To see the other types of publications on this topic, follow the link: Orthornavirae.
Journal articles on the topic 'Orthornavirae'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 22 journal articles for your research on the topic 'Orthornavirae.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Calisher, Charles H., and Mattia Calzolari. "Taxonomy of Phleboviruses, Emphasizing Those That Are Sandfly-Borne." Viruses 13, no. 5 (2021): 918. http://dx.doi.org/10.3390/v13050918.
Full textAbstract:
Sandfly-borne phleboviruses (phylum Negarnavaricota, realm Riboviria, kingdom Orthornavirae, genus Phlebovirus) comprise three genome segments of ribonucleic acid (RNA) and which encode an RNA-dependent RNA polymerase, which they use to transcribe the viral RNA genome into messenger RNA and to replicate the genome. At least some of these viruses cause mild 3-day fevers in humans but some also have been associated with more severe illnesses in humans. The 67 recognized phleboviruses are listed here in a table composed by the authors from International Committee on Taxonomy of Viruses reports as well as the scientific literature.
2
Kuhn, Jens H., Scott Adkins, Daniela Alioto, et al. "2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales." Archives of Virology 165, no. 12 (2020): 3023–72. http://dx.doi.org/10.1007/s00705-020-04731-2.
Full text
3
Fuji, Shin-ichi, Tomofumi Mochizuki, Mitsuru Okuda, et al. "Plant viruses and viroids in Japan." Journal of General Plant Pathology 88, no. 2 (2022): 105–27. http://dx.doi.org/10.1007/s10327-022-01051-y.
Full textAbstract:
AbstractAn increasing number of plant viruses and viroids have been reported from all over the world due largely to metavirogenomics approaches with technological innovation. Herein, the official changes of virus taxonomy, including the establishment of megataxonomy and amendments of the codes of virus classification and nomenclature, recently made by the International Committee on Taxonomy of Viruses were summarized. The continued efforts of the plant virology community of Japan to index all plant viruses and viroids occurring in Japan, which represent 407 viruses, including 303 virus species and 104 unclassified viruses, and 25 viroids, including 20 species and 5 unclassified viroids, as of October 2021, were also introduced. These viruses and viroids are collectively classified into 81 genera within 26 families of 3 kingdoms (Shotokuvirae, Orthornavirae, Pararnavirae) across 2 realms (Monodnaviria and Riboviria). This review also overviewed how Japan’s plant virus/viroid studies have contributed to advance virus/viroid taxonomy.
4
Rosario, Karyna, Noémi Van Bogaert, Natalia B. López-Figueroa, Haris Paliogiannis, Mason Kerr, and Mya Breitbart. "Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom Orthornavirae." PeerJ 10 (August 16, 2022): e13875. http://dx.doi.org/10.7717/peerj.13875.
Full textAbstract:
Research on aquatic plant viruses is lagging behind that of their terrestrial counterparts. To address this knowledge gap, here we identified viruses associated with freshwater macrophytes, a taxonomically diverse group of aquatic phototrophs that are visible with the naked eye. We surveyed pooled macrophyte samples collected at four spring sites in Florida, USA through next generation sequencing of RNA extracted from purified viral particles. Sequencing efforts resulted in the detection of 156 freshwater macrophyte associated (FMA) viral contigs, 37 of which approximate complete genomes or segments. FMA viral contigs represent putative members from all five major phyla of the RNA viral kingdom Orthornavirae. Similar to viral types found in land plants, viral sequences identified in macrophytes were dominated by positive-sense RNA viruses. Over half of the FMA viral contigs were most similar to viruses reported from diverse hosts in aquatic environments, including phototrophs, invertebrates, and fungi. The detection of FMA viruses from orders dominated by plant viruses, namely Patatavirales and Tymovirales, indicate that members of these orders may thrive in aquatic hosts. PCR assays confirmed the presence of putative FMA plant viruses in asymptomatic vascular plants, indicating that viruses with persistent lifestyles are widespread in macrophytes. The detection of potato virus Y and oat blue dwarf virus in submerged macrophytes suggests that terrestrial plant viruses infect underwater plants and highlights a potential terrestrial-freshwater plant virus continuum. Defining the virome of unexplored macrophytes will improve our understanding of virus evolution in terrestrial and aquatic primary producers and reveal the potential ecological impacts of viral infection in macrophytes.
