, Farkas K, Kraberger S, Filloux D, Fernandez E, Galzi S, Ferdinand R, Granier M, Marais A, Monge Blasco P, Candresse T, Escriu F, Varsani A, Harkins GW, Martin DP, Roumagnac P. Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa. Virology 2016; 493:142-53. [PMID: 27038709 DOI: 10.1016/j.virol.2016.03.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 01/25/2023]
Abstract
Little is known about the prevalence, diversity, evolutionary processes, genomic structures and population dynamics of viruses in the divergent geminivirus lineage known as the capulaviruses. We determined and analyzed full genome sequences of 13 Euphorbia caput-medusae latent virus (EcmLV) and 26 Alfalfa leaf curl virus (ALCV) isolates, and partial genome sequences of 23 EcmLV and 37 ALCV isolates. While EcmLV was asymptomatic in uncultivated southern African Euphorbia caput-medusae, severe alfalfa disease symptoms were associated with ALCV in southern France. The prevalence of both viruses exceeded 10% in their respective hosts. Besides using patterns of detectable negative selection to identify ORFs that are probably functionally expressed, we show that ALCV and EcmLV both display evidence of inter-species recombination and biologically functional genomic secondary structures. Finally, we show that whereas the EcmLV populations likely experience restricted geographical dispersion, ALCV is probably freely moving across the French Mediterranean region.
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Affiliation(s)
- Pauline Bernardo
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Brejnev Muhire
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Sarah François
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France; INRA, UMR 1333, DGIMI, Montpellier, France; CNRS-IRD-UM1-UM2, UMR 5290, MIVEGEC, Avenue Agropolis, Montpellier, France
| | - Maëlle Deshoux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Penelope Hartnady
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Kata Farkas
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Denis Filloux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Emmanuel Fernandez
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Serge Galzi
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Romain Ferdinand
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Martine Granier
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Armelle Marais
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France; Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France
| | - Pablo Monge Blasco
- Unidad de Sanidad Vegetal, Centro de Investigacion y Tecnologıa Agroalimentaria de Aragon (CITA), Av. Montañana 930, 50059 Zaragoza, Spain
| | - Thierry Candresse
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France; Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France
| | - Fernando Escriu
- Unidad de Sanidad Vegetal, Centro de Investigacion y Tecnologıa Agroalimentaria de Aragon (CITA), Av. Montañana 930, 50059 Zaragoza, Spain; Unidad de Sanidad Vegetal, Instituto Agroalimentario de Aragón IA2 (CITA - Universidad de Zaragoza), Av. Montañana 930, 50059 Zaragoza, Spain
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, South Africa
| | - Gordon W Harkins
- South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Cape Town, South Africa
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Philippe Roumagnac
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
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154
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Karlsson OE, Larsson J, Hayer J, Berg M, Jacobson M. The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets. PLoS One 2016; 11:e0151481. [PMID: 26982708 PMCID: PMC4794121 DOI: 10.1371/journal.pone.0151481] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/29/2016] [Indexed: 12/29/2022] Open
Abstract
Neonatal porcine diarrhoea of uncertain aetiology has been reported from a number of European countries. The aim of the present study was to use viral metagenomics to examine a potential viral involvement in this diarrhoea and to describe the intestinal virome with focus on eukaryotic viruses. Samples from the distal jejunum of 50 diarrhoeic and 19 healthy piglets from 10 affected herds were analysed. The viral fraction of the samples was isolated and nucleic acids (RNA and DNA fractions) were subjected to sequence independent amplification. Samples from diarrhoeic piglets from the same herds were pooled whereas samples from healthy piglets were analysed individually. In total, 29 clinical samples, plus two negative controls and one positive control consisting of a mock metagenome were sequenced using the Ion Torrent platform. The resulting sequence data was subjected to taxonomic classification using Kraken, Diamond and HMMER. In the healthy specimens, eight different mammalian virus families were detected (Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picornaviridae, and Reoviridae) compared to four in the pooled diarrhoeic samples (Anelloviridae, Circoviridae, Picornaviridae, and Reoviridae). It was not possible to associate a particular virus family with the investigated diarrhoea. In conclusion, this study does not support the hypothesis that the investigated diarrhoea was caused by known mammalian viruses. The results do, however, indicate that known mammalian viruses were present in the intestine as early as 24–48 hours after birth, indicating immediate infection post-partum or possibly transplacental infection.
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Affiliation(s)
- Oskar E. Karlsson
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics (HGEN), SLU, Uppsala, Sweden
- The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden
- * E-mail:
| | - Jenny Larsson
- Department of Clinical Sciences (KV), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics (HGEN), SLU, Uppsala, Sweden
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden
| | - Magdalena Jacobson
- Department of Clinical Sciences (KV), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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155
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Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem. INFECTION GENETICS AND EVOLUTION 2016; 39:304-316. [PMID: 26873065 DOI: 10.1016/j.meegid.2016.02.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 11/24/2022]
Abstract
Over the last five years next-generation sequencing has become a cost effective and efficient method for identifying known and unknown microorganisms. Access to this technique has dramatically changed the field of virology, enabling a wide range of environmental viral metagenome studies to be undertaken of organisms and environmental samples from polar to tropical regions. These studies have led to the discovery of hundreds of highly divergent single stranded DNA (ssDNA) virus-like sequences encoding replication-associated proteins. Yet, few studies have explored how viruses might be shared in an ecosystem through feeding relationships. Here we identify 169 circular molecules (160 CRESS DNA molecules, nine circular molecules) recovered from a New Zealand freshwater lake, that we have tentatively classified into 51 putatively novel species and five previously described species (DflaCV-3, -5, -6, -8, -10). The CRESS DNA viruses identified in this study were recovered from molluscs (Echyridella menzeisii, Musculium novaezelandiae, Potamopyrgus antipodarum and Physella acuta) and insect larvae (Procordulia grayi, Xanthocnemis zealandica, and Chironomus zealandicus) collected from Lake Sarah, as well as from the lake water and benthic sediments. Extensive diversity was observed across most CRESS DNA molecules recovered. The putative capsid protein of one viral species was found to be most similar to those of members of the Tombusviridae family, thus expanding the number of known RNA-DNA hybrid viruses in nature. We noted a strong association between the CRESS DNA viruses and circular molecules identified in the water and browser organisms (C. zealandicus, P. antipodarum and P. acuta), and between water sediments and undefended prey species (C. zealandicus). However, we were unable to find any significant correlation of viral assemblages to the potential feeding relationships of the host aquatic invertebrates.
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156
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Male MF, Kraberger S, Stainton D, Kami V, Varsani A. Cycloviruses, gemycircularviruses and other novel replication-associated protein encoding circular viruses in Pacific flying fox (Pteropus tonganus) faeces. INFECTION GENETICS AND EVOLUTION 2016; 39:279-292. [PMID: 26873064 DOI: 10.1016/j.meegid.2016.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/27/2016] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Viral metagenomic studies have demonstrated that animal faeces can be a good sampling source for exploring viral diversity associated with the host and its environment. As part of an continuing effort to identify novel circular replication-associated protein encoding single-stranded (CRESS) DNA viruses circulating in the Tongan archipelago, coupled with the fact that bats are a reservoir species of a large number of viruses, we used a metagenomic approach to investigate the CRESS DNA virus diversity in Pacific flying fox (Pteropus tonganus) faeces. Faecal matter from four roosting sites located in Ha'avakatolo, Kolovai, Ha'ateiho and Lapaha on Tongatapu Island was collected in April 2014 and January 2015. From these samples we identified five novel cycloviruses representing three putative species, 25 gemycircularviruses representing at least 14 putative species, 17 other CRESS DNA viruses (15 putative species), two circular DNA molecules and a putative novel multi-component virus for which we have identified three cognate molecules. This study demonstrates that there exists a large diversity of CRESS DNA viruses in Pacific flying fox faeces.
