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Mokili JL, Rohwer F, Dutilh BE. Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2012; 2:63-77. [PMID: 22440968 PMCID: PMC7102772 DOI: 10.1016/j.coviro.2011.12.004] [Citation(s) in RCA: 386] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 12/09/2011] [Accepted: 12/12/2011] [Indexed: 01/21/2023]
Abstract
Monitoring the emergence and re-emergence of viral diseases with the goal of containing the spread of viral agents requires both adequate preparedness and quick response. Identifying the causative agent of a new epidemic is one of the most important steps for effective response to disease outbreaks. Traditionally, virus discovery required propagation of the virus in cell culture, a proven technique responsible for the identification of the vast majority of viruses known to date. However, many viruses cannot be easily propagated in cell culture, thus limiting our knowledge of viruses. Viral metagenomic analyses of environmental samples suggest that the field of virology has explored less than 1% of the extant viral diversity. In the last decade, the culture-independent and sequence-independent metagenomic approach has permitted the discovery of many viruses in a wide range of samples. Phylogenetically, some of these viruses are distantly related to previously discovered viruses. In addition, 60-99% of the sequences generated in different viral metagenomic studies are not homologous to known viruses. In this review, we discuss the advances in the area of viral metagenomics during the last decade and their relevance to virus discovery, clinical microbiology and public health. We discuss the potential of metagenomics for characterization of the normal viral population in a healthy community and identification of viruses that could pose a threat to humans through zoonosis. In addition, we propose a new model of the Koch's postulates named the 'Metagenomic Koch's Postulates'. Unlike the original Koch's postulates and the Molecular Koch's postulates as formulated by Falkow, the metagenomic Koch's postulates focus on the identification of metagenomic traits in disease cases. The metagenomic traits that can be traced after healthy individuals have been exposed to the source of the suspected pathogen.
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Affiliation(s)
- John L Mokili
- Department of Biology, San Diego State University, San Diego, CA 92182, USA.
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252
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Wang C, Lan D, Cui L, Yang Z, Yuan C, Hua X. Molecular characterization of a porcine kobuvirus strain in China. Arch Virol 2011; 157:573-8. [DOI: 10.1007/s00705-011-1205-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/22/2011] [Indexed: 01/11/2023]
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253
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Canuti M, Eis-Huebinger AM, Deijs M, de Vries M, Drexler JF, Oppong SK, Müller MA, Klose SM, Wellinghausen N, Cottontail VM, Kalko EKV, Drosten C, van der Hoek L. Two novel parvoviruses in frugivorous New and Old World bats. PLoS One 2011; 6:e29140. [PMID: 22216187 PMCID: PMC3246463 DOI: 10.1371/journal.pone.0029140] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 11/21/2011] [Indexed: 02/07/2023] Open
Abstract
Bats, a globally distributed group of mammals with high ecological importance, are increasingly recognized as natural reservoir hosts for viral agents of significance to human and animal health. In the present study, we evaluated pools of blood samples obtained from two phylogenetically distant bat families, in particular from flying foxes (Pteropodidae), Eidolon helvum in West Africa, and from two species of New World leaf-nosed fruit bats (Phyllostomidae), Artibeus jamaicensis and Artibeus lituratus in Central America. A sequence-independent virus discovery technique (VIDISCA) was used in combination with high throughput sequencing to detect two novel parvoviruses: a PARV4-like virus named Eh-BtPV-1 in Eidolon helvum from Ghana and the first member of a putative new genus in Artibeus jamaicensis from Panama (Aj-BtPV-1). Those viruses were circulating in the corresponding bat colony at rates of 7–8%. Aj-BtPV-1 was also found in Artibeus lituratus (5.5%). Both viruses were detected in the blood of infected animals at high concentrations: up to 10E8 and to 10E10 copies/ml for Aj-BtPV-1 and Eh-BtPV-1 respectively. Eh-BtPV-1 was additionally detected in all organs collected from bats (brain, lungs, liver, spleen, kidneys and intestine) and spleen and kidneys were identified as the most likely sites where viral replication takes place. Our study shows that bat parvoviruses share common ancestors with known parvoviruses of humans and livestock. We also provide evidence that a variety of Parvovirinae are able to cause active infection in bats and that they are widely distributed in these animals with different geographic origin, ecologies and climatic ranges.
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Affiliation(s)
- Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | | | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Michel de Vries
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Samuel K. Oppong
- Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Marcel A. Müller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Stefan M. Klose
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
| | | | - Veronika M. Cottontail
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Institute of Medical Microbiology and Hygiene, University of Ulm, Ulm, Germany
| | - Elisabeth K. V. Kalko
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Panama
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity (CINIMA), Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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254
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Abstract
A thorough understanding of the diversity of viruses in wildlife provides epidemiological baseline information about potential pathogens. Metagenomic analysis of the enteric viral flora revealed a new anellovirus and bocavirus species in pine martens and a new circovirus-like virus and geminivirus-related DNA virus in European badgers. In addition, sequences with homology to viruses from the families Paramyxo- and Picornaviridae were detected.
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255
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Wang LF, Walker PJ, Poon LLM. Mass extinctions, biodiversity and mitochondrial function: are bats 'special' as reservoirs for emerging viruses? Curr Opin Virol 2011; 1:649-57. [PMID: 22440923 PMCID: PMC7102786 DOI: 10.1016/j.coviro.2011.10.013] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/16/2011] [Accepted: 10/17/2011] [Indexed: 01/11/2023]
Abstract
For the past 10-15 years, bats have attracted growing attention as reservoirs of emerging zoonotic viruses. This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. As bats have ancient evolutionary origins and are the only flying mammals, it has been hypothesized that some of their unique biological features may have made them especially suitable hosts for different viruses. So the question 'Are bats different, special or exceptional?' has become a focal point in the field of virology, bat biology and virus-host co-evolution. In this brief review, we examine the topic in a relatively unconventional way, that is, our discussion will be based on both scientific discoveries and theoretical predictions. This approach was chosen partially because the data in this field are so limited that it is impossible to conduct a useful review based on published results only and also because we believe it is important to provoke original, speculative or even controversial ideas or theories in this important field of research.
