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Journal ArticleDOI

Comparative genomic analysis of the family Iridoviridae : re-annotating and defining the core set of iridovirus genes

19 Jan 2007-Virology Journal (BioMed Central)-Vol. 4, Iss: 1, pp 11-11
TL;DR: The re-analysis of genomes within the Iridoviridae family provides a unifying framework to understand the biology of these viruses, and further re-defining the core set of iridovirus genes will continue to lead to a better understanding of the phylogenetic relationships between individual irids.
Abstract: Members of the family Iridoviridae can cause severe diseases resulting in significant economic and environmental losses. Very little is known about how iridoviruses cause disease in their host. In the present study, we describe the re-analysis of the Iridoviridae family of complex DNA viruses using a variety of comparative genomic tools to yield a greater consensus among the annotated sequences of its members. A series of genomic sequence comparisons were made among, and between the Ranavirus and Megalocytivirus genera in order to identify novel conserved ORFs. Of these two genera, the Megalocytivirus genomes required the greatest number of altered annotations. Prior to our re-analysis, the Megalocytivirus species orange-spotted grouper iridovirus and rock bream iridovirus shared 99% sequence identity, but only 82 out of 118 potential ORFs were annotated; in contrast, we predict that these species share an identical complement of genes. These annotation changes allowed the redefinition of the group of core genes shared by all iridoviruses. Seven new core genes were identified, bringing the total number to 26. Our re-analysis of genomes within the Iridoviridae family provides a unifying framework to understand the biology of these viruses. Further re-defining the core set of iridovirus genes will continue to lead us to a better understanding of the phylogenetic relationships between individual iridoviruses as well as giving us a much deeper understanding of iridovirus replication. In addition, this analysis will provide a better framework for characterizing and annotating currently unclassified iridoviruses.

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Citations
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Journal ArticleDOI
TL;DR: In as much as ranaviral disease is listed as a notifiable disease by the World Organization for Animal Health and is a threat to amphibian survival, biosecurity precautions are implemented by nations to reduce the likelihood of transporting ranavirus virions among populations.
Abstract: Mass mortality of amphibians has occurred globally since at least the early 1990s from viral pathogens that are members of the genus Ranavirus, family Iridoviridae. The pathogen infects multiple amphibian hosts, larval and adult cohorts, and may persist in herpetofaunal and oste- ichthyan reservoirs. Environmental persistence of ranavirus virions outside a host may be several weeks or longer in aquatic systems. Transmission occurs by indirect and direct routes, and includes exposure to contaminated water or soil, casual or direct contact with infected individuals, and inges- tion of infected tissue during predation, cannibalism, or necrophagy. Some gross lesions include swelling of the limbs or body, erythema, swollen friable livers, and hemorrhage. Susceptible amphi- bians usually die from chronic cell death in multiple organs, which can occur within a few days fol- lowing infection or may take several weeks. Amphibian species differ in their susceptibility to rana- viruses, which may be related to their co-evolutionary history with the pathogen. The occurrence of recent widespread amphibian population die-offs from ranaviruses may be an interaction of sup- pressed and naive host immunity, anthropogenic stressors, and novel strain introduction. This review summarizes the ecological research on amphibian ranaviruses, discusses possible drivers of emer- gence and conservation strategies, and presents ideas for future research directions. We also discuss common pathological signs of ranaviral disease, methods for diagnostic evaluation, and ranavirus surveillance methods. Inasmuch as ranaviral disease is listed as a notifiable disease by the World Organization for Animal Health and is a threat to amphibian survival, we recommend that biosecu- rity precautions are implemented by nations to reduce the likelihood of transporting ranavirus virions among populations. Biosecurity precautions include disinfecting footwear and equipment that comes in contact with surface water inhabited by amphibians and testing commercially shipped amphibians for the pathogen. We also encourage natural resource organizations to establish routine surveillance programs for ranaviruses in wild amphibian populations.

292 citations


Cites background from "Comparative genomic analysis of the..."

  • ...Smithsonian Institute, Washington, DC, p 127–136 Chinchar VG (2002) Ranaviruses (family Iridoviridae): emerging cold-blooded killers....

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  • ...However, electron microscopy is only reliable for identification to the family level (Iridoviridae); it cannot be used to definitively verify a ranavirus....