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Affiliation(s)
- Maketalena F Male
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | | | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA.
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157
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Rosario K, Marr C, Varsani A, Kraberger S, Stainton D, Moriones E, Polston JE, Breitbart M. Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae). Viruses 2016; 8:v8020036. [PMID: 26848679 PMCID: PMC4776191 DOI: 10.3390/v8020036] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/15/2016] [Accepted: 01/22/2016] [Indexed: 01/23/2023] Open
Abstract
Monopartite begomoviruses (Geminiviridae), which are whitefly-transmitted single-stranded DNA viruses known for causing devastating crop diseases, are often associated with satellite DNAs. Since begomovirus acquisition or exchange of satellite DNAs may lead to adaptation to new plant hosts and emergence of new disease complexes, it is important to investigate the diversity and distribution of these molecules. This study reports begomovirus-associated satellite DNAs identified during a vector-enabled metagenomic (VEM) survey of begomoviruses using whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Protein-encoding satellite DNAs, including alphasatellites and betasatellites, were identified in Israel, Puerto Rico, and Guatemala. Novel alphasatellites were detected in samples from Guatemala and Puerto Rico, resulting in the description of a phylogenetic clade (DNA-3-type alphasatellites) dominated by New World sequences. In addition, a diversity of small (~640-750 nucleotides) satellite DNAs similar to satellites associated with begomoviruses infecting Ipomoea spp. were detected in Puerto Rico and Spain. A third class of satellite molecules, named gammasatellites, is proposed to encompass the increasing number of reported small (<1 kilobase), non-coding begomovirus-associated satellite DNAs. This VEM-based survey indicates that, although recently recovered begomovirus genomes are variations of known genetic themes, satellite DNAs hold unexplored genetic diversity.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Christian Marr
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental ''La Mayora'', Algarrobo-Costa, Málaga 29750, Spain.
| | - Jane E Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
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158
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The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin. Arch Virol 2016; 161:959-66. [PMID: 26780893 DOI: 10.1007/s00705-016-2756-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/08/2016] [Indexed: 01/14/2023]
Abstract
Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown.
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159
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Ng TFF, Zhang W, Sachsenröder J, Kondov NO, da Costa AC, Vega E, Holtz LR, Wu G, Wang D, Stine CO, Antonio M, Mulvaney US, Muench MO, Deng X, Ambert-Balay K, Pothier P, Vinjé J, Delwart E. A diverse group of small circular ssDNA viral genomes in human and non-human primate stools. Virus Evol 2015; 1:vev017. [PMID: 27774288 PMCID: PMC5014484 DOI: 10.1093/ve/vev017] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Viral metagenomics sequencing of fecal samples from outbreaks of acute gastroenteritis from the US revealed the presence of small circular ssDNA viral genomes encoding a replication initiator protein (Rep). Viral genomes were ∼2.5 kb in length, with bi-directionally oriented Rep and capsid (Cap) encoding genes and a stem loop structure downstream of Rep. Several genomes showed evidence of recombination. By digital screening of an in-house virome database (1.04 billion reads) using BLAST, we identified closely related sequences from cases of unexplained diarrhea in France. Deep sequencing and PCR detected such genomes in 7 of 25 US (28 percent) and 14 of 21 French outbreaks (67 percent). One of eighty-five sporadic diarrhea cases in the Gambia was positive by PCR. Twenty-two complete genomes were characterized showing that viruses from patients in the same outbreaks were closely related suggesting common origins. Similar genomes were also characterized from the stools of captive chimpanzees, a gorilla, a black howler monkey, and a lemur that were more diverse than the human stool-associated genomes. The name smacovirus is proposed for this monophyletic viral clade. Possible tropism include mammalian enteric cells or ingested food components such as infected plants. No evidence of viral amplification was found in immunodeficient mice orally inoculated with smacovirus-positive stool supernatants. A role for smacoviruses in diarrhea, if any, remains to be demonstrated.
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Affiliation(s)
- Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Wen Zhang
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of Microbiology, School of Medicine, Jiangsu University, Jiangsu, Zhenjiang, China
| | - Jana Sachsenröder
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Federal Institute for Risk Assessment, Berlin, Germany
| | - Nikola O Kondov
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA
| | - Antonio Charlys da Costa
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Institute of Tropical Medicine, University of Sao Paulo, São Paulo, Brazil
| | - Everardo Vega
- NCIRD, Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Guang Wu
- Department of Molecular Microbiology, and
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Colin O Stine
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Usha S Mulvaney
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA
| | - Marcus O Muench
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Katia Ambert-Balay
- National Reference Centre for enteric viruses, Dijon University Hospital, Dijon, France and
| | - Pierre Pothier
- National Reference Centre for enteric viruses, Dijon University Hospital, Dijon, France and
| | - Jan Vinjé
- NCIRD, National Calicivirus Laboratory, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
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160
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Breitbart M, Benner BE, Jernigan PE, Rosario K, Birsa LM, Harbeitner RC, Fulford S, Graham C, Walters A, Goldsmith DB, Berger SA, Nejstgaard JC. Discovery, Prevalence, and Persistence of Novel Circular Single-Stranded DNA Viruses in the Ctenophores Mnemiopsis leidyi and Beroe ovata. Front Microbiol 2015; 6:1427. [PMID: 26733971 PMCID: PMC4683175 DOI: 10.3389/fmicb.2015.01427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 11/30/2015] [Indexed: 01/13/2023] Open
Abstract
Gelatinous zooplankton, such as ctenophores and jellyfish, are important components of marine and brackish ecosystems and play critical roles in aquatic biogeochemistry. As voracious predators of plankton, ctenophores have key positions in aquatic food webs and are often successful invaders when introduced to new areas. Gelatinous zooplankton have strong impacts on ecosystem services, particularly in coastal environments. However, little is known about the factors responsible for regulating population dynamics of gelatinous organisms, including biological interactions that may contribute to bloom demise. Ctenophores are known to contain specific bacterial communities and a variety of invertebrate parasites and symbionts; however, no previous studies have examined the presence of viruses in these organisms. Building upon recent studies demonstrating a diversity of single-stranded DNA viruses that encode a replication initiator protein (Rep) in aquatic invertebrates, this study explored the presence of circular, Rep-encoding single-stranded DNA (CRESS-DNA) viruses in the ctenophores Mnemiopsis leidyi and Beroe ovata collected from the Skidaway River Estuary and Savannah River in Georgia, USA. Using rolling circle amplification followed by restriction enzyme digestion, this study provides the first evidence of viruses in ctenophores. Investigation of four CRESS-DNA viruses over an 8-month period using PCR demonstrated temporal trends in viral prevalence and indicated that some of the viruses may persist in ctenophore populations throughout the year. Although future work needs to examine the ecological roles of these ctenophore-associated viruses, this study indicates that viral infection may play a role in population dynamics of gelatinous zooplankton.