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Affiliation(s)
- Lin-Fa Wang
- CSRIO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria 3216, Australia.
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256
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Abstract
The genome of bat adenovirus 2 was sequenced and analyzed. It is similar in size (31,616 bp) to the genomes of bat adenovirus 3 and canine adenoviruses 1 and 2. These four viruses are monophyletic and share an identical genome organization, with one E3 gene and four E4 genes unique to this group among the mastadenoviruses. These findings suggest that canine adenoviruses may have originated by interspecies transfer of a vespertilionid bat adenovirus.
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257
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Sequence analysis of porcine kobuvirus VP1 region detected in pigs in Japan and Thailand. Virus Genes 2011; 44:253-7. [DOI: 10.1007/s11262-011-0692-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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258
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Taylor DJ, Dittmar K, Ballinger MJ, Bruenn JA. Evolutionary maintenance of filovirus-like genes in bat genomes. BMC Evol Biol 2011; 11:336. [PMID: 22093762 PMCID: PMC3229293 DOI: 10.1186/1471-2148-11-336] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Little is known of the biological significance and evolutionary maintenance of integrated non-retroviral RNA virus genes in eukaryotic host genomes. Here, we isolated novel filovirus-like genes from bat genomes and tested for evolutionary maintenance. We also estimated the age of filovirus VP35-like gene integrations and tested the phylogenetic hypotheses that there is a eutherian mammal clade and a marsupial/ebolavirus/Marburgvirus dichotomy for filoviruses. RESULTS We detected homologous copies of VP35-like and NP-like gene integrations in both Old World and New World species of Myotis (bats). We also detected previously unknown VP35-like genes in rodents that are positionally homologous. Comprehensive phylogenetic estimates for filovirus NP-like and VP35-like loci support two main clades with a marsupial and a rodent grouping within the ebolavirus/Lloviu virus/Marburgvirus clade. The concordance of VP35-like, NP-like and mitochondrial gene trees with the expected species tree supports the notion that the copies we examined are orthologs that predate the global spread and radiation of the genus Myotis. Parametric simulations were consistent with selective maintenance for the open reading frame (ORF) of VP35-like genes in Myotis. The ORF of the filovirus-like VP35 gene has been maintained in bat genomes for an estimated 13. 4 MY. ORFs were disrupted for the NP-like genes in Myotis. Likelihood ratio tests revealed that a model that accommodates positive selection is a significantly better fit to the data than a model that does not allow for positive selection for VP35-like sequences. Moreover, site-by-site analysis of selection using two methods indicated at least 25 sites in the VP35-like alignment are under positive selection in Myotis. CONCLUSIONS Our results indicate that filovirus-like elements have significance beyond genomic imprints of prior infection. That is, there appears to be, or have been, functionally maintained copies of such genes in mammals. "Living fossils" of filoviruses appear to be selectively maintained in a diverse mammalian genus (Myotis).
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Affiliation(s)
- Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA.
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259
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Ge X, Li J, Peng C, Wu L, Yang X, Wu Y, Zhang Y, Shi Z. Genetic diversity of novel circular ssDNA viruses in bats in China. J Gen Virol 2011; 92:2646-2653. [DOI: 10.1099/vir.0.034108-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Novel circular ssDNA genomes have recently been detected in animals and in the environment using metagenomic and high-throughput sequencing approaches. In this study, five full-length circular ssDNA genomes were recovered from bat faecal samples using inverse PCR with sequences designed based on circovirus-related sequences obtained from Solexa sequencing data derived from a random amplification method. These five sequences shared a similar genomic organization to circovirus or the recently proposed cyclovirus of the family Circoviridae. The newly obtained circovirus/cyclovirus-like genomes ranged from 1741 to 2177 bp, and each consisted of two major ORFs, ORF1 and ORF2, encoding putative replicase (Rep) and capsid (Cap) proteins, respectively. The potential stem–loop region was predicted in all five genomes, and three of them had the typical conserved nonanucleotide motif of cycloviruses. A set of primers targeting the conserved Rep region was designed and used to detect the prevalence of circovirus/cyclovirus sequences in individual bats. Among 199 samples tested, 47 were positive (23.6 %) for the circovirus genome and two (1.0 %) were positive for the cyclovirus genome. In total, 48 partial Rep sequences plus the five full-length genomes were obtained in this study. Detailed analysis indicated that these sequences are distantly related to known circovirus/cyclovirus genomes and may represent 22 novel species that belong to the family Circoviridae.
