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Max L Nibert - One of the best experts on this subject based on the ideXlab platform.
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Extended genome sequences of penaeid shrimp infectious myonecrosis virus strains from Brazil and Indonesia
Archives of Virology, 2015Co-Authors: Sidrotun Naim, Donald V. Lightner, Kathy F J Tang, May Yang, Max L NibertAbstract:New sequencing studies of the nonsegmented dsRNA genome of penaeid shrimp infectious myonecrosis virus (IMNV), a tentatively assigned member of the family Totiviridae , identified previously unread sequences at both genome termini in three previously analyzed IMNV strains, one from Brazil (the prototype strain of IMNV) and two from Indonesia. The new sequence determinations add >600 nt to the 5′ end of the genomic plus strand of each strain, increasing the length of the 5′ nontranslated region to at least 469–472 nt and the length of the upstream open reading frame (ORF1) translation product by at least 48 aa. These new findings are similar to recent ones for two other IMNV strains (GenBank KF836757.1 and KJ556923.1) and thereby corroborate important amendments to the full-length IMNV genome sequence.
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Three-Dimensional Structure of a Protozoal Double-Stranded RNA Virus That Infects the Enteric Pathogen Giardia lamblia
Journal of Virology, 2014Co-Authors: Mandy E.w. Janssen, Yuko Takagi, Giovanni Cardone, Kristin N. Parent, Max L Nibert, Timothy S. BakerAbstract:Giardia lamblia virus (GLV) is a small, nonenveloped, nonsegmented double-stranded RNA (dsRNA) virus infecting Giardia lamblia, the most common protozoan pathogen of the human intestine and a major agent of waterborne diarrheal disease worldwide. GLV (genus Giardiavirus) is a member of family Totiviridae, along with several other groups of protozoal or fungal viruses, including Leishmania RNA viruses and Trichomonas vaginalis viruses. Interestingly, GLV is more closely related than other Totiviridae members to a group of recently discovered metazoan viruses that includes penaeid shrimp infectious myonecrosis virus (IMNV). Moreover, GLV is the only known protozoal dsRNA virus that can transmit efficiently by extracellular means, also like IMNV. In this study, we used transmission electron cryomicroscopy and icosahedral image reconstruction to examine the GLV virion at an estimated resolution of 6.0 Å. Its outermost diameter is 485 Å, making it the largest totivirus capsid analyzed to date. Structural comparisons of GLV and other totiviruses highlighted a related “T=2” capsid organization and a conserved helix-rich fold in the capsid subunits. In agreement with its unique capacity as a protozoal dsRNA virus to survive and transmit through extracellular environments, GLV was found to be more thermoresistant than Trichomonas vaginalis virus 1, but no specific protein machinery to mediate cell entry, such as the fiber complexes in IMNV, could be localized. These and other structural and biochemical findings provide a basis for future work to dissect the cell entry mechanism of GLV into a “primitive” (early-branching) eukaryotic host and an important enteric pathogen of humans. IMPORTANCE Numerous pathogenic bacteria, including Corynebacterium diphtheriae, Salmonella enterica, and Vibrio cholerae, are infected with lysogenic bacteriophages that contribute significantly to bacterial virulence. In line with this phenomenon, several pathogenic protozoa, including Giardia lamblia, Leishmania species, and Trichomonas vaginalis are persistently infected with dsRNA viruses, and growing evidence indicates that at least some of these protozoal viruses can likewise enhance the pathogenicity of their hosts. Understanding of these protozoal viruses, however, lags far behind that of many bacteriophages. Here, we investigated the dsRNA virus that infects the widespread enteric parasite Giardia lamblia. Using electron cryomicroscopy and icosahedral image reconstruction, we determined the virion structure of Giardia lamblia virus, obtaining new information relating to its assembly, stability, functions in cell entry and transcription, and similarities and differences with other dsRNA viruses. The results of our study set the stage for further mechanistic work on the roles of these viruses in protozoal virulence.
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Trichomonasvirus: a new genus of protozoan viruses in the family Totiviridae
Archives of Virology, 2011Co-Authors: Russell P. Goodman, Said A Ghabrial, Raina N. Fichorova, Max L NibertAbstract:The family Totiviridae includes a number of viruses with monosegmented dsRNA genomes and isometric virions that infect either fungi or a number of medically important protozoan parasites such as Leishmania and Giardia . A new genus, Trichomonasvirus , was recently approved for this family. Its name is based on the genus of its host organism, Trichomonas vaginalis , a protozoan parasite that colonizes the human genitourinary mucosa and is the most common non-viral sexually transmitted infection in the world. The type species of this new genus is Trichomonas vaginalis virus 1 . Distinguishing characteristics of the new genus include infection of a human sexually transmitted parasite, stable mixed infection with more than one distinct Trichomonasvirus species, and sequence-based phylogenetic divergence that distinguishes it from all other family members.