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  • ...Ranavirus is in the family Iridoviridae (Eaton et al. 2007), which contains 5 genera: 2 infect invertebrates (Iridovirus and Chloriridovirus) and 3 infect ectothermic vertebrates (Ranavirus, Megalocytivirus, and Lymphocystivirus; Chinchar et al. 2009)....

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  • ...Virology 306:303–312 Chinchar VG, Essbauer S, He JG, Hyatt A, Miyazaki T, Seligy V, Williams T (2005) Iridoviridae....

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  • ...Ecol Lett 9:1157–1171 Ridenhour BJ, Storfer AT (2008) Geographically variable selection in Ambystoma tigrinum virus (Iridoviridae) throughout the western USA....

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Book ChapterDOI
TL;DR: The molecular and genetic basis of viral replication, pathogenesis, and immunity are described, and viral ecology is discussed with reference to members from each of the invertebrate and vertebrate genera.
Abstract: Members of the family Iridoviridae infect a diverse array of invertebrate and cold-blooded vertebrate hosts and are currently viewed as emerging pathogens of fish and amphibians. Iridovirid replication is unique and involves both nuclear and cytoplasmic compartments, a circularly permuted, terminally redundant genome that, in the case of vertebrate iridoviruses, is also highly methylated, and the efficient shutoff of host macromolecular synthesis. Although initially neglected largely due to the perceived lack of health, environmental, and economic concerns, members of the genus Ranavirus, and the newly recognized genus Megalocytivirus, are rapidly attracting growing interest due to their involvement in amphibian population declines and their adverse impacts on aquaculture. Herein we describe the molecular and genetic basis of viral replication, pathogenesis, and immunity, and discuss viral ecology with reference to members from each of the invertebrate and vertebrate genera.

219 citations


Cites background or methods from "Comparative genomic analysis of the..."

  • ...…of the two largest subunits of host Pol II (designated vPol-IIα and -IIβ) in all iridovirids sequenced to date strongly suggests that late in infection viral transcription is catalyzed by a virus-modified, or virusencoded, DNA-dependent RNA polymerase (Williams et al. 2005; Eaton et al. 2007)....

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  • ...Overall, iridovirids contain a common set of viral genes that encode viral structural and catalytic proteins that permit replication in a broad range of cell types (Eaton et al. 2007)....

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  • ...The numbers shown are averages based on the estimates of Eaton et al. (2007) and Tsai et al. (2007) b11951193-0004ztc.indd 128 8/18/2008 5:51:38 PM...

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  • ...Although there is still some disagreement on the exact numbers, based on the genome size, iridovirids contain between roughly 100 (ATV and FV3) and 200 (IIV-6) open reading frames (ORFs) (Tsai et al. 2007; Eaton et al. 2007; see Table 2 )....

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  • ...Most of the remaining ORFs match putative proteins present in one or more iridovirids, suggesting that they play important roles in iridovirid replication, biogenesis, and survival (Eaton et al. 2007)....

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Book ChapterDOI
01 Jan 2015
TL;DR: FV3 is the type species of the genus Ranavirus, and appears to be the most globally distributed species infecting ectothermic taxonomic across three vertebrate classes.
Abstract: Ranaviruses are globally distributed pathogens in amphibian, fish, and reptile communities that appear to be emerging. Cases of ranavirus infection or disease have been confirmed in at least 105 amphibian species (18 families), 41 fish species (22 families), and 29 reptile species (12 families). Ranaviruses have been documented on all continents except Antarctica, and are frequently associated with mass die-offs. Host susceptibility differs among species, with some species harboring subclinical infections and likely serving as reservoirs for the virus, and other highly susceptible species amplifying the virus. Currently, there are six recognized species of ranavirus, and all are not equally pathogenic among hosts. Frog virus 3 (FV3) is the type species of the genus Ranavirus, and appears to be the most globally distributed species infecting ectothermic taxonomic across three vertebrate classes. International commerce involving subclinically infected ectothermic vertebrates undoubtedly has contributed to the global distribution and emergence of ranaviruses. Herein, we describe the global distributed species infecting ectothermic vertebrates across three taxonomic classes.

