Academic literature on the topic 'Marnaviridae'
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Journal articles on the topic "Marnaviridae"
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Wang, Han, Anna Munke, Siqi Li, Yuji Tomaru, and Kenta Okamoto. "Structural Insights into Common and Host-Specific Receptor-Binding Mechanisms in Algal Picorna-like Viruses." Viruses 14, no. 11 (October 27, 2022): 2369. http://dx.doi.org/10.3390/v14112369.
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Marnaviridae viruses are abundant algal viruses that regulate the dynamics of algal blooms in aquatic environments. They employ a narrow host range because they merely lyse their algal host species. This host-specific lysis is thought to correspond to the unique receptor-binding mechanism of the Marnaviridae viruses. Here, we present the atomic structures of the full and empty capsids of Chaetoceros socialis forma radians RNA virus 1 built-in 3.0 Å and 3.1 Å cryo-electron microscopy maps. The empty capsid structure and the structural variability provide insights into its assembly and uncoating intermediates. In conjunction with the previously reported atomic model of the Chaetoceros tenuissimus RNA virus type II capsid, we have identified the common and diverse structural features of the VP1 surface between the Marnaviridae viruses. We have also tested the potential usage of AlphaFold2 for structural prediction of the VP1s and a subsequent structural phylogeny for classifying Marnaviridae viruses by their hosts. These findings will be crucial for inferring the host-specific receptor-binding mechanism in Marnaviridae viruses.
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Potapov, Sergey, Anna Gorshkova, Andrey Krasnopeev, Galina Podlesnaya, Irina Tikhonova, Maria Suslova, Dmitry Kwon, Maxim Patrushev, Valentin Drucker, and Olga Belykh. "RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters." International Journal of Molecular Sciences 24, no. 15 (July 27, 2023): 12049. http://dx.doi.org/10.3390/ijms241512049.
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In this study, we analyzed the transcriptomes of RNA and DNA viruses from the oligotrophic water of Lake Baikal and the effluent from wastewater treatment plants (WWTPs) discharged into the lake from the towns of Severobaikalsk and Slyudyanka located on the lake shores. Given the uniqueness and importance of Lake Baikal, the issues of biodiversity conservation and the monitoring of potential virological hazards to hydrobionts and humans are important. Wastewater treatment plants discharge treated effluent directly into the lake. In this context, the identification and monitoring of allochthonous microorganisms entering the lake play an important role. Using high-throughput sequencing methods, we found that dsDNA-containing viruses of the class Caudoviricetes were the most abundant in all samples, while Leviviricetes (ssRNA(+) viruses) dominated the treated water samples. RNA viruses of the families Nodaviridae, Tombusviridae, Dicitroviridae, Picobirnaviridae, Botourmiaviridae, Marnaviridae, Solemoviridae, and Endornavirida were found in the pelagic zone of three lake basins. Complete or nearly complete genomes of RNA viruses belonging to such families as Dicistroviridae, Marnaviridae, Blumeviridae, Virgaviridae, Solspiviridae, Nodaviridae, and Fiersviridae and the unassigned genus Chimpavirus, as well as unclassified picorna-like viruses, were identified. In general, the data of sanitary/microbiological and genetic analyses showed that WWTPs inadequately purify the discharged water, but, at the same time, we did not observe viruses pathogenic to humans in the pelagic zone of the lake.
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Han, Zhenzhi, Jinbo Xiao, Yang Song, Mei Hong, Guolong Dai, Huanhuan Lu, Man Zhang, et al. "The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales." Viruses 12, no. 9 (September 7, 2020): 995. http://dx.doi.org/10.3390/v12090995.