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Victorivirus, a new genus of fungal viruses in the family Totiviridae
Archives of Virology, 2009Co-Authors: Said A Ghabrial, Max L NibertAbstract:The family Totiviridae comprises viruses with nonsegmented dsRNA genomes and isometric virions. A new genus, Victorivirus , has been approved for this family, named from the specific epithet of Helminthosporium victoriae, host of the type species, Helminthosporium victoriae virus 190S . Distinguishing characteristics of the 11 viruses so far assigned to this genus include infection of filamentous fungi, an apparently coupled termination–reinitiation mechanism for translating the RNA-dependent RNA polymerase as a separate product from the upstream capsid protein, and sequence-based phylogenetic grouping in a distinct clade from other family members.
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infectious myonecrosis virus has a totivirus like 120 subunit capsid but with fiber complexes at the fivefold axes
Proceedings of the National Academy of Sciences of the United States of America, 2008Co-Authors: Jinghua Tang, Wendy F Ochoa, Robert S Sinkovits, Bonnie T Poulos, Donald V. Lightner, Timothy S. Baker, Said A Ghabrial, Max L NibertAbstract:Infectious myonecrosis virus (IMNV) is an emerging pathogen of penaeid shrimp in global aquaculture. Tentatively assigned to family Totiviridae, it has a nonsegmented dsRNA genome of 7,560 bp and an isometric capsid of the 901-aa major capsid protein. We used electron cryomicroscopy and 3D image reconstruction to examine the IMNV virion at 8.0-A resolution. Results reveal a totivirus-like, 120-subunit T = 1 capsid, 450 A in diameter, but with fiber complexes protruding a further 80 A at the fivefold axes. These protrusions likely mediate roles in the extracellular transmission and pathogenesis of IMNV, capabilities not shared by most other totiviruses. The IMNV structure is also notable in that the genome is centrally organized in five or six concentric shells. Within each of these shells, the densities alternate between a dodecahedral frame that connects the threefold axes vs. concentration around the fivefold axes, implying certain regularities in the RNA packing scheme.
Said A Ghabrial - One of the best experts on this subject based on the ideXlab platform.
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Discovery of Novel dsRNA Viral Sequences by In Silico Cloning and Implications for Viral Diversity, Host Range and Evolution
2016Co-Authors: Huiquan Liu, Jiasen Cheng, Said A Ghabrial, Jiatao Xie, Daohong JiangAbstract:Genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and the interaction between viruses and hosts. Traditional molecular cloning methods for obtaining RNA viral genomes are time-consuming and often difficult because many viruses occur in extremely low titers. DsRNA viruses in the families, Partitiviridae, Totiviridae, Endornaviridae, Chrysoviridae, and other related unclassified dsRNA viruses are generally associated with symptomless or persistent infections of their hosts. These characteristics indicate that samples or materials derived from eukaryotic organisms used to construct cDNA libraries and EST sequencing might carry these viruses, which were not easily detected by the researchers. Therefore, the EST databases may include numerous unknown viral sequences. In this study, we performed in silico cloning, a procedure for obtaining full or partial cDNA sequence of a gene by bioinformatics analysis, using known dsRNA viral sequences as queries to search against NCBI Expressed Sequence Tag (EST) database. From this analysis, we obtained 119 novel virus-like sequences related to members of the families, Endornaviridae, Chrysoviridae, Partitiviridae, and Totiviridae. Many of them were identified in cDNA libraries of eukaryotic lineages, which were not known to be hosts for these viruses. Furthermore, comprehensive phylogenetic analysis of these newly discovered virus-like sequences with known dsRNA viruses revealed that these dsRNA viruses may have co-evolved with respective host supergroups over a long evolutionary time while potential horizontal transmissions of viruses between different hos
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Discovery of Novel dsRNA Viral Sequences by In Silico Cloning and Implications for Viral Diversity, Host Range and Evolution
PloS one, 2012Co-Authors: Huiquan Liu, Jiasen Cheng, Said A Ghabrial, Jiatao Xie, Daohong JiangAbstract:Genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and the interaction between viruses and hosts. Traditional molecular cloning methods for obtaining RNA viral genomes are time-consuming and often difficult because many viruses occur in extremely low titers. DsRNA viruses in the families, Partitiviridae, Totiviridae, Endornaviridae, Chrysoviridae, and other related unclassified dsRNA viruses are generally associated with symptomless or persistent infections of their hosts. These characteristics indicate that samples or materials derived from eukaryotic organisms used to construct cDNA libraries and EST sequencing might carry these viruses, which were not easily detected by the researchers. Therefore, the EST databases may include numerous unknown viral sequences. In this study, we performed in silico cloning, a procedure for obtaining full or partial cDNA sequence of a gene by bioinformatics analysis, using known dsRNA viral sequences as queries to search against NCBI Expressed Sequence Tag (EST) database. From this analysis, we obtained 119 novel virus-like sequences related to members of the families, Endornaviridae, Chrysoviridae, Partitiviridae, and Totiviridae. Many of them were identified in cDNA libraries of eukaryotic lineages, which were not known to be hosts for these viruses. Furthermore, comprehensive phylogenetic analysis of these newly discovered virus-like sequences with known dsRNA viruses revealed that these dsRNA viruses may have co-evolved with respective host supergroups over a long evolutionary time while potential horizontal transmissions of viruses between different host supergroups also is possible. We also found that some of the plant partitiviruses may have originated from fungal viruses by horizontal transmissions. These findings extend our knowledge of the diversity and possible host range of dsRNA viruses and offer insight into the origin and evolution of relevant viruses with their hosts.