157 citations

Journal ArticleDOI
TL;DR: The wealth of genetic and genomic information from studies on a diverse range of aquatic viruses is reviewed, and some major advances in the understanding of virus-host interactions in animals used in aquaculture are outlined.
Abstract: Over the last 30 years, aquaculture has become the fastest growing form of agriculture production in the world, but its development has been hampered by a diverse range of pathogenic viruses. During the last decade, a large number of viruses from aquatic animals have been identified, and more than 100 viral genomes have been sequenced and genetically characterized. These advances are leading to better understanding about antiviral mechanisms and the types of interaction occurring between aquatic viruses and their hosts. Here, based on our research experience of more than 20 years, we review the wealth of genetic and genomic information from studies on a diverse range of aquatic viruses, including iridoviruses, herpesviruses, reoviruses, and rhabdoviruses, and outline some major advances in our understanding of virus-host interactions in animals used in aquaculture.

148 citations

Journal ArticleDOI
TL;DR: The data indicate that RNAi provides antiviral defense against dsDNA viruses in animals that provides protection against all major classes of viruses.
Abstract: RNA viruses in insects are targets of an RNA interference (RNAi)-based antiviral immune response, in which viral replication intermediates or viral dsRNA genomes are processed by Dicer-2 (Dcr-2) into viral small interfering RNAs (vsiRNAs). Whether dsDNA virus infections are controlled by the RNAi pathway remains to be determined. Here, we analyzed the role of RNAi in DNA virus infection using Drosophila melanogaster infected with Invertebrate iridescent virus 6 (IIV-6) as a model. We show that Dcr-2 and Argonaute-2 mutant flies are more sensitive to virus infection, suggesting that vsiRNAs contribute to the control of DNA virus infection. Indeed, small RNA sequencing of IIV-6–infected WT and RNAi mutant flies identified abundant vsiRNAs that were produced in a Dcr-2–dependent manner. We observed a highly uneven distribution with strong clustering of vsiRNAs to small defined regions (hotspots) and modest coverage at other regions (coldspots). vsiRNAs mapped in similar proportions to both strands of the viral genome, suggesting that long dsRNA derived from convergent overlapping transcripts serves as a substrate for Dcr-2. In agreement, strand-specific RT-PCR and Northern blot analyses indicated that antisense transcripts are produced during infection. Moreover, we show that vsiRNAs are functional in silencing reporter constructs carrying fragments of the IIV-6 genome. Together, our data indicate that RNAi provides antiviral defense against dsDNA viruses in animals. Thus, RNAi is the predominant antiviral defense mechanism in insects that provides protection against all major classes of viruses.

145 citations


Cites background or methods from "Comparative genomic analysis of the..."

  • ...(34) was used to analyze read density per ORF....

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  • ...The IIV-6 genome is predicted to encode 211 ORFs, of which 45% and 55% derive from the upper and lower strands, respectively (34)....

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  • ...IIV-6 is a large, complex virus with a dsDNA genome of 212,482 bp that encodes 211 putative ORFs distributed along the two strands of the viral genome (33, 34)....

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References
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Journal ArticleDOI
TL;DR: The role of these diseases in the global decline of amphibian populations is examined and hypotheses for the origins and impact of these panzootics are proposed.
Abstract: We review recent research on the pathology, ecology, and biogeography of two emerging infectious wildlife diseases, chytridiomycosis and ranaviral disease, in the context of host-parasite population biology. We examine the role of these diseases in the global decline of amphibian populations and propose hypotheses for the origins and impact of these panzootics. Finally, we discuss emerging infectious diseases as a global threat to wildlife populations.

956 citations

Journal ArticleDOI
TL;DR: It is suggested that, in common with many emerging infectious diseases of humans, domestic animals and other wildlife species, emergence of chytridiomycosis may be driven by anthropogenic introduction (pathogen pollution).
Abstract: . A series of recent papers have implicated pathogens and parasites in amphibian population declines. Here, we review evidence on the link between infectious disease and amphibian population declines. We conclude that available data provide the clearest link for the fungal disease amphibian chytridiomycosis, although other pathogens are also implicated. We suggest additional experimental and observational data that need to be collected to provide further support that these other pathogens are associated with declines. We suggest that, in common with many emerging infectious diseases (EIDs) of humans, domestic animals and other wildlife species, emergence of chytridiomycosis may be driven by anthropogenic introduction (pathogen pollution). Finally, we review a number of recent advances in the host–parasite ecology of chytridiomycosis that help explain its emergence and impact.