5
Kuhn, Jens H., Scott Adkins, Bernard R. Agwanda, et al. "Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales." Archives of Virology 166, no. 12 (2021): 3567–79. http://dx.doi.org/10.1007/s00705-021-05266-w.
Full text
6
Kuhn, Jens H., Junya Abe, Scott Adkins, et al. "Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)." Journal of General Virology 104, no. 8 (2023): 001864. https://doi.org/10.5281/zenodo.13531936.
Full textAbstract:
(Uploaded by Plazi for the Bat Literature Project) In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
7
Kuhn, Jens H., Junya Abe, Scott Adkins, et al. "Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)." Journal of General Virology 104, no. 8 (2023): 001864. https://doi.org/10.5281/zenodo.13531936.
Full textAbstract:
(Uploaded by Plazi for the Bat Literature Project) In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
8
Glotov, Alexander G., Anton G. Yuzhakov, Tatyana I. Glotova, et al. "Occurrence in sick animals and genetic heterogeneity of Siberian isolates of bovine respiratory syncytial virus (Pneumoviridae: <i>Orthopneumovirus</i>; BRSV) identified in the territories of the Ural, Siberian Federal District and the Republic of Kazakhstan." Problems of Virology 69, no. 1 (2024): 76–87. http://dx.doi.org/10.36233/0507-4088-216.
Full textAbstract:
Introduction. Bovine respiratory syncytial virus (Pneumoviridae: Orthornavirae, Orthopneumovirus; Bovine orthopneumovirus, Bovine respiratory syncytial virus, BRSV) is one of causative agents of respiratory diseases in animals. The study of the occurrence and genetic diversity of this pathogen is of particular importance.
 Objective. To study the frequency of virus in animals using RT-PCR and genetic heterogeneity of isolates based on determining the complete nucleotide sequence of glycoprotein G gene.
 Materials and methods. A 381-bp region of glycoprotein F gene was used for identification of virus genome, while complete nucleotide sequences of G gene were used for phylogenetic analysis. Phylogenetic trees were constructed using the maximum likelihood method in MEGA 7.0 software.
 Results. During outbreaks of respiratory diseases, BRSV RNA was detected in animals of all ages in samples of lungs, nasal secretions, pulmonary lymph nodes. Complete nucleotide sequences of glycoprotein G gene, 771 bp in length were obtained for five isolates and 789 bp in length ‒ for two isolates. Nucleotide similarity between them was 87–100%. Phylogenetic analysis assigned the isolates to subgroups II and III, each of which included two isolates. A separate clade formed by K18 isolate from animals imported from Canada and sequences from vaccines containing the attenuated «375» strain.
 Conclusion. The virus genome was identified in cows and heifers (20.0 and 14.3%), in calves up 1 month of age (3.05%), and in calves from 1 to 6 months of age (6.7%). Complete G gene nucleotide sequence analysis is a useful tool for studying the molecular epidemiology of BRSV on particular territories.
9
Kalinina, O. S. "Modern taxonomy of viruses of vertebrates." Scientific Messenger of LNU of Veterinary Medicine and Biotechnologies 22, no. 98 (2020): 113–18. http://dx.doi.org/10.32718/nvlvet9820.
Full textAbstract:
The modern taxonomy of viruses of vertebrates is presented according to the information of ICTV issue 07.2019, ratification 03.2020. The leading criteria of taxonomy of viruses are named: type and structure of viral genome, mechanism of replication and morphology of virion. The periods of formation of taxonomic ranks of viruses are characterized: in 1966–1970 genera of viruses were formed, in 1971–1975 – families and subfamilies, since 1990 – orders, in 2018–2019 – realms, kingdoms, phylums, subphylums, classes, suborders, subgenеres. The nomenclature of viruses is described. Viruses belong to the Viruses domain. Viruses of vertebrates (1878 species) belong to 4 realms, 5 kingdoms, 10 phylums, 2 subphylums, 20 classes, 26 orders, 3 suborders, 45 families (of which 15 – DNA-genomic and 30 – RNA-genomic), 33 subfamilies, 345 genera and 49 subgenera. Taxonomic ranks of DNA- and RNA-genomic viruses of vertebrates are described. The DNA-genome family Anelloviridae and the unclassified RNA-genomic genus Deltavirus are not included in any realm. The family Birnaviridae is not classified within the kingdom Orthornavirae. The family of DNA-genomic Hepadnaviridae is included in the realm of RNA-containing viruses Riboviria on the grounds that the replication of hepadnaviruses occurs through the stage of RNA on the principle of reverse transcription, as in the family Retroviridae. The main taxonomic features of DNA- and RNA-genomic viruses of vertebrates are described: type and structure of viral genome (DNA or RNA, number of strands, conformation, fragmentation, polarity), shape and size of virions, presence of outer lipoprotein shell, type of capsid symmetry (spiral, iсosahedral). Some families, in addition to viruses of vertebrates, contain viruses of invertebrates and plants, in particular: families Poxviridae, Iridoviridae, Parvoviridae, Circoviridae, Smacoviridae, Genomoviridae, Rhabdoviridae, Nyamiviridae, Peribunyaviridae, Phenuiviridae, Nairoviviridae, Nodaviridae, Reoviridae and Birnaviridae – viruses of insects; families Genomoviridae, Rhabdoviridae, Phenuiviridae and Reoviridae – viruses of plants; family Nyamiviridae – viruses of nematodes, cestodes, sipunculidеs and echinoderms; family Rhabdoviridae – viruses of nematodes; family Reoviridae – Eriocheir sinensis reovirus; family Birnaviridae – viruses of tellines and rotifers.