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Novel posa-like viral genomes were first identified in swine fecal samples using metagenomics and were designated as unclassified viruses in the order Picornavirales. In the present study, nine husavirus strains were identified in China. Their genomes share 94.1–99.9% similarity, and alignment of these nine husavirus strains identified 697 nucleotide polymorphism sites across their full-length genomes. These nine strains were directly clustered with the Husavirus 1 lineage, and their genomic arrangement showed similar characteristics. These posa-like viruses have undergone a complex evolutionary process, and have a wide geographic distribution, complex host spectrum, deep phylogenetic divergence, and diverse genomic organizations. The clade of posa-like viruses forms a single group, which is evolutionarily distinct from other known families and could represent a distinct family within the Picornavirales. The genomic arrangement of Picornavirales and the new posa-like viruses are different, whereas the posa-like viruses have genomic modules similar to the families Dicistroviridae and Marnaviridae. The present study provides valuable genetic evidence of husaviruses in China, and clarifies the phylogenetic dynamics and the evolutionary characteristics of Picornavirales.
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Chase, Emily E., Sonia Monteil-Bouchard, Angélique Gobet, Felana H. Andrianjakarivony, Christelle Desnues, and Guillaume Blanc. "A High Rate Algal Pond Hosting a Dynamic Community of RNA Viruses." Viruses 13, no. 11 (October 26, 2021): 2163. http://dx.doi.org/10.3390/v13112163.
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Despite a surge of RNA virome sequencing in recent years, there are still many RNA viruses to uncover—as indicated by the relevance of viral dark matter to RNA virome studies (i.e., putative viruses that do not match to taxonomically identified viruses). This study explores a unique site, a high-rate algal pond (HRAP), for culturing industrially microalgae, to elucidate new RNA viruses. The importance of viral-host interactions in aquatic systems are well documented, and the ever-expanding microalgae industry is no exception. As the industry becomes a more important source of sustainable plastic manufacturing, a producer of cosmetic pigments and alternative protein sources, and a means of CO2 remediation in the face of climate change, studying microalgal viruses becomes a vital practice for proactive management of microalgae cultures at the industrial level. This study provides evidence of RNA microalgal viruses persisting in a CO2 remediation pilot project HRAP and uncovers the diversity of the RNA virosphere contained within it. Evidence shows that family Marnaviridae is cultured in the basin, alongside other potential microalgal infecting viruses (e.g., family Narnaviridae, family Totitiviridae, and family Yueviridae). Finally, we demonstrate that the RNA viral diversity of the HRAP is temporally dynamic across two successive culturing seasons.
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Wolf, Yuri I., Sukrit Silas, Yongjie Wang, Shuang Wu, Michael Bocek, Darius Kazlauskas, Mart Krupovic, Andrew Fire, Valerian V. Dolja, and Eugene V. Koonin. "Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome." Nature Microbiology 5, no. 10 (July 20, 2020): 1262–70. http://dx.doi.org/10.1038/s41564-020-0755-4.
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Abstract RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.
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Lang, Andrew S., Marli Vlok, Alexander I. Culley, Curtis A. Suttle, Yoshitake Takao, and Yuji Tomaru. "ICTV Virus Taxonomy Profile: Marnaviridae 2021." Journal of General Virology 102, no. 8 (August 6, 2021). http://dx.doi.org/10.1099/jgv.0.001633.
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The family Marnaviridae comprises small non-enveloped viruses with positive-sense RNA genomes of 8.6–9.6 kb. Isolates infect marine single-celled eukaryotes (protists) that come from diverse lineages. Some members are known from metagenomic studies of ocean virioplankton, with additional unclassified viruses described from metagenomic datasets derived from marine and freshwater environments. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Marnaviridae, which is available at ictv.global/report/marnaviridae.
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Vlok, Marli, Andrew S. Lang, and Curtis A. Suttle. "Application of a sequence-based taxonomic classification method to uncultured and unclassified marine single-stranded RNA viruses in the order Picornavirales." Virus Evolution 5, no. 2 (July 1, 2019). http://dx.doi.org/10.1093/ve/vez056.