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Affiliation(s)
- Mya Breitbart
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Bayleigh E Benner
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Parker E Jernigan
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Karyna Rosario
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Laura M Birsa
- Skidaway Institute of Oceanography, University of Georgia Savannah, GA, USA
| | - Rachel C Harbeitner
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Sidney Fulford
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Carina Graham
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Anna Walters
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Dawn B Goldsmith
- College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA
| | - Stella A Berger
- Skidaway Institute of Oceanography, University of GeorgiaSavannah, GA, USA; Department III, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB)Stechlin, Germany
| | - Jens C Nejstgaard
- Skidaway Institute of Oceanography, University of GeorgiaSavannah, GA, USA; Department III, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB)Stechlin, Germany
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161
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A novel, highly divergent ssDNA virus identified in Brazil infecting apple, pear and grapevine. Virus Res 2015; 210:27-33. [DOI: 10.1016/j.virusres.2015.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/02/2015] [Accepted: 07/03/2015] [Indexed: 11/22/2022]
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162
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Zhou C, Zhang S, Gong Q, Hao A. A novel gemycircularvirus in an unexplained case of child encephalitis. Virol J 2015; 12:197. [PMID: 26596706 PMCID: PMC4657213 DOI: 10.1186/s12985-015-0431-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/17/2015] [Indexed: 12/21/2022] Open
Abstract
Background Recently, a diverse group of viruses with circular, replication initiator protein(Rep) encoding, single stranded DNA (CRESS-DNA) genomes, were discovered from wide range of eukaryotic organisms ranging from mammals to fungi. Gemycircularvirus belongs to a distinct group of CRESS-DNA genomes and is classified under the genus name of Gemycircularvirus. Findings Here, a novel gemycircularvirus named GeTz1 from cerebrospinal fluid sample of a child with unexplainable encephalitis was characterized. The novel gemycircularvirus encodes two major proteins, including a capsid protein (Cap) and a replication-associated protein (Rep). Phylogenetic analysis based on the amino acid sequence of Rep indicated that GeTz1 clusters with one gemycircularvirus discovered from bird (KF371633), sharing 46.6 % amino acid sequence identity with each other. Conclusion A novel gemycircularvirus was discovered from cerebrospinal fluid sample of a child with unexplainable encephalitis. Further studies, such as testing human sera for specific antibodies, should be performed to investigate whether gemycircularvirus infects human and is associated with encephalitis.
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Affiliation(s)
- Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, 225300, China.
| | - Shibing Zhang
- Department of Laboratory Medicine, the First People's Hospital of Suqian, Suqian, Jiangsu, 223800, China.
| | - Qin Gong
- Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, 225300, China.
| | - Aimin Hao
- Department of Laboratory Medicine, the Second People's Hospital of Wuxi, Wuxi, Jiangsu, 214002, China.
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163
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New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics. PLoS One 2015; 10:e0141952. [PMID: 26559957 PMCID: PMC4641689 DOI: 10.1371/journal.pone.0141952] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/15/2015] [Indexed: 12/31/2022] Open
Abstract
Rattus norvegicus (R. norvegicus) are ubiquitous and their presence has several effects on the human populations in our urban areas on a global scale. Both historically and presently, this close interaction has facilitated the dissemination of many pathogens to humans, making screening for potentially zoonotic and emerging viruses in rats highly relevant. We have investigated faecal samples from R. norvegicus collected from urban areas using a protocol based on metagenomic enrichment of circular DNA genomes and subsequent sequencing. We found a new type of papillomavirus, with a L1 region 82% identical to that of the known R. norvegicus Papillomavirus 2. Additionally, we found 20 different circular replication associated protein (Rep)-encoding single stranded DNA (CRESS-DNA) virus-like genomes, one of which has homology to the replication-associated gene of Beak and feather disease virus. Papillomaviruses are a group of viruses known for their carcinogenic potential, and although they are known to infect several different vertebrates, they are mainly studied and characterised in humans. CRESS-DNA viruses are found in many different environments and tissue types. Both papillomaviruses and CRESS-DNA viruses are known to have pathogenic potential and screening for novel and known viruses in R. norvegicus could help identify viruses with pathogenic potential.
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164
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Rosario K, Seah YM, Marr C, Varsani A, Kraberger S, Stainton D, Moriones E, Polston JE, Duffy S, Breitbart M. Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Reveal Novel Begomovirus Species in the New and Old Worlds. Viruses 2015; 7:5553-70. [PMID: 26516898 PMCID: PMC4632403 DOI: 10.3390/v7102895] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 01/16/2023] Open
Abstract
Whitefly-transmitted viruses belonging to the genus Begomovirus (family Geminiviridae) represent a substantial threat to agricultural food production. The rapid evolutionary potential of these single-stranded DNA viruses combined with the polyphagous feeding behavior of their whitefly vector (Bemisia tabaci) can lead to the emergence of damaging viral strains. Therefore, it is crucial to characterize begomoviruses circulating in different regions and crops globally. This study utilized vector-enabled metagenomics (VEM) coupled with high-throughput sequencing to survey begomoviruses directly from whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Begomoviruses were detected in all locations, with the highest diversity identified in Guatemala where up to seven different species were identified in a single field. Both bipartite and monopartite viruses were detected, including seven new begomovirus species from Guatemala, Puerto Rico, and Spain. This begomovirus survey extends the known diversity of these highly damaging plant viruses. However, the new genomes described here and in the recent literature appear to reflect the outcome of interactions between closely-related species, often resulting from recombination, instead of unique, highly divergent species.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Yee Mey Seah
- Microbiology and Molecular Genetics, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Christian Marr
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora", Algarrobo-Costa, Málaga 29750, Spain.
| | - Jane E Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
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165
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Abstract
Viruses are notorious for rapidly exchanging genetic information between close relatives and with the host cells they infect. This exchange has profound effects on the nature and rapidity of virus and host evolution. Recombination between dsDNA viruses is common, as is genetic exchange between dsDNA viruses or retroviruses and host genomes. Recombination between RNA virus genomes is also well known. In contrast, genetic exchange across viral kingdoms, for instance between nonretroviral RNA viruses or ssDNA viruses and host genomes or between RNA and DNA viruses, was previously thought to be practically nonexistent. However, there is now growing evidence for both RNA and ssDNA viruses recombining with host dsDNA genomes and, more surprisingly, RNA virus genes recombining with ssDNA virus genomes. Mechanisms are still unclear, but this deep recombination greatly expands the breadth of virus evolution and confounds virus taxonomy.