10
Kalinina, O. S., and I. K. Avdosieva. "Coronaviruses: modern taxonomy and research chronology." Scientific Messenger of LNU of Veterinary Medicine and Biotechnologies 24, no. 107 (2022): 49–57. http://dx.doi.org/10.32718/nvlvet10709.
Full textAbstract:
The classification of coronaviruses began in 1968 when five viruses (IBV, MHV, B814, 229E, and OC43) were united into an independent group, “coronaviruses”, based on the characteristic morphology of the virions. In 1971, the genus Coronavirus was formed, and in 1975, the family Coronaviridae, which in 1996 was included in the order Nidovirales. In 2009, the Coronaviridae family was divided into subfamilies. In 2018, new taxa of viruses were created – region, suborder, and subgenus, and in 2019 – kingdom, type, and class. According to the International Committee on Taxonomy of Viruses, issue No. 37 of 07.2021 (ratification of 03.2022), the family Coronaviridae belongs to the region Riboviria, kingdom Orthornavirae, phylum Pisuviricota, class Pisoniviricetes, order Nidovirales, suborder Cornidovirineae. The Coronaviridae family includes 54 viruses, which are grouped into three subfamilies (Letovirinae, Orthocoronavirinae, Pitovirinae), six genera (Alphaletovirus, Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus, Alphapironavirus) and 28 subgenera. Representatives of the most numerous subfamily Orthocoronavirinae infect various species of mammals and birds, causing various pathologies: respiratory and intestinal infections, polyserositis, myocarditis, hepatitis, nephritis, neuroinfections, immunopathology. In particular, viruses that cause infectious bronchitis in chickens, transmissible gastroenteritis in pigs, epidemic diarrhea in pigs, encephalomyelitis in pigs, coronavirus infection in cattle, and epizootic catarrhal gastroenteritis in minks are relevant for veterinary practice. The natural reservoirs of coronaviruses from the genera Alphacoronavirus and Betacoronavirus are bats and birds from the genera Gammacoronavirus and Deltacoronavirus. Particularly dangerous human coronaviruses are SARS-CoV, MERS-CoV and SARS-CoV-2, which cause emergent infections. The circulation of SARS-CoV, MERS-CoV, and SARS-CoV-2 among animals is shown. The natural reservoir of these viruses is bats, and the intermediate hosts for SARS-CoV are Himalayan civets, one-humped camels for MERS-CoV, and pangolins for SARS-CoV-2. The circulation of SARS-CoV-2 among different species of domestic and wild animals leads to the accumulation of mutations, which causes the adaptation of the virus to new hosts and ecological niches and its subsequent introduction into the human population.
11
White, William T., Shannon Corrigan, Lei Yang, et al. "Phylogeny of the manta and devilrays (Chondrichthyes: obulidae), with an updated taxonomic arrangement for the family." Zoological Journal of the Linnean Society 182, no. 1 (2018): 50–75. https://doi.org/10.1093/zoolinnean/zlx018.