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Affiliation(s)
- Xingyi Ge
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Jialu Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Cheng Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Lijun Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Xinglou Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Yongquan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Yunzhi Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, PR China
| | - Zhengli Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
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260
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Shan T, Li L, Simmonds P, Wang C, Moeser A, Delwart E. The fecal virome of pigs on a high-density farm. J Virol 2011; 85:11697-708. [PMID: 21900163 PMCID: PMC3209269 DOI: 10.1128/jvi.05217-11] [Citation(s) in RCA: 260] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/23/2011] [Indexed: 12/14/2022] Open
Abstract
Swine are an important source of proteins worldwide but are subject to frequent viral outbreaks and numerous infections capable of infecting humans. Modern farming conditions may also increase viral transmission and potential zoonotic spread. We describe here the metagenomics-derived virome in the feces of 24 healthy and 12 diarrheic piglets on a high-density farm. An average of 4.2 different mammalian viruses were shed by healthy piglets, reflecting a high level of asymptomatic infections. Diarrheic pigs shed an average of 5.4 different mammalian viruses. Ninety-nine percent of the viral sequences were related to the RNA virus families Picornaviridae, Astroviridae, Coronaviridae, and Caliciviridae, while 1% were related to the small DNA virus families Circoviridae, and Parvoviridae. Porcine RNA viruses identified, in order of decreasing number of sequence reads, consisted of kobuviruses, astroviruses, enteroviruses, sapoviruses, sapeloviruses, coronaviruses, bocaviruses, and teschoviruses. The near-full genomes of multiple novel species of porcine astroviruses and bocaviruses were generated and phylogenetically analyzed. Multiple small circular DNA genomes encoding replicase proteins plus two highly divergent members of the Picornavirales order were also characterized. The possible origin of these viral genomes from pig-infecting protozoans and nematodes, based on closest sequence similarities, is discussed. In summary, an unbiased survey of viruses in the feces of intensely farmed animals revealed frequent coinfections with a highly diverse set of viruses providing favorable conditions for viral recombination. Viral surveys of animals can readily document the circulation of known and new viruses, facilitating the detection of emerging viruses and prospective evaluation of their pathogenic and zoonotic potentials.
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Affiliation(s)
- Tongling Shan
- Blood Systems Research Institute, San Francisco, California
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
- Zoonosis and Comparative Medicine Group, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, California
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Peter Simmonds
- Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Chunlin Wang
- Stanford Genome Technology Center, Stanford, California
| | - Adam Moeser
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
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261
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Abstract
At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity. Importance At this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that the viral universe is far more vast and diverse than previously suspected. At this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that the viral universe is far more vast and diverse than previously suspected.
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262
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Barry AF, Ribeiro J, Alfieri AF, van der Poel WH, Alfieri AA. First detection of kobuvirus in farm animals in Brazil and the Netherlands. INFECTION GENETICS AND EVOLUTION 2011; 11:1811-4. [DOI: 10.1016/j.meegid.2011.06.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 06/28/2011] [Accepted: 06/29/2011] [Indexed: 11/27/2022]
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263
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Lau SKP, Woo PCY, Lai KKY, Huang Y, Yip CCY, Shek CT, Lee P, Lam CSF, Chan KH, Yuen KY. Complete genome analysis of three novel picornaviruses from diverse bat species. J Virol 2011; 85:8819-28. [PMID: 21697464 PMCID: PMC3165794 DOI: 10.1128/jvi.02364-10] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 06/14/2011] [Indexed: 12/21/2022] Open
Abstract
Although bats are important reservoirs of diverse viruses that can cause human epidemics, little is known about the presence of picornaviruses in these flying mammals. Among 1,108 bats of 18 species studied, three novel picornaviruses (groups 1, 2, and 3) were identified from alimentary specimens of 12 bats from five species and four genera. Two complete genomes, each from the three picornaviruses, were sequenced. Phylogenetic analysis showed that they fell into three distinct clusters in the Picornaviridae family, with low homologies to known picornaviruses, especially in leader and 2A proteins. Moreover, group 1 and 2 viruses are more closely related to each other than to group 3 viruses, which exhibit genome features distinct from those of the former two virus groups. In particular, the group 3 virus genome contains the shortest leader protein within Picornaviridae, a putative type I internal ribosome entry site (IRES) in the 5'-untranslated region instead of the type IV IRES found in group 1 and 2 viruses, one instead of two GXCG motifs in 2A, an L→V substitution in the DDLXQ motif in 2C helicase, and a conserved GXH motif in 3C protease. Group 1 and 2 viruses are unique among picornaviruses in having AMH instead of the GXH motif in 3C(pro). These findings suggest that the three picornaviruses belong to two novel genera in the Picornaviridae family. This report describes the discovery and complete genome analysis of three picornaviruses in bats, and their presence in diverse bat genera/species suggests the ability to cross the species barrier.
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Affiliation(s)
- Susanna K. P. Lau
- State Key Laboratory of Emerging Infectious Diseases
- Research Centre of Infection and Immunology
- Carol Yu Centre for Infection
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Patrick C. Y. Woo
- State Key Laboratory of Emerging Infectious Diseases
- Research Centre of Infection and Immunology
- Carol Yu Centre for Infection
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | | | - Yi Huang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Cyril C. Y. Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Chung-Tong Shek
- Agriculture, Fisheries and Conservation Department, The Government of Hong Kong Special Administrative Region, Hong Kong
| | - Paul Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Carol S. F. Lam
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases
- Research Centre of Infection and Immunology
- Carol Yu Centre for Infection
- Department of Microbiology, The University of Hong Kong, Hong Kong
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264
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Phan TG, Kapusinszky B, Wang C, Rose RK, Lipton HL, Delwart EL. The fecal viral flora of wild rodents. PLoS Pathog 2011; 7:e1002218. [PMID: 21909269 PMCID: PMC3164639 DOI: 10.1371/journal.ppat.1002218] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 06/28/2011] [Indexed: 12/30/2022] Open
Abstract
The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals. Rodents are the natural reservoir of numerous zoonotic viruses causing serious diseases in humans. We used an unbiased metagenomic approach to characterize the viral diversity in rodent feces. In addition to diet-derived insect and plant viruses mammalian viral sequences were abundant and diverse. Most notably, multiple new circular viral DNA families, two new picornaviridae genera, and the first murine astrovirus and picobirnaviruses were characterized. A mouse kobuvirus was a close relative to the Aichi virus human pathogen. This study significantly increases the known genetic diversity of eukaryotic viruses in rodents and provides an initial description of their enteric viromes.