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Affiliation(s)
- Kenneth M Stedman
- Biology Department and Center for Life in Extreme Environments, Portland State University, Portland, Oregon 97207;
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166
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Simmonds P. Methods for virus classification and the challenge of incorporating metagenomic sequence data. J Gen Virol 2015; 96:1193-1206. [PMID: 26068186 DOI: 10.1099/jgv.0.000016] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The division of viruses into orders, families, genera and species provides a classification framework that seeks to organize and make sense of the diversity of viruses infecting animals, plants and bacteria. Classifications are based on similarities in genome structure and organization, the presence of homologous genes and sequence motifs and at lower levels such as species, host range, nucleotide and antigenic relatedness and epidemiology. Classification below the level of family must also be consistent with phylogeny and virus evolutionary histories. Recently developed methods such as PASC, DEMaRC and NVR offer alternative strategies for genus and species assignments that are based purely on degrees of divergence between genome sequences. They offer the possibility of automating classification of the vast number of novel virus sequences being generated by next-generation metagenomic sequencing. However, distance-based methods struggle to deal with the complex evolutionary history of virus genomes that are shuffled by recombination and reassortment, and where taxonomic lineages evolve at different rates. In biological terms, classifications based on sequence distances alone are also arbitrary whereas the current system of virus taxonomy is of utility precisely because it is primarily based upon phenotypic characteristics. However, a separate system is clearly needed by which virus variants that lack biological information might be incorporated into the ICTV classification even if based solely on sequence relationships to existing taxa. For these, simplified taxonomic proposals and naming conventions represent a practical way to expand the existing virus classification and catalogue our rapidly increasing knowledge of virus diversity.
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Affiliation(s)
- Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
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167
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López-Bueno A, Rastrojo A, Peiró R, Arenas M, Alcamí A. Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Mol Ecol 2015. [DOI: 10.1111/mec.13321] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- A. López-Bueno
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - A. Rastrojo
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - R. Peiró
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - M. Arenas
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - A. Alcamí
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
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168
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Bzhalava D, Hultin E, Arroyo Mühr LS, Ekström J, Lehtinen M, de Villiers EM, Dillner J. Viremia during pregnancy and risk of childhood leukemia and lymphomas in the offspring: Nested case-control study. Int J Cancer 2015; 138:2212-20. [PMID: 26132655 DOI: 10.1002/ijc.29666] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/24/2015] [Accepted: 06/01/2015] [Indexed: 01/29/2023]
Abstract
A possible role for infections of the pregnant mother in the development of childhood acute leukemias and lymphomas has been suggested. However, no specific infectious agent has been identified. Offspring of 74,000 mothers who had serum samples taken during pregnancy and stored in a large-scale biobank were followed up to the age of 15 years (750,000 person years) through over-generation linkages between the biobank files, the Swedish national population and cancer registers to identify incident leukemia/lymphoma cases in the offspring. First-trimester sera from mothers of 47 cases and 47 matched controls were retrieved and analyzed using next generation sequencing. Anelloviruses were the most common viruses detected, found in 37/47 cases and in 40/47 controls, respectively (OR: 0.6, 95% CI: 0.2-1.9). None of the detected viruses was associated with leukemia/lymphoma in the offspring. Viremia during pregnancy was common, but no association with leukemia/lymphoma risk in the offspring was found.
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Affiliation(s)
- Davit Bzhalava
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, SE-141 86, Sweden
| | - Emilie Hultin
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, SE-141 86, Sweden
| | | | - Johanna Ekström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Matti Lehtinen
- National Institute for Health and Welfare, Oulu, Finland
| | - Ethel-Michele de Villiers
- Abteilung Tumorvirus-Charakterisierung, Deutsches Krebsforschungszentrum, Heidelberg, 69120, Germany
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, SE-141 86, Sweden.,Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, SE-171 77, Sweden
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169
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Rosario K, Schenck RO, Harbeitner RC, Lawler SN, Breitbart M. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins. Front Microbiol 2015. [PMID: 26217327 PMCID: PMC4498126 DOI: 10.3389/fmicb.2015.00696] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Ryan O Schenck
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Rachel C Harbeitner
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Stephanie N Lawler
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
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170
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Sudarshana MR, Perry KL, Fuchs MF. Grapevine Red Blotch-Associated Virus, an Emerging Threat to the Grapevine Industry. PHYTOPATHOLOGY 2015; 105:1026-1032. [PMID: 25738551 DOI: 10.1094/phyto-12-14-0369-fi] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Grapevine red blotch-associated virus (GRBaV) is a newly identified virus of grapevines and a putative member of a new genus within the family Geminiviridae. This virus is associated with red blotch disease that was first reported in California in 2008. It affects the profitability of vineyards by substantially reducing fruit quality and ripening. In red-berried grapevine cultivars, foliar disease symptoms consist of red blotches early in the season that can expand and coalesce across most of the leaf blade later in the season. In white-berried grapevine cultivars, foliar disease symptoms are less conspicuous and generally involve irregular chlorotic areas that may become necrotic late in the season. Determining the GRBaV genome sequence yielded critical information for the design of primers for polymerase chain reaction-based diagnostics. To date, GRBaV has been reported in the major grape-growing areas in North America and two distinct phylogenetic clades have been described. Spread of GRBaV is suspected in certain vineyards but a vector of epidemiological significance has yet to be identified. Future research will need to focus on virus spread, the production of clean planting stocks, and the development of management options that are effective, economical, and environmentally friendly.
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Affiliation(s)
- Mysore R Sudarshana
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Keith L Perry
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Marc F Fuchs
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
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171
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Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi. Arch Virol 2015; 160:2349-51. [DOI: 10.1007/s00705-015-2503-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
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172
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Sato G, Kawashima T, Kiuchi M, Tohya Y. Novel cyclovirus detected in the intestinal contents of Taiwan squirrels (Callosciurus erythraeus thaiwanensis). Virus Genes 2015; 51:148-51. [DOI: 10.1007/s11262-015-1217-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/06/2015] [Indexed: 11/25/2022]
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173
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Simmonds P. Methods for virus classification and the challenge of incorporating metagenomic sequence data. J Gen Virol 2015. [DOI: 10.1099/vir.0.000016] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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174
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Li L, Giannitti F, Low J, Keyes C, Ullmann LS, Deng X, Aleman M, Pesavento PA, Pusterla N, Delwart E. Exploring the virome of diseased horses. J Gen Virol 2015; 96:2721-2733. [PMID: 26044792 DOI: 10.1099/vir.0.000199] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C virus and equid herpesvirus 2 were identified in the cerebrospinal fluid of horses with neurological signs. Four co-infecting picobirnaviruses, including an unusual genome with fused RNA segments, and a divergent anellovirus were found in the plasma of two febrile horses. A novel cyclovirus genome was characterized from the nasal secretion of another febrile animal. Lastly, a small circular DNA genome with a Rep gene, from a virus we called kirkovirus, was identified in the liver and spleen of a horse with fatal idiopathic hepatopathy. This study expands the number of viruses found in horses, and characterizes their genomes to assist future epidemiological studies of their transmission and potential association with various equine diseases.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Federico Giannitti
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA.,Instituto Nacional de Investigación Agropecuaria, La Estanzuela, Colonia, Uruguay
| | - Jason Low
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Casey Keyes
- Department of Biology, University of San Francisco, San Francisco, CA, USA
| | - Leila S Ullmann
- Department of Microbiology and Immunology, UNESP Sao Paulo State University, Sao Paulo, Brazil
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Monica Aleman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, USA
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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175
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Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Arch Virol 2015; 160:1593-619. [PMID: 25894478 DOI: 10.1007/s00705-015-2398-y] [Citation(s) in RCA: 294] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
Abstract
Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.
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176
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Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol Mol Biol Rev 2015; 78:278-303. [PMID: 24847023 DOI: 10.1128/mmbr.00049-13] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host.