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Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages
BMC Evolutionary Biology, 2012Co-Authors: Huiquan Liu, Jiasen Cheng, Said A Ghabrial, Jiatao Xie, Youliang Peng, Daohong JiangAbstract:Background Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses.
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Clinical Isolates of Trichomonas vaginalis Concurrently Infected by Strains of Up to Four Trichomonasvirus Species (Family Totiviridae)
Journal of virology, 2011Co-Authors: Russell P. Goodman, Said A Ghabrial, Taylor S. Freret, Tomasz Kula, Alexander M. Geller, Megan W. T. Talkington, Vanessa Tang-fernandez, Olimpia Suciu, Aleksander A. Demidenko, David H. BeachAbstract:Trichomonas vaginalis, which causes the most common nonviral sexually transmitted disease worldwide, is itself commonly infected by nonsegmented double-stranded RNA (dsRNA) viruses from the genus Trichomonasvirus, family Totiviridae. To date, cDNA sequences of one or more strains of each of three trichomonasvirus species have been reported, and gel electrophoresis showing several different dsRNA molecules obtained from a few T. vaginalis isolates has suggested that more than one virus strain might concurrently infect the same parasite cell. Here, we report the complete cDNA sequences of 3 trichomonasvirus strains, one from each of the 3 known species, infecting a single, agar-cloned clinical isolate of T. vaginalis, confirming the natural capacity for concurrent (in this case, triple) infections in this system. We furthermore report the complete cDNA sequences of 11 additional trichomonasvirus strains, from 4 other clinical isolates of T. vaginalis. These additional strains represent the three known trichomonasvirus species, as well as a newly identified fourth species. Moreover, 2 of these other T. vaginalis isolates are concurrently infected by strains of all 4 trichomonasvirus species (i.e., quadruple infections). In sum, the full-length cDNA sequences of these 14 new trichomonasviruses greatly expand the existing data set for members of this genus and substantiate our understanding of their genome organizations, protein-coding and replication signals, diversity, and phylogenetics. The complexity of this virus-host system is greater than has been previously well recognized and suggests a number of important questions relating to the pathogenesis and disease outcomes of T. vaginalis infections of the human genital mucosa.
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Trichomonasvirus: a new genus of protozoan viruses in the family Totiviridae
Archives of Virology, 2011Co-Authors: Russell P. Goodman, Said A Ghabrial, Raina N. Fichorova, Max L NibertAbstract:The family Totiviridae includes a number of viruses with monosegmented dsRNA genomes and isometric virions that infect either fungi or a number of medically important protozoan parasites such as Leishmania and Giardia . A new genus, Trichomonasvirus , was recently approved for this family. Its name is based on the genus of its host organism, Trichomonas vaginalis , a protozoan parasite that colonizes the human genitourinary mucosa and is the most common non-viral sexually transmitted infection in the world. The type species of this new genus is Trichomonas vaginalis virus 1 . Distinguishing characteristics of the new genus include infection of a human sexually transmitted parasite, stable mixed infection with more than one distinct Trichomonasvirus species, and sequence-based phylogenetic divergence that distinguishes it from all other family members.
Jie Zhong - One of the best experts on this subject based on the ideXlab platform.