Full textAbstract:
White, William T, Corrigan, Shannon, Yang, Lei, Henderson, Aaron C, Bazinet, Adam L, Swofford, David L, Naylor, Gavin J P (2018): Phylogeny of the manta and devilrays (Chondrichthyes: obulidae), with an updated taxonomic arrangement for the family. Zoological Journal of the Linnean Society 182 (1): 50-75, DOI: 10.1093/zoolinnean/zlx018, URL: http://academic.oup.com/zoolinnean/article/182/1/50/3886052
12
Cheng, Dong-Qiang, Sandra Kolundžija, and Federico M. Lauro. "Global phylogenetic analysis of the RNA-dependent RNA polymerase with OrViT (OrthornaVirae Tree)." Frontiers in Virology 2 (September 5, 2022). http://dx.doi.org/10.3389/fviro.2022.981177.
Full textAbstract:
Viruses of the kingdom Orthornavirae are the causative agents of many diseases in humans, animals and plants and play an important role in the ecology of the biosphere. Novel orthornaviral viral sequences are constantly being discovered from environmental datasets, but generating high-quality and comprehensive phylogenetic trees of Orthornavirae to resolve their taxonomic and phylogenetic relationships is still a challenge. To assist microbial ecologists and virologists with this task, we developed OrViT (OrthornaVirae Tree), a pipeline that integrates and updates published methods and bridges various public software to generate a global phylogenetic tree of the RNA-dependent RNA polymerase (RdRp) encoded by all orthornaviral genomes. The pipeline can infer the phylogenetic relationships between RdRp sequences extracted from the RefSeq viral database and the users’ own assembled contigs or protein datasets. The results from OrViT can be used for the taxonomic identification of novel viruses and suggest revisions of the existing phylogeny of RNA viruses. OrViT includes several Perl and Bash scripts assembled into a Makefile, making it portable between different Linux-based operating systems and easy to use. OrViT is freely available from https://github.com/chengdongqiang/OrViT.
13
Mutz, Pascal, Antonio Pedro Camargo, Harutyun Sahakyan, et al. "The protein structurome of Orthornavirae and its dark matter." mBio, December 23, 2024. https://doi.org/10.1128/mbio.03200-24.
Full textAbstract:
ABSTRACT Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in the realm Riboviria. Thorough protein annotation and comparison are essential to get insights into the functions of viral proteins and virus evolution. In addition to sequence- and hmm profile‑based methods, protein structure comparison adds a powerful tool to uncover protein functions and relationships. We constructed an Orthornavirae “structurome” consisting of already annotated as well as unannotated (“dark matter”) proteins and domains encoded in viral genomes. We used protein structure modeling and similarity searches to illuminate the remaining dark matter in hundreds of thousands of orthornavirus genomes. The vast majority of the dark matter domains showed either “generic” folds, such as single α-helices, or no high confidence structure predictions. Nevertheless, a variety of lineage-specific globular domains that were new either to orthornaviruses in general or to particular virus families were identified within the proteomic dark matter of orthornaviruses, including several predicted nucleic acid-binding domains and nucleases. In addition, we identified a case of exaptation of a cellular nucleoside monophosphate kinase as an RNA-binding protein in several virus families. Notwithstanding the continuing discovery of numerous orthornaviruses, it appears that all the protein domains conserved in large groups of viruses have already been identified. The rest of the viral proteome seems to be dominated by poorly structured domains including intrinsically disordered ones that likely mediate specific virus-host interactions. IMPORTANCE Advanced methods for protein structure prediction, such as AlphaFold2, greatly expand our capability to identify protein domains and infer their likely functions and evolutionary relationships. This is particularly pertinent for proteins encoded by viruses that are known to evolve rapidly and as a result often cannot be adequately characterized by analysis of the protein sequences. We performed an exhaustive structure prediction and comparative analysis for uncharacterized proteins and domains (“dark matter”) encoded by viruses with RNA genomes. The results show the dark matter of RNA virus proteome consists mostly of disordered and all-α-helical domains that cannot be readily assigned a specific function and that likely mediate various interactions between viral proteins and between viral and host proteins. The great majority of globular proteins and domains of RNA viruses are already known although we identified several unexpected domains represented in individual viral families.
14
Coy, Samantha R., Budi Utama, James W. Spurlin, et al. "Visualization of RNA virus infection in a marine protist with a universal biomarker." Scientific Reports 13, no. 1 (2023). http://dx.doi.org/10.1038/s41598-023-31507-w.