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177
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Distinct circular single-stranded DNA viruses exist in different soil types. Appl Environ Microbiol 2015; 81:3934-45. [PMID: 25841004 DOI: 10.1128/aem.03878-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/23/2015] [Indexed: 02/03/2023] Open
Abstract
The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family Microviridae (icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of Microviridae major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily Gokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family Circoviridae in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the Circoviridae showed that they are a novel clade of Circoviridae-related CRESS-DNA viruses distinct from known Circoviridae genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.
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178
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Krupovic M, Zhi N, Li J, Hu G, Koonin EV, Wong S, Shevchenko S, Zhao K, Young NS. Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing. Genome Biol Evol 2015; 7:993-1001. [PMID: 25840414 PMCID: PMC4419787 DOI: 10.1093/gbe/evv034] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viruses with single-stranded (ss) DNA genomes infect hosts in all three domains of life and include many medically, ecologically, and economically important pathogens. Recently, a new group of ssDNA viruses with chimeric genomes has been discovered through viral metagenomics. These chimeric viruses combine capsid protein genes and replicative protein genes that, respectively, appear to have been inherited from viruses with positive-strand RNA genomes, such as tombusviruses, and ssDNA genomes, such as circoviruses, nanoviruses or geminiviruses. Here, we describe the genome sequence of a new representative of this virus group and reveal an additional layer of chimerism among ssDNA viruses. We show that not only do these viruses encompass genes for capsid proteins and replicative proteins that have distinct evolutionary histories, but also the replicative genes themselves are chimeras of functional domains inherited from viruses of different families. Our results underscore the importance of horizontal gene transfer in the evolution of ssDNA viruses and the role of genetic recombination in the emergence of novel virus groups.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Ning Zhi
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Jungang Li
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Gangqing Hu
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Susan Wong
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sofiya Shevchenko
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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179
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Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, Bucardo-Rivera F, Orlandi P, Ahmed K, Delwart E. Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage. Virology 2015; 482:98-104. [PMID: 25839169 DOI: 10.1016/j.virol.2015.03.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 02/16/2015] [Accepted: 03/03/2015] [Indexed: 01/02/2023]
Abstract
Viruses with small circular ssDNA genomes encoding a replication initiator protein can infect a wide range of eukaryotic organisms ranging from mammals to fungi. The genomes of two such viruses, a cyclovirus (CyCV-SL) and gemycircularvirus (GemyCV-SL) were detected by deep sequencing of the cerebrospinal fluids of Sri Lankan patients with unexplained encephalitis. One and three out of 201 CSF samples (1.5%) from unexplained encephalitis patients tested by PCR were CyCV-SL and GemyCV-SL DNA positive respectively. Nucleotide similarity searches of pre-existing metagenomics datasets revealed closely related genomes in feces from unexplained cases of diarrhea from Nicaragua and Brazil and in untreated sewage from Nepal. Whether the tropism of the cyclovirus and gemycircularvirus reported here include humans or other cellular sources in or on the human body remains to be determined.
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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
| | - Daisuke Mori
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Shaman Rajindrajith
- Department of Pediatrics, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Udaya Ranawaka
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | | | | | - Kamruddin Ahmed
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; Research Promotion Institute, Oita University, Yufu 879-5593, Oita, Japan; Department of Pathobiology and Medical Diagnostics, Faculty of Medicine, Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah, Malaysia
| | - 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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180
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Diverse small circular DNA viruses circulating amongst estuarine molluscs. INFECTION GENETICS AND EVOLUTION 2015; 31:284-95. [DOI: 10.1016/j.meegid.2015.02.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 01/22/2023]
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181
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Koonin EV, Dolja VV, Krupovic M. Origins and evolution of viruses of eukaryotes: The ultimate modularity. Virology 2015; 479-480:2-25. [PMID: 25771806 PMCID: PMC5898234 DOI: 10.1016/j.virol.2015.02.039] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 01/04/2023]
Abstract
Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order "Megavirales" that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
| | - Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015, France.
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182
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Dayaram A, Potter KA, Pailes R, Marinov M, Rosenstein DD, Varsani A. Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA. INFECTION GENETICS AND EVOLUTION 2015; 30:278-287. [DOI: 10.1016/j.meegid.2014.12.037] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/17/2014] [Accepted: 12/31/2014] [Indexed: 12/16/2022]
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183
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Marton S, Ihász K, Lengyel G, Farkas S, Dán Á, Paulus P, Bányai K, Fehér E. Ubiquiter circovirus sequences raise challenges in laboratory diagnosis: the case of honey bee and bee mite, reptiles, and free living amoebae. Acta Microbiol Immunol Hung 2015; 62:57-73. [PMID: 25823454 DOI: 10.1556/amicr.62.2015.1.5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Circoviruses of pigs and birds are established pathogens, however, the exact role of other, recently described circoviruses and circovirus-like viruses remains to be elucidated. The aim of this study was the detection of circoviruses in neglected host species, including honey bees, exotic reptiles and free-living amoebae by widely used broad-spectrum polymerase chain reaction (PCR) assays specific for the replication initiation protein coding gene of these viruses. The majority of sequences obtained from honey bees were highly similar to canine and porcine circoviruses, or, were distantly related to dragonfly cycloviruses. Other rep sequences detected in some honey bees, reptiles and amoebae showed similarities to various rep sequences deposited in the GenBank. Back-to-back PCR primers designed for the amplification of whole viral genomes failed to work that suggested the existence of integrated rep-like elements in many samples. Rolling circle amplification and exonuclease treatment confirmed the absence of small circular DNA genomes in the specimens analysed. In case of honey bees Varroa mite DNA contamination might be a source of the identified endogenous rep-like elements. The reptile and amoebae rep-like sequences were nearly identical with each other and with sequences detected in chimpanzee feces raising the possibility that detection of novel or unusual rep-like elements in some host species might originate from the microbial community of the host. Our results indicate that attention is needed when broad-spectrum rep gene specific polymerase chain reaction is chosen for laboratory diagnosis of circovirus infections.
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Affiliation(s)
- Szilvia Marton
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
| | - Katalin Ihász
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
| | - György Lengyel
- 2 Hungarian Defence Forces Military Medical Centre Budapest Hungary
| | - Szilvia Farkas
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
| | - Ádám Dán
- 3 National Food Chain Safety Office Veterinary Diagnostic Directorate Budapest Hungary
| | - Petra Paulus
- 3 National Food Chain Safety Office Veterinary Diagnostic Directorate Budapest Hungary
| | - Krisztián Bányai
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
| | - Enikő Fehér
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
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184
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Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Arch Virol 2015; 160:1303-11. [PMID: 25701210 DOI: 10.1007/s00705-015-2358-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/29/2015] [Indexed: 12/17/2022]
Abstract
The genomes of a large number of highly diverse novel circular DNA viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) viruses that share similarities with plant-infecting ssDNA viruses of the family Geminiviridae. Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiviruses or gemycircularviruses (a new group of ssDNA viruses that are closely related to geminiviruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share >99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these viruses, this is the first report of circular DNA viruses associated with grasses in New Zealand.