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Abstract Metagenomics has altered our understanding of microbial diversity and ecology. This includes its applications to viruses in marine environments that have demonstrated their enormous diversity. Within these are RNA viruses, many of which share genetic features with members of the order Picornavirales; yet, very few of these have been taxonomically classified. The only recognized family of marine RNA viruses is the Marnaviridae, which was founded based on discovery and characterization of the species Heterosigma akashiwo RNA virus. Two additional genera of marine RNA viruses, Labyrnavirus (one species) and Bacillarnavirus (three species), were subsequently defined within the order Picornavirales but not assigned to a family. We have defined a sequence-based framework for taxonomic classification of twenty marine RNA viruses into the family Marnaviridae. Using RNA-dependent RNA polymerase (RdRp) phylogeny and distance-based analyses, we assigned the genera Labyrnavirus and Bacillarnavirus to the family Marnaviridae and created four additional genera in the family: Locarnavirus (four species), Kusarnavirus (one species), Salisharnavirus (four species) and Sogarnavirus (six species). We used pairwise capsid protein comparisons to delineate species within families, with 75 per cent identity as the species demarcation threshold. The family displays high sequence diversities and Jukes–Cantor distances for both the RdRp and capsid genes, suggesting that the classified viruses are not representative of all of the virus diversity within the family and that there are many more extant taxa. Our proposed taxonomic framework provides a sound classification system for this group of viruses that will have broadly applicable principles for other viral groups. It is based on sequence data alone and provides a robust taxonomic framework to include viruses discovered via metagenomic studies, thereby greatly expanding the realm of viruses subject to taxonomic classification.
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Xu, Ailan, Shan Xu, Qihang Tu, Huanao Qiao, Wei Lin, Jing Li, Yugan He, et al. "A novel virus in the family Marnaviridae as a potential pathogen of Penaeus vannamei glass post-larvae disease." Virus Research, December 2022, 199026. http://dx.doi.org/10.1016/j.virusres.2022.199026.
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Charon, Justine, Shauna Murray, and Edward C. Holmes. "Revealing RNA virus diversity and evolution in unicellular algae transcriptomes." Virus Evolution 7, no. 2 (August 14, 2021). http://dx.doi.org/10.1093/ve/veab070.
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Abstract Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified thirty new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants, and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA (ds-RNA) Partitiviridae, as well as tentative evidence for one negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.
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Shen, Lixin, Ziqiang Zhang, Rui Wang, Shuang Wu, Yongjie Wang, and Songzhe Fu. "Metatranscriptomic data mining together with microfluidic card uncovered the potential pathogens and seasonal RNA viral ecology in a drinking water source." Journal of Applied Microbiology, December 21, 2023. http://dx.doi.org/10.1093/jambio/lxad310.
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Abstract Aims Despite metatranscriptomics becoming an emerging tool for pathogen surveillance, very little is known about the feasibility of this approach for understanding the fate of human-derived pathogens in drinking water sources. Methods and results We conducted multiplexed microfluidic cards and metatranscriptomic sequencing of the drinking water source in a border city of North Korea in four seasons. Microfluidic card detected norovirus, hepatitis B virus (HBV), enterovirus and Vibrio cholerae in the water. Phylogenetic analyses showed that environmental-derived sequences from norovirus GII.17, genotype C of HBV and coxsackievirus A6 (CA6) were genetically related to the local clinical isolates. Meanwhile, metatranscriptomic assembly suggested that several bacterial pathogens including Acinetobacter johnsonii, and V. cholerae might be prevalent in the studied region. Metatranscriptomic analysis recovered 349 species-level groups with substantial viral diversity without detection of norovirus, HBV and CA6. Seasonally distinct virus communities were also found. Specifically, 126, 73, 126 and 457 types of viruses were identified in spring, summer, autumn and winter, respectively. The viromes were dominated by Pisuviricota phylum including members from Marnaviridae, Dicistroviridae, Luteoviridae, Potyviridae, Picornaviridae, Astroviridae and Picobirnaviridae families. Further phylogenetic analyses of RNA-dependent RNA polymerase (RdRp) sequences showed a diverse set of picorna-like viruses associated with shellfish, of which several novel picorna-like viruses were also identified. Additionally, potential animal pathogens including infectious bronchitis virus, Bat dicibavirus, Bat nodavirus, Bat picornavirus 2, infectious bursal disease virus, and Macrobrachium rosenbergii nodavirus were also identified. Conclusions Our data illustrate the divergence between microfluidic cards and metatranscriptomics, highlighting that the combination of both methods facilitates the source tracking of human viruses in challenging settings without sufficient clinical surveillance.