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Affiliation(s)
- Tung G. Phan
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, United States of America
| | - Beatrix Kapusinszky
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, United States of America
- Department of Viral Diagnostics, National Center for Epidemiology, Budapest, Hungary
| | - Chunlin Wang
- Division of Infectious Diseases, Stanford University Medical Center, Stanford, California, United States of America
| | - Robert K. Rose
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, United States of America
| | - Howard L. Lipton
- Department of Neurology and Microbiology-Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Eric L. Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, United States of America
- * E-mail:
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265
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Puechmaille SJ, Frick WF, Kunz TH, Racey PA, Voigt CC, Wibbelt G, Teeling EC. White-nose syndrome: is this emerging disease a threat to European bats? Trends Ecol Evol 2011; 26:570-6. [PMID: 21835492 DOI: 10.1016/j.tree.2011.06.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/17/2011] [Accepted: 06/21/2011] [Indexed: 12/15/2022]
Abstract
White-nose syndrome (WNS) is a newly emergent disease that potentially threatens all temperate bat species. A recently identified fungus, Geomyces destructans, is the most likely causative agent of this disease. Until 2009, WNS and G. destructans were exclusively known from North America, but recent studies have confirmed this fungus is also present in Europe. We assembled an international WNS consortium of 67 scientists from 29 countries and identified the most important research and conservation priorities to assess the risk of WNS to European bats. Here, we review what is known about WNS and G. destructans and detail the conservation and research recommendations aimed at understanding and containing this emerging infectious disease.
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Affiliation(s)
- Sébastien J Puechmaille
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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266
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Abstract
New diseases continue to emerge in both human and animal populations, and the importance of animals, as reservoirs for viruses that can cause zoonoses are evident. Thus, an increased knowledge of the viral flora in animals, both in healthy and diseased individuals, is important both for animal and human health. Viral metagenomics is a culture-independent approach that is used to investigate the complete viral genetic populations of a sample. This review describes and discusses the different possible steps of a viral metagenomic study utilizing sequence-independent amplification, high-throughput sequencing, and bioinformatics to identify viruses. With this technology, multiple viruses can be detected simultaneously and novel and highly divergent viruses can be discovered and genetically characterized for the first time. This review also briefly discusses the applications of viral metagenomics in veterinary science and lists some of the viruses discovered within this field.
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Affiliation(s)
- Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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267
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Abstract
California sea lions are one of the major marine mammal species along the Pacific coast of North America. Sea lions are susceptible to a wide variety of viruses, some of which can be transmitted to or from terrestrial mammals. Using an unbiased viral metagenomic approach, we surveyed the fecal virome in California sea lions of different ages and health statuses. Averages of 1.6 and 2.5 distinct mammalian viral species were shed by pups and juvenile sea lions, respectively. Previously undescribed mammalian viruses from four RNA virus families (Astroviridae, Picornaviridae, Caliciviridae, and Reoviridae) and one DNA virus family (Parvoviridae) were characterized. The first complete or partial genomes of sapeloviruses, sapoviruses, noroviruses, and bocavirus in marine mammals are reported. Astroviruses and bocaviruses showed the highest prevalence and abundance in California sea lion feces. The diversity of bacteriophages was higher in unweaned sea lion pups than in juveniles and animals in rehabilitation, where the phage community consisted largely of phages related to the family Microviridae. This study increases our understanding of the viral diversity in marine mammals, highlights the high rate of enteric viral infections in these highly social carnivores, and may be used as a baseline viral survey for comparison with samples from California sea lions during unexplained disease outbreaks.
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268
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Li L, Pesavento PA, Shan T, Leutenegger CM, Wang C, Delwart E. Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses. J Gen Virol 2011; 92:2534-2541. [PMID: 21775584 DOI: 10.1099/vir.0.034611-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The close interactions of dogs with humans and surrounding wildlife provide frequent opportunities for cross-species virus transmissions. In order to initiate an unbiased characterization of the eukaryotic viruses in the gut of dogs, this study used deep sequencing of partially purified viral capsid-protected nucleic acids from the faeces of 18 diarrhoeic dogs. Known canine parvoviruses, coronaviruses and rotaviruses were identified, and the genomes of the first reported canine kobuvirus and sapovirus were characterized. Canine kobuvirus, the first sequenced canine picornavirus and the closest genetic relative of the diarrhoea-causing human Aichi virus, was detected at high frequency in the faeces of both healthy and diarrhoeic dogs. Canine sapovirus constituted a novel genogroup within the genus Sapovirus, a group of viruses also associated with human and animal diarrhoea. These results highlight the high frequency of new virus detection possible even in extensively studied animal species using metagenomics approaches, and provide viral genomes for further disease-association studies.
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Affiliation(s)
- Linlin Li
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Tongling Shan
- Zoonosis and Comparative Medicine Group, Shanghai Jiao Tong University, Shanghai, Republic of China
- Blood Systems Research Institute, San Francisco, CA, USA
| | | | - Chunlin Wang
- Stanford Genome Technology Center, Stanford, CA, USA
| | - Eric Delwart
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
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269
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Scheets K, Blinkova O, Melcher U, Palmer MW, Wiley GB, Ding T, Roe BA. Detection of members of the Tombusviridae in the Tallgrass Prairie Preserve, Osage County, Oklahoma, USA. Virus Res 2011; 160:256-63. [PMID: 21762736 DOI: 10.1016/j.virusres.2011.06.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 06/27/2011] [Accepted: 06/29/2011] [Indexed: 12/16/2022]
Abstract
Viruses are most frequently discovered because they cause disease in organisms of importance to humans. To expand knowledge of plant-associated viruses beyond these narrow constraints, non-cultivated plants of the Tallgrass Prairie Preserve, Osage County, Oklahoma, USA were systematically surveyed for evidence of the presence of viruses. This report discusses viruses of the family Tombusviridae putatively identified by the survey. Evidence of two carmoviruses, a tombusvirus, a panicovirus and an unclassifiable tombusvirid was found. The complete genome sequence was obtained for putative TGP carmovirus 1 from the legume Lespedeza procumbens, and the virus was detected in several other plant species including the fern Pellaea atropurpurea. Phylogenetic analysis of the sequence and partial sequence of a related virus supported strongly the placement of these viruses in the genus Carmovirus. Polymorphisms in the sequences suggested existence of two populations of TGP carmovirus 1 in the study area and year-to-year variations in infection by TGP carmovirus 3.