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185
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Lima FEDS, Cibulski SP, dos Santos HF, Teixeira TF, Varela APM, Roehe PM, Delwart E, Franco AC. Genomic characterization of novel circular ssDNA viruses from insectivorous bats in Southern Brazil. PLoS One 2015; 10:e0118070. [PMID: 25688970 PMCID: PMC4331541 DOI: 10.1371/journal.pone.0118070] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/04/2015] [Indexed: 11/18/2022] Open
Abstract
Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirus and the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop.
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Affiliation(s)
- Francisco Esmaile de Sales Lima
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul (RS), Brazil
- * E-mail:
| | - Samuel Paulo Cibulski
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul (RS), Brazil
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Helton Fernandes dos Santos
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Thais Fumaco Teixeira
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Ana Paula Muterle Varela
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Paulo Michel Roehe
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul (RS), Brazil
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America; University of California, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Ana Cláudia Franco
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul (RS), Brazil
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186
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Kraberger S, Argüello-Astorga GR, Greenfield LG, Galilee C, Law D, Martin DP, Varsani A. Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond. INFECTION GENETICS AND EVOLUTION 2015; 31:73-86. [PMID: 25583447 DOI: 10.1016/j.meegid.2015.01.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/23/2014] [Accepted: 01/02/2015] [Indexed: 12/20/2022]
Abstract
Our knowledge of circular replication-associated protein encoding single-stranded (CRESS) DNA virus diversity has increased dramatically in recent years, largely due to advances in high-throughput sequencing technologies. These viruses are apparently major virome components in most terrestrial and aquatic environments and it is therefore of interest to determine their diversity at the interfaces between these environments. Treated sewage water is a particularly interesting interface between terrestrial and aquatic viromes in that it is directly pumped into waterways and is likely to contain virus populations that have been strongly impacted by humans. We used a combination of high-throughput sequencing, full genome PCR amplification, cloning and Sanger sequencing to investigate the diversity of CRESS DNA viruses present in a sewage oxidation pond. Using this approach, we recovered 50 putatively complete novel CRESS viral genomes (it remains possible that some are components of multipartite viral genomes) and 11 putatively sub-genome-length circular DNA molecules which may be either defective genomes or components of multipartite genomes. Thirteen of the genomes have bidirectional genome organisations and share similar conserved replication-associated protein (Rep) motifs to those of the gemycircularviruses: a group that in turn is most closely related to the geminiviruses. The remaining 37 viral genomes share very low degrees of Rep similarity to those of all other known CRESS DNA viruses. This number of highly divergent CRESS DNA virus genomes within a single sewage treatment pond further reinforces the notion that there likely exist hundreds of completely unknown genus/family level CRESS DNA virus groupings.
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Affiliation(s)
- Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Gerardo R Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, S.L.P., Mexico
| | - Laurence G Greenfield
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Craig Galilee
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Donald Law
- The Laboratories, Christchurch City Council, Christchurch, New Zealand
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.
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187
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Garigliany MM, Börstler J, Jöst H, Badusche M, Desmecht D, Schmidt-Chanasit J, Cadar D. Characterization of a novel circo-like virus in Aedes vexans mosquitoes from Germany: evidence for a new genus within the family Circoviridae. J Gen Virol 2014; 96:915-920. [PMID: 25535324 DOI: 10.1099/vir.0.000036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Over recent decades, metagenomic studies have expanded the number of newly described, often unclassified, viruses within the family Circoviridae. Using broad-spectrum circovirus and cyclovirus PCRs, we characterized a novel circo-like virus in Aedes vexans mosquitoes from Germany whose main putative ORFs shared very low amino acid identity with those of previously characterized circoviruses and cycloviruses. Phylogenetic and genetic distance analysis revealed that this new virus species defined, together with previously described mosquito- and bat faeces-derived circo-like viruses, a different genus, tentatively called Krikovirus, within the family Circoviridae. We further demonstrated that viruses of the putative genus Krikovirus all shared a genomic organization that was unique among the family Circoviridae. Further investigations are needed to determine the host range, tissue tropism and transmission route(s). This report increases the current knowledge of the genetic diversity and evolution of the members of the family Circoviridae.
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Affiliation(s)
- Mutien-Marie Garigliany
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,University of Liège, Faculty of Veterinary Medicine, Department of Veterinary Pathology, Liège, Belgium
| | - Jessica Börstler
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Hanna Jöst
- German Centre for Infection Research (DZIF), Hamburg-Luebeck-Borstel, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Marlis Badusche
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Daniel Desmecht
- University of Liège, Faculty of Veterinary Medicine, Department of Veterinary Pathology, Liège, Belgium
| | - Jonas Schmidt-Chanasit
- German Centre for Infection Research (DZIF), Hamburg-Luebeck-Borstel, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany
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188
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Kraberger S, Kumari SG, Hamed AA, Gronenborn B, Thomas JE, Sharman M, Harkins GW, Muhire BM, Martin DP, Varsani A. Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains. INFECTION GENETICS AND EVOLUTION 2014; 29:203-15. [PMID: 25444941 DOI: 10.1016/j.meegid.2014.11.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.
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Affiliation(s)
- Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Safaa G Kumari
- Virology Laboratory, International Centre for Agricultural Research in the Dry Areas (ICARDA), Tunis, Tunisia.
| | - Abdelmagid A Hamed
- Plant Pathology Research Program, Agricultural Research Corporation, P.O. Box 126, Wadmedani, Sudan
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - John E Thomas
- Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Murray Sharman
- Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Gordon W Harkins
- South African National Bioinformatics Institute, SA Medical Research Unit for Bioinformatics Capacity Development, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Brejnev M Muhire
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
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189
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Ng TFF, Chen LF, Zhou Y, Shapiro B, Stiller M, Heintzman PD, Varsani A, Kondov NO, Wong W, Deng X, Andrews TD, Moorman BJ, Meulendyk T, MacKay G, Gilbertson RL, Delwart E. Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci U S A 2014; 111:16842-7. [PMID: 25349412 PMCID: PMC4250163 DOI: 10.1073/pnas.1410429111] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses preserved in ancient materials provide snapshots of past viral diversity and a means to trace viral evolution through time. Here, we use a metagenomics approach to identify filterable and nuclease-resistant nucleic acids preserved in 700-y-old caribou feces frozen in a permanent ice patch. We were able to recover and characterize two viruses in replicated experiments performed in two different laboratories: a small circular DNA viral genome (ancient caribou feces associated virus, or aCFV) and a partial RNA viral genome (Ancient Northwest Territories cripavirus, or aNCV). Phylogenetic analysis identifies aCFV as distantly related to the plant-infecting geminiviruses and the fungi-infecting Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 and aNCV as within the insect-infecting Cripavirus genus. We hypothesize that these viruses originate from plant material ingested by caribou or from flying insects and that their preservation can be attributed to protection within viral capsids maintained at cold temperatures. To investigate the tropism of aCFV, we used the geminiviral reverse genetic system and introduced a multimeric clone into the laboratory model plant Nicotiana benthamiana. Evidence for infectivity came from the detection of viral DNA in newly emerged leaves and the precise excision of the viral genome from the multimeric clones in inoculated leaves. Our findings indicate that viral genomes may in some circumstances be protected from degradation for centuries.