779 citations


"Comparative genomic analysis of the..." refers background in this paper

  • ...In addition, iridovirus infections have been implicated in amphibian population declines, representing a set of emerging infectious diseases whose spread has been accelerated by human activities [10-14]....

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Journal ArticleDOI

442 citations


"Comparative genomic analysis of the..." refers background in this paper

  • ...The first step in the re-annotation of the Ranavirus genus was a comparative genomic analysis of FV3, TFV, and ATV....

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  • ...Results: A series of genomic sequence comparisons were made among, and between the Ranavirus and Megalocytivirus genera in order to identify novel conserved ORFs....

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  • ...Subsequent reanalysis of the second Ranavirus group, containing SGIV and GIV, resulted in an increase from 131 to 138 conserved annotated ORFs (Table 4)....

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  • ...After re-annotating the Megalocytivirus genus, we applied the same comparative genomic analysis to the Ranavirus genus....

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  • ...Although this approach proved extremely successful for the Ranavirus and Megalocytivirus genera, we were unable to use it for the Chloriridovirus, Iridovirus, and Lymphocystivirus genera....

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Journal ArticleDOI
TL;DR: A hierarchy of rates at which genomes have changed during evolution is established and it is shown that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes.
Abstract: The determination of complete genome sequences provides us with an opportunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to their protein coding genes at two levels: (i) we compare genomes as "bags of genes" and measure the fraction of orthologs shared between genomes and (ii) we quantify correlations between genes with respect to their relative positions in genomes. Distances between the genomes are related to their divergence times, measured as the number of amino acid substitutions per site in a set of 34 orthologous genes that are shared among all the genomes compared. We establish a hierarchy of rates at which genomes have changed during evolution. Protein sequence identity is the most conserved, followed by the complement of genes within the genome. Next is the degree of conservation of the order of genes, whereas gene regulation appears to evolve at the highest rate. Finally, we show that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes.

437 citations


"Comparative genomic analysis of the..." refers background in this paper

  • ...This type of analysis is rarely consistent due to horizontal gene transfer [28] and variable rates of evolution [29]....

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Journal ArticleDOI
05 Dec 2001-Virology
TL;DR: It is suggested that ISKNV, RSIV, sea bass iridovirus, grouper iridvirus, and African lampeye iridavirus may belong to a new genus of the Iridoviridae family and are tentatively referred to as cell hypertrophy iridOViruses.

235 citations


"Comparative genomic analysis of the..." refers background in this paper

  • ...Frog virus 3 FV3 Ranavirus 105903 97 AY548484 [27] Tiger frog virus TFV Ranavirus 105057 103 AF389451 [1] Ambystoma tigrinum virus ATV Ranavirus 106332 92 AY150217 [30] Grouper iridovirus GIV Ranavirus 139793 139 AY666015 [21] Singapore grouper iridovirus SGIV Ranavirus 140131 139 AY521625 [22] Lymphocystis disease virus 1 LCDV-1 Lymphocystivirus 102653 108 L63545 [34] Lymphocystis disease virus China LCDV-China Lymphocystivirus 186250 178 AY380826 [24] Infectious spleen and kidney necrosis virus ISKNV Megalocytivirus 111362 117 AF371960 [20] Rock bream iridovirus RBIV Megalocytivirus 112080 116 AY532606 [19] Orange-spotted grouper iridovirus OSGIV Megalocytivirus 112636 116 AY894343 [18] Invertebrate iridescent virus 6 IIV-6 Iridovirus 212482 211 AF303741 [2] Invertebrate iridescent virus 3 IIV-3 Chloriridovirus 191100 126 DQ643392 [26]...

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  • ...A number of past phylogenetic analyses of Iridoviridae have used phylogenic trees constructed from aligned protein sequences [1,18-20,22,24,27]....

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  • ...It is interesting to note that the genomic sequence of ISKNV (sequenced using subcloned fragments rather than PCR products) [20], had significantly fewer annotation changes made during our re-analysis....

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