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Affiliation(s)
- Kay Scheets
- Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA.
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270
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Rosario K, Breitbart M. Exploring the viral world through metagenomics. Curr Opin Virol 2011; 1:289-97. [PMID: 22440785 DOI: 10.1016/j.coviro.2011.06.004] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 06/07/2011] [Indexed: 01/07/2023]
Abstract
Viral metagenomics, or shotgun sequencing of purified viral particles, has revolutionized the field of environmental virology by allowing the exploration of viral communities in a variety of sample types throughout the biosphere. The introduction of viral metagenomics has demonstrated that dominant viruses in environmental communities are not well-represented by the cultured viruses in existing sequence databases. Viral metagenomic studies have provided insights into viral ecology by elucidating the genetic potential, community structure, and biogeography of environmental viruses. In addition, viral metagenomics has expanded current knowledge of virus-host interactions by uncovering genes that may allow viruses to manipulate their hosts in unexpected ways. The intrinsic potential for virus discovery through viral metagenomics can help advance a wide array of disciplines including evolutionary biology, pathogen surveillance, and biotechnology.
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Affiliation(s)
- Karyna Rosario
- University of South Florida, College of Marine Science, 140 7th Avenue South, Saint Petersburg, FL 33701, USA
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271
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Ng TFF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, Breitbart M. Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One 2011; 6:e20579. [PMID: 21674005 PMCID: PMC3108952 DOI: 10.1371/journal.pone.0020579] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 05/04/2011] [Indexed: 11/30/2022] Open
Abstract
Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes.
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Affiliation(s)
- Terry Fei Fan Ng
- College of Marine Science, University of South Florida, St. Petersburg, Florida, United States of America
| | - Dana L. Willner
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Yan Wei Lim
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Genome Institute of Singapore, Singapore
| | - Robert Schmieder
- Computational Science Research Center, San Diego State University, San Diego, California, United States of America
| | - Betty Chau
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | | | - Simon Anthony
- Wildlife Disease Labs, San Diego Zoo's Institute for Conservation Research, San Diego, California, United States of America
| | - Yijun Ruan
- Genome Institute of Singapore, Singapore
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, Florida, United States of America
- * E-mail:
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272
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Abstract
Kobuviruses are members of the large and growing family Picornaviridae. Until now, two official, Aichi virus and Bovine kobuvirus, and one candidate kobuvirus species, 'porcine kobuvirus', have been identified in human, cattle and swine, respectively. In addition, kobu-like viruses were detected very recently in the bat. Aichi virus could be one of the causative agents of gastroenteritis in humans, and kobuviruses probably also cause diarrhoea in cattle and swine. Although Aichi virus has been detected relatively infrequently (0-3%) in human diarrhoea, high seroprevalence, up to 80-95% at the age of 30-40, was found indicating the general nature of infection in different human populations. In the previous years, much new information has accumulated relating to kobuviruses and their host species. This review summarises the current knowledge on kobuviruses including taxonomy, biology and viral characteristics, and covers all aspects of infection including epidemiology, clinical picture, host species diversity, laboratory diagnosis and it gives a summary about possible future perspectives.
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Affiliation(s)
- Gábor Reuter
- National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.
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273
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Osborne C, Cryan PM, O'Shea TJ, Oko LM, Ndaluka C, Calisher CH, Berglund AD, Klavetter ML, Bowen RA, Holmes KV, Dominguez SR. Alphacoronaviruses in New World bats: prevalence, persistence, phylogeny, and potential for interaction with humans. PLoS One 2011; 6:e19156. [PMID: 21589915 PMCID: PMC3093381 DOI: 10.1371/journal.pone.0019156] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/20/2011] [Indexed: 11/19/2022] Open
Abstract
Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.
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Affiliation(s)
- Christina Osborne
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Paul M. Cryan
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Thomas J. O'Shea
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Lauren M. Oko
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Christina Ndaluka
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Charles H. Calisher
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Andrew D. Berglund
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Mead L. Klavetter
- Pinon Canyon Maneuver Site, Model, Colorado, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kathryn V. Holmes
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Samuel R. Dominguez
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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274
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Osborne C, Cryan PM, O'Shea TJ, Oko LM, Ndaluka C, Calisher CH, Berglund AD, Klavetter ML, Bowen RA, Holmes KV, Dominguez SR. Alphacoronaviruses in New World bats: prevalence, persistence, phylogeny, and potential for interaction with humans. PLoS One 2011; 6:e19156. [PMID: 21589915 DOI: 10.1371/journal.pone.0019156pone-d-11-00052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/20/2011] [Indexed: 05/24/2023] Open
Abstract
Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.
