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Article
Microbiology
Eugene Koonin et al.
Summary: Viruses are the most abundant biological entities on earth and show great genetic diversity. The number of virus species is estimated to be astronomically large, ranging from 10^7 to 10^9. Virus origins involve non-viral replicators capturing cellular proteins to become virus capsid subunits. The number of realms in the global virome is expected to significantly increase with the discovery of new distinct groups.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Peter Simmonds et al.
Review
Biology
Peter T. S. van der Gulik et al.
Summary: Enormous progress has been made in understanding biological diversity in the last century, but it has not been fully integrated into a formal taxonomic system. The Linnaean system, although advantageous, has some challenges and limitations. This article proposes amendments to the system and discusses the shortcomings of the cladistic approach, suggesting a semi-cladistic system as a way forward.
BIOLOGICAL REVIEWS
(2023)
Article
Microbiology
Guillermo Dominguez-Huerta et al.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Virology
Francisco Murilo Zerbini et al.
Summary: Following the ICTV Ratification Vote in March 2021, a standard two-part binomial nomenclature is now the standard for naming virus species. The adoption of this new nomenclature is still in its early stages, making it timely to clarify the distinction between viruses and virus species and provide guidelines for their correct naming and writing.
ARCHIVES OF VIROLOGY
(2022)
Article
Multidisciplinary Sciences
Robert C. Edgar et al.
Summary: Public databases contain a vast amount of nucleic acid sequences, but efficient methods for systematic exploration of this library have been lacking. In this study, we developed a cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at the petabase scale. By searching millions of diverse samples, we identified over 10(5) novel RNA viruses and characterized their environmental reservoirs. To facilitate viral discovery, we established a comprehensive database of these data and tools. Expanding the known sequence diversity of viruses has important implications for understanding emerging pathogens and improving pathogen surveillance.
Article
Multidisciplinary Sciences
Mart Krupovic et al.
Summary: The double jelly-roll major capsid protein (DJR-MCP) is not a unique innovation of viruses, but has a common ancestry with a family of cellular proteins involved in carbohydrate metabolism. The findings suggest that bamfordviruses evolved from nonviral replicators by recruiting host proteins for capsid formation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Virology
Alexander E. Gorbalenya et al.
Summary: Genome sequencing plays a crucial role in virus taxonomy, allowing scientists to classify viruses systematically based on evolutionary knowledge. Researchers use various methods and metrics to cluster and classify viruses, while advancing computational tools is critical for improving virus classification and addressing research questions.
CURRENT OPINION IN VIROLOGY
(2022)
Article
Microbiology
Nicholas A. T. Irwin et al.
Summary: This study systematically characterized viral-eukaryotic gene exchange, identifying thousands of transfers and revealing their frequency, taxonomic distribution, and predicted functions. The findings highlight the impact of virus-host interactions on evolutionary changes, as well as common strategies employed by viruses to manipulate hosts, such as metabolic reprogramming, proteolytic degradation, and extracellular modification. Additionally, the study implicates genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases impacting a wide range of structures.
NATURE MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Maria Benko et al.
Summary: The family Adenoviridae consists of non-enveloped viruses with linear dsDNA genomes and medium-sized icosahedral capsids. Adenoviruses have been found in vertebrates from fish to humans. The family is divided into six genera, each of which is more prevalent in certain animal groups. The outcome of infection can range from subclinical to lethal disease.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Multidisciplinary Sciences
Ahmed A. Zayed et al.
Summary: This study expands Earth's RNA virus catalogs and their taxonomy, investigates their evolutionary origins and marine biogeography, and reveals the need for substantive revisions of taxonomy for RNA viruses. The efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
Article
Biotechnology & Applied Microbiology
Thomas S. Postler et al.
Summary: The International Committee on Taxonomy of Viruses has adopted a binomial naming format for virus species, which is comparable with other biological taxonomies. Latinization of these names is optional, but it provides the advantage of cultural neutrality and compatibility with other taxonomies.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Annette Mankertz et al.
JOURNAL OF GENERAL VIROLOGY
(2022)
Review
Microbiology
Eugene Koonin et al.
Summary: Viruses are parasites that rely on host cells, but they have their own genomes and independent evolutionary trajectories. Virus genes responsible for genome replication descended from primordial replicators, while most other genes were acquired from hosts. Host gene capture occurs through two main routes: recruitment of genes that benefit virus reproduction and repurposing of host proteins for unique virus functions. This leads to varying levels of similarity between virus and host homologs.
CELL HOST & MICROBE
(2022)
Article
Biochemistry & Molecular Biology
Chris Lauber et al.
Summary: Virus discovery has entered a new phase of data-driven approaches, primarily computational, that utilize publicly available data to study viruses without relying on sample collection and processing. This approach offers significant benefits to classical virology and molecular biology.
Article
Biochemistry & Molecular Biology
Uri Neri et al.