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Affiliation(s)
- Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, CA 94118; Department of Laboratory Medicine, University of California, San Francisco, CA 94118
| | - Li-Fang Chen
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Yanchen Zhou
- Blood Systems Research Institute, San Francisco, CA 94118; Department of Laboratory Medicine, University of California, San Francisco, CA 94118
| | - Beth Shapiro
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Mathias Stiller
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Peter D Heintzman
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
| | | | - Walt Wong
- Blood Systems Research Institute, San Francisco, CA 94118
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118; Department of Laboratory Medicine, University of California, San Francisco, CA 94118
| | - Thomas D Andrews
- Prince of Wales Northern Heritage Centre, Government of the Northwest Territories, Yellowknife, NT, Canada X1A2L9
| | - Brian J Moorman
- Department of Geography, University of Calgary, Calgary, AB, Canada T2N1N4; and
| | - Thomas Meulendyk
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto, Ontario, Canada M1C1A4
| | - Glen MacKay
- Prince of Wales Northern Heritage Centre, Government of the Northwest Territories, Yellowknife, NT, Canada X1A2L9
| | | | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA 94118; Department of Laboratory Medicine, University of California, San Francisco, CA 94118;
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190
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Sasaki M, Orba Y, Ueno K, Ishii A, Moonga L, Hang'ombe BM, Mweene AS, Ito K, Sawa H. Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses. J Gen Virol 2014; 96:440-452. [PMID: 25381053 DOI: 10.1099/vir.0.071209-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Shrews are small insectivorous mammals that are distributed worldwide. Similar to rodents, shrews live on the ground and are commonly found near human residences. In this study, we investigated the enteric virome of wild shrews in the genus Crocidura using a sequence-independent viral metagenomics approach. A large portion of the shrew enteric virome was composed of insect viruses, whilst novel viruses including cyclovirus, picornavirus and picorna-like virus were also identified. Several cycloviruses, including variants of human cycloviruses detected in cerebrospinal fluid and stools, were detected in wild shrews at a high prevalence rate. The identified picornavirus was distantly related to human parechovirus, inferring the presence of a new genus in this family. The identified picorna-like viruses were characterized as different species of calhevirus 1, which was discovered previously in human stools. Complete or nearly complete genome sequences of these novel viruses were determined in this study and then were subjected to further genetic characterization. Our study provides an initial view of the diversity and distinctiveness of the shrew enteric virome and highlights unique novel viruses related to human stool-associated viruses.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Keisuke Ueno
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiro Ishii
- Hokudai Center for Zoonosis Control in Zambia, PO Box 32379, Lusaka, Zambia
| | - Ladslav Moonga
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Bernard M Hang'ombe
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Global Institution for Collaborative Research and Education, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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191
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Fehér E, Pazár P, Lengyel G, Phan TG, Bányai K. Sequence and phylogenetic analysis identifies a putative novel gyrovirus 3 genotype in ferret feces. Virus Genes 2014; 50:137-41. [DOI: 10.1007/s11262-014-1128-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
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192
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Cheung AK, Ng TFF, Lager KM, Alt DP, Delwart E, Pogranichniy RM. Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces. Arch Virol 2014; 160:353-8. [DOI: 10.1007/s00705-014-2234-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
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193
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Rodríguez-Negrete EA, Sánchez-Campos S, Cañizares MC, Navas-Castillo J, Moriones E, Bejarano ER, Grande-Pérez A. A sensitive method for the quantification of virion-sense and complementary-sense DNA strands of circular single-stranded DNA viruses. Sci Rep 2014; 4:6438. [PMID: 25241765 PMCID: PMC5377365 DOI: 10.1038/srep06438] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/01/2014] [Indexed: 12/16/2022] Open
Abstract
Circular single-stranded DNA (ssDNA) viruses are the smallest viruses known to infect eukaryotes. High recombination and mutation rates have conferred these viruses with an evolutionary potential that has facilitated their emergence. Their damaging effects on livestock (circoviruses) and crops (geminiviruses and nanoviruses), and the ubiquity of anelloviruses in human populations and other mammalian species, have resulted in increased interest in better understanding their epidemiology and infection mechanisms. Circular ssDNA viral replication involves the synthesis of dsDNA intermediates containing complementary-sense (CS) and virion-sense (VS) strands. Precise quantification of VS and CS accumulation during viral infections can provide insights into the molecular mechanisms underlying viral replication and the host invasion process. Although qPCR protocols for quantifying viral molecules exist, none of them discriminate VS and CS strands. Here, using a two-step qPCR protocol we have quantified VS and CS molecule accumulation during the infection process of Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) (genus Begomovirus, family Geminiviridae). Our results show that the VS/CS strand ratio and overall dsDNA amounts vary throughout the infection process. Moreover, we show that these values depend on the virus-host combination, and that most CS strands are present as double-stranded molecules.
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Affiliation(s)
- Edgar A. Rodríguez-Negrete
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
- Current address: Centro de Investigación y Estudios Avanzados (Cinvestav) Irapuato Km. 9.6 Libramiento Norte Irapuato, Guanajuato. 36821 Mexico
| | - Sonia Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - M. Carmen Cañizares
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Eduardo R. Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, (IHSM-UMA-CSIC) Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
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194
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Mycovirus-like DNA virus sequences from cattle serum and human brain and serum samples from multiple sclerosis patients. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00848-14. [PMID: 25169858 PMCID: PMC4148726 DOI: 10.1128/genomea.00848-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Myco-like viruses have been isolated from fungi, feces of various animals, and plant leaves. We report here the isolation of 3 complete genome sequences of gemycircularvirus-related viruses from healthy bovine serum and human brain and serum samples from patients with multiple sclerosis (MS). Their putative capsid proteins share similarity to Torque teno virus (TTV) open reading frame 1 (ORF1) proteins.
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195
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Sachsenröder J, Braun A, Machnowska P, Ng TFF, Deng X, Guenther S, Bernstein S, Ulrich RG, Delwart E, Johne R. Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus. J Gen Virol 2014; 95:2734-2747. [PMID: 25121550 DOI: 10.1099/vir.0.070029-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rats are known as reservoirs and vectors for several zoonotic pathogens. However, information on the viruses shed by urban wild rats that could pose a zoonotic risk to human health is scare. Here, intestinal contents from 20 wild Norway rats (Rattus norvegicus) collected in the city of Berlin, Germany, were subjected to metagenomic analysis of viral nucleic acids. The determined faecal viromes of rats consisted of a variety of known and unknown viruses, and were highly variable among the individuals. Members of the families Parvoviridae and Picobirnaviridae represented the most abundant species. Novel picornaviruses, bocaviruses, sapoviruses and stool-associated circular ssDNA viruses were identified, which showed only low sequence identity to known representatives of the corresponding taxa. In addition, noroviruses and rotaviruses were detected as potential zoonotic gastroenteritis viruses. However, partial-genome sequence analyses indicated that the norovirus was closely related to the recently identified rat norovirus and the rotavirus B was closely related to the rat rotavirus strain IDIR; both viruses clustered separately from respective human virus strains in phylogenetic trees. In contrast, the rotavirus A sequences showed high identity to human and animal strains. Analysis of the nearly complete genome of this virus revealed the known genotypes G3, P[3] and N2 for three of the genome segments, whereas the remaining eight genome segments represented the novel genotypes I20-R11-C11-M10-A22-T14-E18-H13. Our results indicated a high heterogeneity of enteric viruses present in urban wild rats; their ability to be transmitted to humans remains to be assessed in the future.