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Affiliation(s)
- Christina Osborne
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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275
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Molecular detection and genetic characterization of kobuviruses in fecal samples collected from diarrheic cattle in Korea. INFECTION GENETICS AND EVOLUTION 2011; 11:1178-82. [PMID: 21382521 DOI: 10.1016/j.meegid.2011.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 02/18/2011] [Accepted: 02/28/2011] [Indexed: 11/21/2022]
Abstract
Kobuviruses are small, non-enveloped viruses with single-stranded, positive-sense genomic RNA, belonging to the family Picornaviridae, a highly diverse family of important pathogens of humans and animals. In spite of discovery of bovine kobuvirus was first reported in 2003, which is several years ago, information about the virus is lacking. In this study, we first identified bovine kobuviruses from Korean diarrheic cattle by RT-PCR using the generic kobuvirus primers with subsequent cloning and sequencing, and reported genetic characterization of Korean bovine kobuviruses by phylogenetic analysis. Among 62 diarrheic fecal samples collected from 36 cattle farms in 2008-2010 in Korea, 16 (25.8%) samples and 13 (36.1%) farms were positive for kobuvirus, and this indicated that kobuvirus infections are endemic in diarrheic cattle in Korea. The rates of evolutionary substitution of kobuvirus and age of MRCA of Korean kobuvirus were estimated on the basis of temporal information of the sequences by divergence analysis. Phylogenetic analysis showed that six strains except CPF4293 belonged to bovine kobuviruses and formed the exclusive branch with other bovine kobuvirus reference strains; The CPF4293 strain, however, was especially close to porcine kobuviruses rather than to any other kobuviruses, and showed the close genetic relationship with porcine kobuvirus strains isolated in 2009 in Japan, even though it was originated from bovine fecal sample. These data raise questions as to whether interspecies transmission of porcine kobuvirus to cattle may occur in nature.
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276
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Rosario K, Marinov M, Stainton D, Kraberger S, Wiltshire EJ, Collings DA, Walters M, Martin DP, Breitbart M, Varsani A. Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). J Gen Virol 2011; 92:1302-1308. [PMID: 21367985 DOI: 10.1099/vir.0.030338-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Dragonfly cyclovirus (DfCyV), a new species of ssDNA virus discovered using viral metagenomics in dragonflies (family Libellulidae) from the Kingdom of Tonga. Metagenomic sequences of DfCyV were similar to viruses of the recently proposed genus Cyclovirus within the family Circoviridae. Specific PCRs resulted in the recovery of 21 DfCyV genomes from three dragonfly species (Pantala flavescens, Tholymis tillarga and Diplacodes bipunctata). The 1741 nt DfCyV genomes share >95 % nucleotide identity and are classified into 11 subtypes representing a single strain. The DfCyV genomes share 48-63 % genome-wide nucleotide identity with cycloviruses identified in human faecal samples. Recombination analysis revealed three recombinant DfCyV genomes, suggesting that recombination plays an important role in cyclovirus evolution. To our knowledge, this is the first report of a circular ssDNA virus identified in insects, and the data may help elucidate evolutionary links among novel Circoviridae recently identified in animals and environmental samples.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
| | - Milen Marinov
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
| | - Elizabeth J Wiltshire
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
| | - David A Collings
- Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
| | - Darren P Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch 7701, Cape Town, South Africa.,Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
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277
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Mechanism of translation initiation by Dicistroviridae IGR IRESs. Virology 2011; 411:355-61. [PMID: 21284991 DOI: 10.1016/j.virol.2011.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 01/04/2011] [Indexed: 01/02/2023]
Abstract
The Dicistroviridae is a growing virus family characterized by a dicistronic genome, wherein each open reading frame (ORF) is translated from an independent internal ribosome entry site (IRES). The 5' IRES that translates the first open reading frame (ORF1) is similar to the picornaviral IRESs. However the second IRES, referred to as the intergenic region (IGR) IRES, - translates ORF2 by and uses an unusual mechanism of initiating protein synthesis. It folds into a compact RNA structure that can bind directly to 40S ribosomal subunits and form 80S complexes to initiate translation in the absence of any initiation factors. Despite its unusual mechanism, the IGR IRES has proven to be an elegant model for elucidating initiation mechanisms employed by IRESs, as well as making it a powerful research tool with diverse applications.
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278
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Jimenez RM, Delwart E, Lupták A. Structure-based search reveals hammerhead ribozymes in the human microbiome. J Biol Chem 2011; 286:7737-7743. [PMID: 21257745 DOI: 10.1074/jbc.c110.209288] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deep sequencing of viral or bacterial nucleic acids monitors the presence and diversity of microbes in select populations and locations. Metagenomic study of mammalian viromes can help trace paths of viral transmissions within or between species. High throughput sequencing of patient and untreated sewage microbiomes showed many sequences with no similarity to genomic sequences of known function or origin. To estimate the distribution of functional RNAs in these microbiomes, we used the hammerhead ribozyme (HHR) motif to search for sequences capable of assuming its three-way junction fold. Although only two of the three possible natural HHR topologies had been known, our analysis revealed highly active ribozymes that terminated in any of the three stems. The most abundant of these are type II HHRs, one of which is the fastest natural cis-acting HHR yet discovered. Altogether, 13 ribozymes were confirmed in vitro, but only one showed sequence similarity to previously described HHRs. Sequences surrounding the ribozymes do not generally show similarity to known genes, except in one case, where a ribozyme is immediately preceded by a bacterial RadC gene. We demonstrate that a structure-based search for a known functional RNA is a powerful tool for analysis of metagenomic datasets, complementing sequence alignments.
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Affiliation(s)
| | - Eric Delwart
- the Blood Systems Research Institute and; Department of Laboratory Medicine, University of California, San Francisco, California 94118
| | - Andrej Lupták
- From the Departments of Pharmaceutical Sciences,; Chemistry, and; Molecular Biology and Biochemistry, University of California, Irvine, California 92697 and.
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279
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Abstract
Several new enterovirus serotypes and a new human rhinovirus species have been characterized in the Enterovirus genus recently, raising a question about the origin of the new viruses. In this article we attempt to outline the general patterns of enterovirus evolution, ultimately leading to the emergence of new serotypes or species. Different evolutionary and epidemiological patterns can be deduced between different enterovirus species, between entero- and rhino-viruses and between different serotypes within a species. This article presents a hypothesis that the divergent evolution leading to a new serotype is likely to involve adaptation to a new ecological niche either within a single host species or due to interspecies transmission. By contrast, evolution within a serotype appears to occur primarily by genetic drift.