Full textAbstract:
AbstractHalf of the marine virosphere is hypothesized to be RNA viruses (kingdom Orthornavirae) that infect abundant micro-eukaryotic hosts (e.g. protists). To test this, quantitative approaches that broadly track infections in situ are needed. Here, we describe a technique—dsRNA-Immunofluorescence (dsRIF)—that uses a double-stranded RNA (dsRNA) targeting monoclonal antibody to assess host infection status based on the presence of dsRNA, a replicative intermediate of all Orthornavirae infections. We show that the dinoflagellate Heterocapsa circularisquama produces dsRIF signal ~ 1000 times above background autofluorescence when infected by the + ssRNA virus HcRNAV. dsRNA-positive virocells were detected across > 50% of the 48-h infection cycle and accumulated to represent at least 63% of the population. Photosynthetic and chromosomal integrity remained intact during peak replication, indicating HcRNAV infection does not interrupt these processes. This work validates the use of dsRIF on marine RNA viruses and their hosts, setting the stage for quantitative environmental applications that will accelerate understanding of virus-driven ecosystem impacts.
15
Kuhn, Jens H., Scott Adkins, Bernard R. Agwanda, et al. "2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales." Archives of Virology, August 31, 2021. http://dx.doi.org/10.1007/s00705-021-05143-6.
Full text
16
Kuhn, Jens H., Scott Adkins, Sergey V. Alkhovsky, et al. "2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales." Archives of Virology, November 28, 2022. http://dx.doi.org/10.1007/s00705-022-05546-z.
Full text
17
Nino Barreat, Jose Gabriel, and Aris Katzourakis. "Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes." Nature Microbiology, October 22, 2024. http://dx.doi.org/10.1038/s41564-024-01825-4.
Full textAbstract:
AbstractIntegration of viruses into host genomes can give rise to endogenous viral elements (EVEs), which provide insights into viral diversity, host range and evolution. A systematic search for EVEs is becoming computationally challenging given the available genomic data. We used a cloud-computing approach to perform a comprehensive search for EVEs in the kingdoms Shotokuvirae and Orthornavirae across vertebrates. We identified 2,040 EVEs in 295 vertebrate genomes and provide evidence for EVEs belonging to the families Chuviridae, Paramyxoviridae, Nairoviridae and Benyviridae. We also find an EVE from the Hepacivirus genus of flaviviruses with orthology across murine rodents. In addition, our analyses revealed that reptarenaviruses and filoviruses probably acquired their glycoprotein ectodomains three times independently from retroviral elements. Taken together, these findings encourage the addition of 4 virus families and the Hepacivirus genus to the growing virus fossil record of vertebrates, providing key insights into their natural history and evolution.
18
Kuhn, Jens H., Leticia Botella, Marcos de la Peña, et al. "Ambiviricota , a novel ribovirian phylum for viruses with viroid-like properties." Journal of Virology, June 10, 2024. http://dx.doi.org/10.1128/jvi.00831-24.
Full textAbstract:
ABSTRACT Fungi harbor a vast diversity of mobile genetic elements (MGEs). Recently, novel fungal MGEs, tentatively referred to as ‘ambiviruses,’ were described. ‘Ambiviruses’ have single-stranded RNA genomes of about 4–5 kb in length that contain at least two open reading frames (ORFs) in non-overlapping ambisense orientation. Both ORFs are conserved among all currently known ‘ambiviruses,’ and one of them encodes a distinct viral RNA-directed RNA polymerase (RdRP), the hallmark gene of ribovirian kingdom Orthornavirae . However, ‘ambivirus’ genomes are circular and predicted to replicate via a rolling-circle mechanism. Their genomes are also predicted to form rod-like structures and contain ribozymes in various combinations in both sense and antisense orientations—features reminiscent of viroids, virusoids, ribozyvirian kolmiovirids, and yet-unclassified MGEs (such as ‘epsilonviruses,’ ‘zetaviruses,’ and some ‘obelisks’). As a first step toward the formal classification of ‘ambiviruses,’ the International Committee on Taxonomy of Viruses (ICTV) recently approved the establishment of a novel ribovirian phylum, Ambiviricota , to accommodate an initial set of 20 members with well-annotated genome sequences.
19
Kuhn, Jens H., Junya Abe, Scott Adkins, et al. "Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)." Journal of General Virology 104, no. 8 (2023). http://dx.doi.org/10.1099/jgv.0.001864.
Full textAbstract:
In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
20
Wu, Lilin, Yongqin Liu, Wenqing Shi, et al. "Uncovering the hidden RNA virus diversity in Lake Nam Co: Evolutionary insights from an extreme high-altitude environment." Proceedings of the National Academy of Sciences 122, no. 6 (2025). https://doi.org/10.1073/pnas.2420162122.