Dissertations / Theses on the topic "Marnaviridae"
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Chase, Emily. "PHYCOVIR : diversity and dynamics of viruses in a high-density microalgae culture." Electronic Thesis or Diss., Aix-Marseille, 2021. http://www.theses.fr/2021AIXM0554.
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Ce travail de thèse a été consacrée à l'étude d'un bassin de culture de microalgues (HRAP) avec l'objectif d'examiner les épisodes de mortalité massive, dont la cause est inconnue. Nous avons testé l'hypothèse que des virus de microalgues pourraient être responsables. Cette étude représente la première tentative d'exploration de la diversité virale dans un HRAP, en même temps que la collecte de données des hôtes potentiels grâce au métabarcodage 18S. L’analyse bioinformatique de métagénomes a permis d’identifier des virus présents dans le HRAP, et la dynamique de leurs populations a été suivie par (RT)-qPCR sur une série d'échantillons d'eau prélevés sur deux ans de culture. Ces virus appartiennent à la famille Marnaviridae (Ordre des Picornavirales ; virus à ARN), les Nucleocytoviricota de la famille Phycodnaviridae et de la famille Mimiviridae, un membre de la famille Lavidaviridae (virophage), et les « polinton-like viruses » (PLVs), tous ayant des associations connues avec les microalgues. Le dernier chapitre de la thèse décrit une étude bioinfomatique des séquences génomiques d’algues vertes unicellulaires du genre Tetraselmis qui a permis d’identifier et de caractériser des formes virales intégrées (i.e., ADN viral inséré dans les chromosomes de l’algue) apparentées au virus Tsv-N1, aux PLVs mis en évidence dans le HRAP, ainsi qu’au virus géant TetV-1. Cette analyse étend nos connaissances sur la diversité des virus des Tetraselmis et la complexité des interactions biologiques et évolutives entre ces partenairesThis thesis is devoted to the study of an industrial scale microalgae culturing system, called a high rate algal pond (HRAP), situated in Palavas-les-Flots, France. The objective of the study was to investigate culture crashes (i.e. microalgae die-offs) occurring in the HRAP, of which the source is unknown. We hypothesized that microalgal viruses were contained within the culture, and could potentially cause or contribute to the microalgae die-offs. We assessed the viral diversity by sequencing both RNA and DNA viromes. Using in silico analyses, putative viruses were identified in the HRAP, and tracked over a series of water samples taken over two years of culturing by (RT)-qPCR methods. A number of putative viruses of microalgae were uncovered. These include key players such as family Marnaviridae, families Phycodnaviridae and Mimiviridae (so-called “giant viruses”), a member of family Lavidaviridae (i.e. a virophage), and polinton-like viruses (PLVs), all with known associations to microalgae. An in-depth exploration of these key players was conducted, and host inferences were made using 18S metabarcoding, coupled with dynamics data from our (RT)-qPCR approach. The results are a comprehensive look at HRAP viruses. Finally, the thesis describes a bioinformatic study of the genomic sequences of unicellular green algae of the genus Tetraselmis to identify and characterize integrated viral forms related to the Tsv-N1 virus, to the PLVs identified in the HRAP, and to the giant TetV-1 virus. This analysis extends our knowledge on the diversity of Tetraselmis viruses
Book chapters on the topic "Marnaviridae"
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"Marnaviridae." In Virus Taxonomy, 850–54. Elsevier, 2012. http://dx.doi.org/10.1016/b978-0-12-384684-6.00073-2.
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Vlok, Marli, Curtis A. Suttle, and Andrew S. Lang. "Family Marnaviridae." In Reference Module in Life Sciences. Elsevier, 2020. http://dx.doi.org/10.1016/b978-0-12-809633-8.21323-x.
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