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Affiliation(s)
| | - Carita Savolainen-Kopra
- National Institute for Health and Welfare (THL), Division of Health Protection, Department of Infectious Disease Surveillance & Control, Intestinal Viruses Unit, P.O. Box 30, FI-00271 Helsinki, Finland; National Institute for Health & Welfare (THL), PO Box 30, FI-00271 Helsinki, Finland
| | - Merja Roivainen
- National Institute for Health and Welfare (THL), Division of Health Protection, Department of Infectious Disease Surveillance & Control, Intestinal Viruses Unit, P.O. Box 30, FI-00271 Helsinki, Finland; National Institute for Health & Welfare (THL), PO Box 30, FI-00271 Helsinki, Finland
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280
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The limited distribution of Helitrons to vesper bats supports horizontal transfer. Gene 2010; 474:52-8. [PMID: 21193022 DOI: 10.1016/j.gene.2010.12.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 12/20/2010] [Indexed: 11/21/2022]
Abstract
Transposable elements (TEs) have the unique ability to move and replicate within the genome and therefore engender dramatic changes to genome architecture. Among different types of TEs, rolling-circle transposons (Helitrons) are well known for their ability to capture and amplify host gene fragments. Bioinformatic analysis revealed that Helitrons constitute ~3% of the Myotis lucifugus, (little brown bat) genome, while no Helitrons were found in any of the other 44+ sequenced mammalian genomes. Recently horizontal transfer has been implicated for some of the M. lucifugus Helitrons, in part explaining this disparate distribution among mammals. The purpose of this work is to determine both the distribution of Helitrons among bats and to estimate the number of independent invasions. We employed a combination of in silico, PCR and hybridization based techniques to identify Helitrons from diverse bat species belonging to ten different families. This work reveals that Helitrons invaded the vesper bat lineage, at least once. Indeed, Helitrons were not identified in the sister taxa 'Miniopterus', which suggests that the amplification of Helibat occurred (30-36 mya) only in the vesper bat lineage. The estimated age of amplification of the Helibats and the rapid radiation of vesper bats are roughly coincidental and suggest that the invasion and amplification of these elements might have influenced their evolutionary trajectory potentially contributing to phenotypic and genotypic diversity.
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281
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Li L, Shan T, Soji OB, Alam MM, Kunz TH, Zaidi SZ, Delwart E. Possible cross-species transmission of circoviruses and cycloviruses among farm animals. J Gen Virol 2010; 92:768-72. [PMID: 21177928 DOI: 10.1099/vir.0.028704-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circoviruses consist of highly prevalent and genetically diverse porcine and avian pathogens. The genomes of cycloviruses, a proposed new genus in the family Circoviridae, were recently identified in human and chimpanzee faeces. Here, six cyclovirus and four circovirus genomes from the tissues of chickens, goats, cows, and a bat were amplified and sequenced using rolling-circle amplification and inverse PCR. A goat cyclovirus was nearly identical to a cyclovirus from a cow. USA beef contained circoviruses with >99% similarity to porcine circovirus 2b. Circoviruses in chicken were related to those of pigeons. The close genetic similarity of a subset of cycloviruses and circoviruses replicating in distinct animal species may reflect recent cross-species transmissions. Further studies will be required to determine the impact of these highly prevalent infections on the health of farm animals.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA 94118, USA
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282
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Metagenomics and the molecular identification of novel viruses. Vet J 2010; 190:191-198. [PMID: 21111643 PMCID: PMC7110547 DOI: 10.1016/j.tvjl.2010.10.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 10/16/2010] [Accepted: 10/20/2010] [Indexed: 12/16/2022]
Abstract
There have been rapid recent developments in establishing methods for identifying and characterising viruses associated with animal and human diseases. These methodologies, commonly based on hybridisation or PCR techniques, are combined with advanced sequencing techniques termed ‘next generation sequencing’. Allied advances in data analysis, including the use of computational transcriptome subtraction, have also impacted the field of viral pathogen discovery. This review details these molecular detection techniques, discusses their application in viral discovery, and provides an overview of some of the novel viruses discovered. The problems encountered in attributing disease causality to a newly identified virus are also considered.
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Deuzing I, Fagrouch Z, Groenewoud MJ, Niphuis H, Kondova I, Bogers W, Verschoor EJ. Detection and characterization of two chimpanzee polyomavirus genotypes from different subspecies. Virol J 2010; 7:347. [PMID: 21110837 PMCID: PMC3003640 DOI: 10.1186/1743-422x-7-347] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/26/2010] [Indexed: 11/10/2022] Open
Abstract
The complete nucleotide sequences of three chimpanzee polyomavirus genetic variants were determined. Phylogenetic analysis indicated that the viruses form two different genotypes of ChPyV. Comparison with other primate polyomaviruses revealed a putative agnogene, and an unusually long VP1 open reading frame. The transcriptional control regions (TCR) of the viruses were extremely short (155 nucleotides), and highly conserved amongst the genotypes. Analysis of the TCR from different chimpanzee subspecies, and from a series of tissues from five individuals confirmed its genetic stability, and also indicates that double-infections with different genotypes can occur.
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Affiliation(s)
- Ilona Deuzing
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
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284
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A microbial detection array (MDA) for viral and bacterial detection. BMC Genomics 2010; 11:668. [PMID: 21108826 PMCID: PMC3017867 DOI: 10.1186/1471-2164-11-668] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 11/25/2010] [Indexed: 12/21/2022] Open
Abstract
Background Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. Methods We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to have no significant matches to the human genome sequence. Results In blinded testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Conclusions The MDA can be used to identify the suite of viruses and bacteria present in complex samples.