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mycoviruses in the plant pathogen ustilaginoidea virens are not correlated with the genetic backgrounds of its hosts
International Journal of Molecular Sciences, 2017Co-Authors: Jie Zhong, Chuan Yuan Cheng, Qian ZhouAbstract:Ustilaginoidea virens, the causal agent of rice false smut, is one of the most devastating grain diseases that causes loss of yield in most rice-growing areas worldwide. In this study, we performed a dsRNA screen to isolate mycoviruses from 35 U. virens strains. The results revealed that 34 of the tested isolates were infected by various dsRNA elements, displaying highly viral diversity and mixed infections. We characterized a 5.3 kbp dsRNA from a typical isolate containing dsRNA segments with sizes ranging from 0.5 to 5.3 kbp. Sequence analysis of its genomic properties indicated that it is a novel victorivirus, named Ustilaginoidea virens RNA virus 5 (UvRV5), that belongs to the family Totiviridae. RT-PCR detection was performed and indicated that not all the dsRNA bands that were 5.3 kbp in size contained UvRV5. Moreover, the genetic relatedness of all the U. virens strains was estimated according to phylogenetic analysis of the partial intergenic spacer region (IGS) sequences. However, concordance was not found between the dsRNA profiles and the IGS-based genetic relatedness of their host fungi.
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molecular identification of a novel victorivirus from the phytopathogenic fungus nigrospora oryzae
Virus Genes, 2016Co-Authors: Jie Zhong, Qian Zhou, Yue HuAbstract:Nigrospora oryzae is a worldwide phytopathogenic fungus that can infect many plant host species. In this study, complete sequence of a novel mycovirus from N. oryzae was reported. The viral genome is 5100 base pairs in length and possesses two overlapping open reading frames (ORFs). The two ORFs potentially encode proteins that showed significant similarity to the capsid protein and RNA-dependent RNA polymerase, in the family Totiviridae, respectively. Phylogenetic tree showed that this novel mycovirus is a new member of the genus Victorivirus in the family Totiviridae. We here designated the virus as Nigrospora oryzae victorivirus 1 (NoRV1), the first putative victorivirus identified in N. oryzae.
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the complete nucleotide sequence and genomic organization of a novel victorivirus with two non overlapping orfs identified in the plant pathogenic fungus phomopsis vexans
Archives of Virology, 2015Co-Authors: Ru Jia Zhang, Jie Zhong, Hong Hong ShangAbstract:In this study, a novel virus designated Phomopsis vexans RNA virus 1 (PvRV1) was identified in a strain of Phomopsis vexans. The complete genomic nucleotide sequence was determined and analyzed. Sequence analysis indicated that PvRV1 is closely related to viruses in the genus Victorivirus of the family Totiviridae. Two open reading frames (ORF1 and 2) were found in the PvRV1 sequence, and these showed significant similarity to the capsid protein (CP) and RNA-dependent RNA polymerase (RdRp), respectively, of members of the family Totiviridae. The two ORFs were spaced 98 nt apart, which is unique to PvRV1 and different from the overlapping arrangement in most victoriviruses. The expression strategies of the CP and RdRp are discussed based on in silico RNA secondary structure analysis.
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The nucleotide sequence and genome organization of two victoriviruses from the rice false smut fungus Ustilaginoidea virens.
Virus Genes, 2014Co-Authors: Jie Zhong, Qian Zhou, Dan Chen, Hong Hong ShangAbstract:Ustilaginoidea virens is the causal agent of false smut disease of rice. The dsRNA-Ls from a U. virens strain of Uv0901 containing three dsRNA bands were separated and sequenced. The dsRNA-Ls, with molecular weight of 5 kbp, were demonstrated to be two dsRNA segments referenced as dsRNA-L1 and dsRNA-L2. The two dsRNAs each contained two overlapped open reading frames, and showed significant similarity to those of capsid protein and RNA-directed RNA polymerase, respectively, of members of the family Totiviridae. Homology research and phylogenic analysis indicated that the dsRNA-L1 was a conspecific species of the previous reported Ustilaginoidea virens RNA virus 1, named Ustilaginoidea virens RNA virus Uv0901, and the dsRNA-L2 was a new number of the Victorivirus in the family Totiviridae, designed as Ustilaginoidea virens RNA virus 3.
Sven Martin Jørgensen - One of the best experts on this subject based on the ideXlab platform.