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Affiliation(s)
- Jana Sachsenröder
- Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Anne Braun
- Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Patrycja Machnowska
- Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Terry Fei Fan Ng
- Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
| | - Xutao Deng
- Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
| | - Sebastian Guenther
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Strasse 7-13, 14163 Berlin, Germany
| | - Samuel Bernstein
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Eric Delwart
- Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
| | - Reimar Johne
- Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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196
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Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses. Nat Commun 2014; 4:2700. [PMID: 24193254 DOI: 10.1038/ncomms3700] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 10/02/2013] [Indexed: 02/07/2023] Open
Abstract
Metagenomic studies have uncovered an astonishing diversity of ssDNA viruses encoding replication proteins (Reps) related to those of eukaryotic Circoviridae, Geminiviridae or Nanoviridae; however, exact evolutionary relationships among these viruses remain obscure. Recently, a unique chimeric virus (CHIV) genome, which has apparently emerged via recombination between ssRNA and ssDNA viruses, has been discovered. Here we report on the assembly of 13 new CHIV genomes recovered from various environments. Our results indicate a single event of capsid protein (CP) gene capture from an RNA virus in the history of this virus group. The domestication of the CP gene was followed by an unprecedented recurrent replacement of the Rep genes in CHIVs with distant counterparts from diverse ssDNA viruses. We suggest that parasitic and symbiotic interactions between unicellular eukaryotes were central for the emergence of CHIVs and that such turbulent evolution was primarily dictated by incongruence between the CP and Rep proteins.
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197
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Krupovic M, Koonin EV. Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses. Sci Rep 2014; 4:5347. [PMID: 24939392 PMCID: PMC4061559 DOI: 10.1038/srep05347] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/30/2014] [Indexed: 12/20/2022] Open
Abstract
Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015, France
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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198
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Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica). INFECTION GENETICS AND EVOLUTION 2014; 26:132-8. [PMID: 24859088 DOI: 10.1016/j.meegid.2014.05.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 12/23/2022]
Abstract
Antarctica has some of the harshest environmental conditions for existence of life on Earth. In this pilot study we recovered eight diverse circular single-stranded DNA (ssDNA) viral genome sequences (1904-3120 nts) from benthic mats dominated by filamentous cyanobacteria in a freshwater pond on the McMurdo Ice Shelf sampled in 1988. All genomes contain two to three major open reading frames (ORFs) that are uni- or bi-directionally transcribed and all have an ORF encoding a replication-associated protein (Rep). In one genome, the second ORF has similarity to a capsid protein (CP) of Nepavirus which is most closely related to geminiviruses. Additionally, all genomes have two intergenic regions that contain putative stem loop structures, six genomes have NANTATTAC as the nonanucleotide motif, while one has CCTTATTAC, and another has a non-canonical stem loop. In the large intergenic region, we identified iterative sequences flanking the putative stem-loop elements which are a hallmark of most circular ssDNA viruses encoding rolling circle replication (RCR) initiators of the HUH endonuclease superfamily. The Reps encoded by ssDNA viral genomes recovered in this study shared <38% pairwise identity to all other Reps of known ssDNA viruses. A previous study on Lake Limnopolar (Livingston Island, South Shetland Islands), using next-generation sequencing identified circular ssDNA viruses and their putative Reps share <35% pairwise identity to those from the viral genomes removed in this study. It is evident from our pilot study that the global diversity of ssDNA viruses is grossly underestimated and there is limited knowledge on ssDNA viruses in Antarctica.
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199
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Grigoras I, Ginzo AIDC, Martin DP, Varsani A, Romero J, Mammadov AC, Huseynova IM, Aliyev JA, Kheyr-Pour A, Huss H, Ziebell H, Timchenko T, Vetten HJ, Gronenborn B. Genome diversity and evidence of recombination and reassortment in nanoviruses from Europe. J Gen Virol 2014; 95:1178-1191. [DOI: 10.1099/vir.0.063115-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The recent identification of a new nanovirus, pea necrotic yellow dwarf virus, from pea in Germany prompted us to survey wild and cultivated legumes for nanovirus infections in several European countries. This led to the identification of two new nanoviruses: black medic leaf roll virus (BMLRV) and pea yellow stunt virus (PYSV), each considered a putative new species. The complete genomes of a PYSV isolate from Austria and three BMLRV isolates from Austria, Azerbaijan and Sweden were sequenced. In addition, the genomes of five isolates of faba bean necrotic yellows virus (FBNYV) from Azerbaijan and Spain and those of four faba bean necrotic stunt virus (FBNSV) isolates from Azerbaijan were completely sequenced, leading to the first identification of FBNSV occurring in Europe. Sequence analyses uncovered evolutionary relationships, extensive reassortment and potential remnants of mixed nanovirus infections, as well as intra- and intercomponent recombination events within the nanovirus genomes. In some virus isolates, diverse types of the same genome component (paralogues) were observed, a type of genome complexity not described previously for any member of the family Nanoviridae. Moreover, infectious and aphid-transmissible nanoviruses from cloned genomic DNAs of FBNYV and BMLRV were reconstituted that, for the first time, allow experimental reassortments for studying the genome functions and evolution of these nanoviruses.
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Affiliation(s)
- Ioana Grigoras
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - Ana Isabel del Cueto Ginzo
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Carretera de La Coruna Km. 7.0, Madrid 28040, Spain
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8140, New Zealand
| | - Javier Romero
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Carretera de La Coruna Km. 7.0, Madrid 28040, Spain
| | - Alamdar Ch. Mammadov
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | - Irada M. Huseynova
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | - Jalal A. Aliyev
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | | | - Herbert Huss
- Lehr- und Forschungszentrum für Landwirtschaft (LFZ) Raumberg-Gumpenstein, Versuchsstation Lambach/Stadl-Paura, 4651 Stadl-Paura, Austria
| | - Heiko Ziebell
- Julius Kühn Institut, Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, 38104 Braunschweig, Germany
| | - Tatiana Timchenko
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - Heinrich-Josef Vetten
- Julius Kühn Institut, Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, 38104 Braunschweig, Germany
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
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200
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Norman JM, Handley SA, Virgin HW. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology 2014; 146:1459-69. [PMID: 24508599 PMCID: PMC4009354 DOI: 10.1053/j.gastro.2014.02.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/27/2014] [Accepted: 02/03/2014] [Indexed: 12/13/2022]
Abstract
Advanced sequencing techniques have shown that bacteria are not the only complex and important microbes in the human intestine. Nonbacterial organisms, particularly the virome and the mycobiome, are important regulators of intestinal immunity and inflammation. The virome is mucosal and systemic; it can alter the host response to bacteria and interact with host genes and bacteria to contribute to disease pathogenesis. The human mycobiome is also complex and can contribute to intestinal inflammation. We review what has recently been learned about the nonbacterial and nonarchaeal microbes in the gastrointestinal tract, discussing their potential effects on health and disease and analytical approaches for their study. Studies of associations between the microbiome and intestinal pathology should incorporate kingdom-agnostic approaches if we are to fully understand intestinal health and disease.
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Affiliation(s)
| | | | - Herbert W. Virgin
- Reprint requests Address requests for reprints to: Herbert W. Virgin, MD, PhD, Washington University School of Medicine, Box 8118, 660 South Euclid Avenue, St Louis, Missouri 63110.
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