Full textAbstract:
Alpine lakes, characterized by isolation, low temperatures, oligotrophic conditions, and intense ultraviolet radiation, remain a poorly explored ecosystem for RNA viruses. Here, we present the first comprehensive metatranscriptomic study of RNA viruses in Lake Nam Co, a high-altitude alkaline saline lake on the Tibetan Plateau. Using a combination of sequence- and structure-based homology searches, we identified 742 RNA virus species, including 383 novel genus-level groups and 84 novel family-level groups exclusively found in Lake Nam Co. These findings significantly expand the known diversity of the Orthornavirae , uncovering evolutionary adaptations such as permutated RNA-dependent RNA polymerase motifs and distinct RNA secondary structures. Notably, 14 additional RNA virus families potentially infecting prokaryotes were predicted, broadening the known host range of RNA viruses and questioning the traditional assumption that RNA viruses predominantly target eukaryotes. The presence of auxiliary metabolic genes in viral genomes suggested that RNA viruses (families f . 0102 and Nam-Co_family_51) exploit host energy production mechanisms in energy-limited alpine lakes. Low nucleotide diversity, single nucleotide polymorphism frequencies, and pN/pS ratios indicate strong purifying selection in Nam Co viral populations. Our findings offer insights into RNA virus evolution and ecology, highlighting the importance of extreme environments in uncovering hidden viral diversity and further shed light into their potential ecological implications, particularly in the context of climate change.
21
Kondo, Hideki, Leticia Botella, and Nobuhiro Suzuki. "Mycovirus Diversity and Evolution Revealed/Inferred from Recent Studies." Annual Review of Phytopathology 60, no. 1 (2022). http://dx.doi.org/10.1146/annurev-phyto-021621-122122.
Full textAbstract:
High-throughput virome analyses with various fungi, from cultured or uncultured sources, have led to the discovery of diverse viruses with unique genome structures and even neo-lifestyles. Examples in the former category include splipalmiviruses and ambiviruses. Splipalmiviruses, related to yeast narnaviruses, have multiple positive-sense (+) single-stranded (ss) RNA genomic segments that separately encode the RNA-dependent RNA polymerase motifs, the hallmark of RNA viruses (members of the kingdom Orthornavirae ). Ambiviruses appear to have an undivided ssRNA genome of 3∼5 kb with two large open reading frames (ORFs) separated by intergenic regions. Another narna-like virus group has two fully overlapping ORFs on both strands of a genomic segment that span more than 90% of the genome size. New virus lifestyles exhibited by mycoviruses include the yado-kari/yado-nushi nature characterized by the partnership between the (+)ssRNA yadokarivirus and an unrelated dsRNA virus (donor of the capsid for the former) and the hadaka nature of capsidless 10–11 segmented (+)ssRNA accessible by RNase in infected mycelial homogenates. Furthermore, dsRNA polymycoviruses with phylogenetic affinity to (+)ssRNA animal caliciviruses have been shown to be infectious as dsRNA–protein complexes or deproteinized naked dsRNA. Many previous phylogenetic gaps have been filled by recently discovered fungal and other viruses, which have provided interesting evolutionary insights. Phylogenetic analyses and the discovery of natural and experimental cross-kingdom infections suggest that horizontal virus transfer may have occurred and continue to occur between fungi and other kingdoms. Expected final online publication date for the Annual Review of Phytopathology, Volume 60 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
22
Denison, Elizabeth R., Brittany N. Zepernick, R. Michael L. McKay, and Steven W. Wilhelm. "Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie." mSystems, June 28, 2024. http://dx.doi.org/10.1128/msystems.00753-24.
Full textAbstract:
ABSTRACT Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage ( Caudoviricetes ), giant viruses ( Nucleocytoviricota , or NCLDV), and RNA viruses ( Orthornavirae ). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent. IMPORTANCE As seasonal ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities might respond to changing ice conditions. Although it is widely recognized that viruses impact microbial community structure and function, there is little known regarding wintertime viral activity or the relationship between viral activity and ice cover extent. Our metatranscriptomic analyses indicated that viruses were transcriptionally active in the winter surface waters of Lake Erie. These findings also expanded the known diversity of viral lineages in the Great Lakes. Notably, viral community activity metrics were significantly different between the two sampled winters. The pronounced differences we observed in active viral communities between the ice-covered and ice-free samples merit further research regarding how viral communities will function in future, potentially ice-free, freshwater systems.