Summary: High-throughput RNA sequencing allows us to explore the diversity of RNA viruses on Earth. By analyzing diverse metatranscriptomes and RNA-dependent RNA polymerases, we discovered a 5-fold increase in the known diversity of RNA viruses, as well as new protein domains and virus-host interactions. Additionally, we identified two new bacteriophage phyla and potential new classes and orders.
Article
Virology
Jens H. Kuhn et al.
Summary: This article presents the updated taxonomy of Negarnaviricota, including the addition of new families, genera, and species, renaming and moving of species, and correction of misspelled names as accepted by the International Committee on Taxonomy of Viruses (ICTV).
ARCHIVES OF VIROLOGY
(2022)
Review
Microbiology
Hugh M. B. Harris et al.
Summary: Viruses are everywhere on Earth and play a significant role in evolution despite being excluded from the Tree of Life. Research has shown that viruses and cellular organisms engage in frequent horizontal gene transfer and mutual development, demonstrating their close ecological and evolutionary relationship.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Derek Gatherer et al.
Summary: Members of the family Herpesviridae have complex structures and adapt well to their hosts, establishing lifelong latent infections with limited gene expression. Severe diseases are usually observed in specific populations like foetuses, infants, immunocompromised individuals, or alternative hosts. This summary is based on the ICTV Report on Herpesviridae, available at ictv.global/report/herpesviridae.
JOURNAL OF GENERAL VIROLOGY
(2021)
Article
Virology
Heli A. M. Monttinen et al.
Summary: RNA viruses evolve rapidly, making traditional sequence-based phylogenetic methods less effective in reconstructing relationships among them. Protein structures evolve more slowly and can show similarity even when sequences do not. The structure-based phylogenetic tree of viral RdRps reflects their functional differentiation.
Article
Virology
Joanna C. A. Cobbin et al.
Summary: Meta-transcriptomic next-generation sequencing has revolutionized virus discovery by expanding our knowledge of the virosphere, but faces challenges such as errors and limitations in viral sequences in public databases, as well as the lack of bioinformatic tools to identify novel viruses accurately.
CURRENT OPINION IN VIROLOGY
(2021)
Article
Virology
Bas E. Dutilh et al.
Summary: The development of virus taxonomy relies on advances in metagenomic analysis and other technologies, which have brought a wealth of previously unknown virus sequence data and provided unprecedented insights into the vastness of the virosphere. Properly classifying viruses is crucial to understanding the diversity of viruses, and the inclusion of uncultivated viruses has already improved this process.
CURRENT OPINION IN VIROLOGY
(2021)
Article
Virology
Dann Turner et al.
Summary: Bacteriophage taxonomy has been undergoing significant changes in recent years, with the abolition of certain classification units and the establishment of guidelines for delineating species, genus, subfamily, and family-level ranks in tailed phage taxonomy.
Editorial Material
Virology
Mart Krupovic et al.
Summary: The ICTV has established a new virus realm, Adnaviria, which unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins. This realm is considered monophyletic and distinct from other known virus realms.
JOURNAL OF VIROLOGY
(2021)
Review
Microbiology
Eugene Koonin et al.
Summary: David Baltimore's classification of viruses based on genome expression routes has been fundamental in virology for the past fifty years, providing a conceptual framework for understanding virus diversity. Recent studies have focused on the global ecology and biology of viruses within the context of the Baltimore classes, with an exploration of potential extensions to the original scheme.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2021)
Article
Virology
Stuart G. Siddell et al.
ARCHIVES OF VIROLOGY
(2020)
Review
Microbiology
Eugene V. Koonin et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2020)
Article
Microbiology
Alexander E. Gorbalenya et al.
NATURE MICROBIOLOGY
(2020)
Article
Virology
Judit J. Penzes et al.
ARCHIVES OF VIROLOGY
(2020)
Review
Biochemistry & Molecular Biology
Arshan Nasir et al.
TRENDS IN MICROBIOLOGY
(2020)
Review
Mathematical & Computational Biology
Conrad L. Schoch et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2020)
Article
Evolutionary Biology
Charles H. Calisher et al.
SYSTEMATIC BIOLOGY
(2019)
Review
Biotechnology & Applied Microbiology
Peter Simmonds
JOURNAL OF GENERAL VIROLOGY
(2018)
Article
Microbiology
Pakorn Aiewsakun et al.
Review
Microbiology
Peter Simmonds et al.
NATURE REVIEWS MICROBIOLOGY
(2017)
Article
Virology
Evelien M. Adriaenssens et al.
Review
Infectious Diseases
Marcos Perez-Losada et al.
INFECTION GENETICS AND EVOLUTION
(2015)
Article
Virology
Yiming Bao et al.
ARCHIVES OF VIROLOGY
(2014)
Editorial Material
Microbiology
Andrew M. Kropinski et al.
ENVIRONMENTAL MICROBIOLOGY
(2009)
Article
Virology
AJ Gibbs et al.
ARCHIVES OF VIROLOGY
(2006)