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Comparison of Atlantic salmon individuals with different outcomes of cardiomyopathy syndrome (CMS)
BMC genomics, 2012Co-Authors: Gerrit Timmerhaus, Pål Nilsen, Marit Rode, Aleksei Krasnov, Sergey Afanasyev, Harald Takle, Sven Martin JørgensenAbstract:Background Cardiomyopathy syndrome (CMS) is a severe disease of Atlantic salmon (Salmo salar L.) associated with significant economic losses in the aquaculture industry. CMS is diagnosed with a severe inflammation and degradation of myocardial tissue caused by a double-stranded RNA virus named piscine myocarditis virus (PMCV), with structural similarities to the Totiviridae family. In the present study we characterized individual host responses and genomic determinants of different disease outcomes.
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Transcriptome profiling of immune responses to cardiomyopathy syndrome (CMS) in Atlantic salmon
BMC genomics, 2011Co-Authors: Gerrit Timmerhaus, Pål Nilsen, Marit Rode, Aleksei Krasnov, Marta Alarcon, Sergey Afanasyev, Harald Takle, Sven Martin JørgensenAbstract:Background Cardiomyopathy syndrome (CMS) is a disease associated with severe myocarditis primarily in adult farmed Atlantic salmon (Salmo salar L.), caused by a double-stranded RNA virus named piscine myocarditis virus (PMCV) with structural similarities to the Totiviridae family. Here we present the first characterisation of host immune responses to CMS assessed by microarray transcriptome profiling.
Qian Zhou - One of the best experts on this subject based on the ideXlab platform.
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mycoviruses in the plant pathogen ustilaginoidea virens are not correlated with the genetic backgrounds of its hosts
International Journal of Molecular Sciences, 2017Co-Authors: Jie Zhong, Chuan Yuan Cheng, Qian ZhouAbstract:Ustilaginoidea virens, the causal agent of rice false smut, is one of the most devastating grain diseases that causes loss of yield in most rice-growing areas worldwide. In this study, we performed a dsRNA screen to isolate mycoviruses from 35 U. virens strains. The results revealed that 34 of the tested isolates were infected by various dsRNA elements, displaying highly viral diversity and mixed infections. We characterized a 5.3 kbp dsRNA from a typical isolate containing dsRNA segments with sizes ranging from 0.5 to 5.3 kbp. Sequence analysis of its genomic properties indicated that it is a novel victorivirus, named Ustilaginoidea virens RNA virus 5 (UvRV5), that belongs to the family Totiviridae. RT-PCR detection was performed and indicated that not all the dsRNA bands that were 5.3 kbp in size contained UvRV5. Moreover, the genetic relatedness of all the U. virens strains was estimated according to phylogenetic analysis of the partial intergenic spacer region (IGS) sequences. However, concordance was not found between the dsRNA profiles and the IGS-based genetic relatedness of their host fungi.
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molecular identification of a novel victorivirus from the phytopathogenic fungus nigrospora oryzae
Virus Genes, 2016Co-Authors: Jie Zhong, Qian Zhou, Yue HuAbstract:Nigrospora oryzae is a worldwide phytopathogenic fungus that can infect many plant host species. In this study, complete sequence of a novel mycovirus from N. oryzae was reported. The viral genome is 5100 base pairs in length and possesses two overlapping open reading frames (ORFs). The two ORFs potentially encode proteins that showed significant similarity to the capsid protein and RNA-dependent RNA polymerase, in the family Totiviridae, respectively. Phylogenetic tree showed that this novel mycovirus is a new member of the genus Victorivirus in the family Totiviridae. We here designated the virus as Nigrospora oryzae victorivirus 1 (NoRV1), the first putative victorivirus identified in N. oryzae.
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The nucleotide sequence and genome organization of two victoriviruses from the rice false smut fungus Ustilaginoidea virens.
Virus Genes, 2014Co-Authors: Jie Zhong, Qian Zhou, Dan Chen, Hong Hong ShangAbstract:Ustilaginoidea virens is the causal agent of false smut disease of rice. The dsRNA-Ls from a U. virens strain of Uv0901 containing three dsRNA bands were separated and sequenced. The dsRNA-Ls, with molecular weight of 5 kbp, were demonstrated to be two dsRNA segments referenced as dsRNA-L1 and dsRNA-L2. The two dsRNAs each contained two overlapped open reading frames, and showed significant similarity to those of capsid protein and RNA-directed RNA polymerase, respectively, of members of the family Totiviridae. Homology research and phylogenic analysis indicated that the dsRNA-L1 was a conspecific species of the previous reported Ustilaginoidea virens RNA virus 1, named Ustilaginoidea virens RNA virus Uv0901, and the dsRNA-L2 was a new number of the Victorivirus in the family Totiviridae, designed as Ustilaginoidea virens RNA virus 3.