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285
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Katzourakis A, Gifford RJ. Endogenous viral elements in animal genomes. PLoS Genet 2010; 6:e1001191. [PMID: 21124940 PMCID: PMC2987831 DOI: 10.1371/journal.pgen.1001191] [Citation(s) in RCA: 443] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 09/30/2010] [Indexed: 12/31/2022] Open
Abstract
Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs) derived from ten non-retroviral families by systematic in silico screening of animal genomes, including the first endogenous representatives of double-stranded RNA, reverse-transcribing DNA, and segmented RNA viruses, and the first endogenous DNA viruses in mammalian genomes. Phylogenetic and genomic analysis of EVEs across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as mRNA. For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized. The presence of retrovirus sequences in animal genomes has been recognized since the 1970s, but is readily explained by the fact that these viruses integrate into chromosomal DNA as part of their normal replication cycle. Unexpectedly, however, we identified a large and diverse population of sequences in animal genomes that are derived from non-retroviral viruses. Analysis of these sequences—which represent all known virus genome types and replication strategies—reveals new information about the evolutionary history of viruses, in many cases providing the first and only direct evidence for their ancient origins. Additionally, we provide evidence that the functionality of one of these sequences has been maintained in the host genome over many millions of years, raising the possibility that captured viral sequences may have played a larger than expected role in host evolution.
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Affiliation(s)
- Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (RJG); (AK)
| | - Robert J. Gifford
- Aaron Diamond AIDS Research Center, New York, New York, United States of America
- * E-mail: (RJG); (AK)
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A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One 2010; 5:e13381. [PMID: 20976137 PMCID: PMC2956640 DOI: 10.1371/journal.pone.0013381] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 09/21/2010] [Indexed: 12/13/2022] Open
Abstract
Although metagenomics has been previously employed for pathogen discovery, its cost and complexity have prevented its use as a practical front-line diagnostic for unknown infectious diseases. Here we demonstrate the utility of two metagenomics-based strategies, a pan-viral microarray (Virochip) and deep sequencing, for the identification and characterization of 2009 pandemic H1N1 influenza A virus. Using nasopharyngeal swabs collected during the earliest stages of the pandemic in Mexico, Canada, and the United States (n = 17), the Virochip was able to detect a novel virus most closely related to swine influenza viruses without a priori information. Deep sequencing yielded reads corresponding to 2009 H1N1 influenza in each sample (percentage of aligned sequences corresponding to 2009 H1N1 ranging from 0.0011% to 10.9%), with up to 97% coverage of the influenza genome in one sample. Detection of 2009 H1N1 by deep sequencing was possible even at titers near the limits of detection for specific RT-PCR, and the percentage of sequence reads was linearly correlated with virus titer. Deep sequencing also provided insights into the upper respiratory microbiota and host gene expression in response to 2009 H1N1 infection. An unbiased analysis combining sequence data from all 17 outbreak samples revealed that 90% of the 2009 H1N1 genome could be assembled de novo without the use of any reference sequence, including assembly of several near full-length genomic segments. These results indicate that a streamlined metagenomics detection strategy can potentially replace the multiple conventional diagnostic tests required to investigate an outbreak of a novel pathogen, and provide a blueprint for comprehensive diagnosis of unexplained acute illnesses or outbreaks in clinical and public health settings.
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287
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Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat. J Virol 2010; 84:13004-18. [PMID: 20926577 DOI: 10.1128/jvi.01255-10] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Effective prediction of future viral zoonoses requires an in-depth understanding of the heterologous viral population in key animal species that will likely serve as reservoir hosts or intermediates during the next viral epidemic. The importance of bats as natural hosts for several important viral zoonoses, including Ebola, Marburg, Nipah, Hendra, and rabies viruses and severe acute respiratory syndrome-coronavirus (SARS-CoV), has been established; however, the large viral population diversity (virome) of bats has been partially determined for only a few of the ∼1,200 bat species. To assess the virome of North American bats, we collected fecal, oral, urine, and tissue samples from individual bats captured at an abandoned railroad tunnel in Maryland that is cohabitated by 7 to 10 different bat species. Here, we present preliminary characterization of the virome of three common North American bat species, including big brown bats (Eptesicus fuscus), tricolored bats (Perimyotis subflavus), and little brown myotis (Myotis lucifugus). In samples derived from these bats, we identified viral sequences that were similar to at least three novel group 1 CoVs, large numbers of insect and plant virus sequences, and nearly full-length genomic sequences of two novel bacteriophages. These observations suggest that bats encounter and disseminate a large assortment of viruses capable of infecting many different animals, insects, and plants in nature.
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288
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Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses. J Virol 2010; 84:10322-8. [PMID: 20668077 DOI: 10.1128/jvi.00601-10] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nearly complete genome sequences of three novel RNA viruses were acquired from the stool of an Afghan child. Phylogenetic analysis indicated that these viruses belong to the picorna-like virus superfamily. Because of their unique genomic organization and deep phylogenetic roots, we propose these viruses, provisionally named calhevirus, tetnovirus-1, and tetnovirus-2, as prototypes of new viral families. A newly developed nucleotide composition analysis (NCA) method was used to compare mononucleotide and dinucleotide frequencies for RNA viruses infecting mammals, plants, or insects. Using a large training data set of 284 representative picornavirus-like genomic sequences with defined host origins, NCA correctly identified the kingdom or phylum of the viral host for >95% of picorna-like viruses. NCA predicted an insect host origin for the 3 novel picorna-like viruses. Their presence in human stool therefore likely reflects ingestion of insect-contaminated food. As metagenomic analyses of different environments and organisms continue to yield highly divergent viral genomes NCA provides a rapid and robust method to identify their likely cellular hosts.
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