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Journal articles on the topic 'Nucleocytoviricota'

Author: Grafiati

Published: 25 May 2024

Last updated: 31 July 2025

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1

Aylward, Frank O., Mohammad Moniruzzaman, Anh D. Ha, and Eugene V. Koonin. "A phylogenomic framework for charting the diversity and evolution of giant viruses." PLOS Biology 19, no. 10 (2021): e3001430. http://dx.doi.org/10.1371/journal.pbio.3001430.

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Large DNA viruses of the phylum Nucleocytoviricota have recently emerged as important members of ecosystems around the globe that challenge traditional views of viral complexity. Numerous members of this phylum that cannot be classified within established families have recently been reported, and there is presently a strong need for a robust phylogenomic and taxonomic framework for these viruses. Here, we report a comprehensive phylogenomic analysis of the Nucleocytoviricota, present a set of giant virus orthologous groups (GVOGs) together with a benchmarked reference phylogeny, and delineate

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2

Gaïa, Morgan, and Patrick Forterre. "From Mimivirus to Mirusvirus: The Quest for Hidden Giants." Viruses 15, no. 8 (2023): 1758. http://dx.doi.org/10.3390/v15081758.

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Our perception of viruses has been drastically evolving since the inception of the field of virology over a century ago. In particular, the discovery of giant viruses from the Nucleocytoviricota phylum marked a pivotal moment. Their previously concealed diversity and abundance unearthed an unprecedented complexity in the virus world, a complexity that called for new definitions and concepts. These giant viruses underscore the intricate interactions that unfold over time between viruses and their hosts, and are themselves suspected to have played a significant role as a driving force in the evo

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3

de Souza, Fernanda Gil, Jônatas Santos Abrahão, and Rodrigo Araújo Lima Rodrigues. "Comparative Analysis of Transcriptional Regulation Patterns: Understanding the Gene Expression Profile in Nucleocytoviricota." Pathogens 10, no. 8 (2021): 935. http://dx.doi.org/10.3390/pathogens10080935.

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The nucleocytoplasmic large DNA viruses (NCLDV) possess unique characteristics that have drawn the attention of the scientific community, and they are now classified in the phylum Nucleocytoviricota. They are characterized by sharing many genes and have their own transcriptional apparatus, which provides certain independence from their host’s machinery. Thus, the presence of a robust transcriptional apparatus has raised much discussion about the evolutionary aspects of these viruses and their genomes. Understanding the transcriptional process in NCLDV would provide information regarding their

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4

Rodrigues, Rodrigo AL, Fernanda G. de Souza, Bruna L. de Azevedo, Lorena CF da Silva, and Jônatas S. Abrahão. "The morphogenesis of different giant viruses as additional evidence for a common origin of Nucleocytoviricota." Current Opinion in Virology 49 (August 2021): 102–10. http://dx.doi.org/10.1016/j.coviro.2021.05.004.

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5

Moreira, Thaís I. R., João Victor R. P. Carvalho, Clécio A. C. Filho, et al. "Investigations into the Diversity and Distribution of tRNA and Phylogenetics of Translation Factors in Amoebozoa-Infecting Nucleocytoviricota." Viruses 17, no. 3 (2025): 328. https://doi.org/10.3390/v17030328.

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Translation is a sine qua non process for life as we know it. Translation factors (TFs) and tRNAs are rare among viruses but are commonly found in giant viruses of the class Megaviricetes. In this study, we explored the diversity and distribution of tRNAs in giant viruses that were isolated and replicated in amoebae (phylum Amoebozoa), and investigated the evolutionary history of TFs to gain insights into their origins in these viruses. We analyzed the genomes of 77 isolated giant viruses, 52 of which contained at least 1 tRNA. In most of these viruses, tRNA sequences are dispersed throughout

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6

Ruiz Martínez, Eliana, Dean A. Mckeown, Declan C. Schroeder, et al. "Phaeoviruses Present in Cultured and Natural Kelp Species, Saccharina latissima and Laminaria hyperborea (Phaeophyceae, Laminariales), in Norway." Viruses 15, no. 12 (2023): 2331. http://dx.doi.org/10.3390/v15122331.

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Phaeoviruses (Phycodnaviridae) are large icosahedral viruses in the phylum Nucleocytoviricota with dsDNA genomes ranging from 160 to 560 kb, infecting multicellular brown algae (Phaeophyceae). The phaeoviral host range is broader than expected, not only infecting algae from the Ectocarpales but also from the Laminariales order. However, despite phaeoviral infections being reported globally, Norwegian kelp species have not been screened. A molecular analysis of cultured and wild samples of two economically important kelp species in Norway (Saccharina latissima and Laminaria hyperborea) revealed

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7

de Oliveira, Ellen Gonçalves, João Victor Rodrigues Pessoa Carvalho, Bruna Barbosa Botelho, et al. "Giant Viruses as a Source of Novel Enzymes for Biotechnological Application." Pathogens 11, no. 12 (2022): 1453. http://dx.doi.org/10.3390/pathogens11121453.

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The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especiall

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8

Claverie, Jean-Michel. "Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses." Viruses 12, no. 10 (2020): 1130. http://dx.doi.org/10.3390/v12101130.

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The extension of virology beyond its traditional medical, veterinary, or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on Earth. In particular, virus isolations from unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure, gene content, or mode of replication. Complemented by large-scale metagenomic analyses, these discoveries have rekindled interest in the enigma of the origin of viruses, for which

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9

Kukovetz, Kerri, Brigitte Hertel, Christopher R. Schvarcz, et al. "A Functional K+ Channel from Tetraselmis Virus 1, a Member of the Mimiviridae." Viruses 12, no. 10 (2020): 1107. http://dx.doi.org/10.3390/v12101107.

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Potassium ion (K+) channels have been observed in diverse viruses that infect eukaryotic marine and freshwater algae. However, experimental evidence for functional K+ channels among these alga-infecting viruses has thus far been restricted to members of the family Phycodnaviridae, which are large, double-stranded DNA viruses within the phylum Nucleocytoviricota. Recent sequencing projects revealed that alga-infecting members of Mimiviridae, another family within this phylum, may also contain genes encoding K+ channels. Here we examine the structural features and the functional properties of pu

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10

Kyndt, Elliot C., and John A. Kyndt. "Illumina Short-Read Sequencing of the Mitogenomes of Novel Scarites subterraneus Isolates Allows for Taxonomic Refinement of the Genus Scarites Fabricius 1775, within the Carabidae Family." Insects 13, no. 2 (2022): 190. http://dx.doi.org/10.3390/insects13020190.

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We sequenced the complete mitogenomes, 18S and 28S rRNA of two new Scarites isolates, collected in Eastern Nebraska and Northern Arkansas (US). Based on molecular sequence data comparison and morphological characteristics, the new isolates were identified as a subspecies of Scarites subterraneus Fabricius 1775, for which we propose the subspecies names ‘nebraskensis’ and ‘arkansensis’. The new 18S and 28S rRNA sequences were found to be 99% and 98% identical to Scarites subterraneus. There are no other Scarites 18S or 28S rRNA sequences in the Genbank database, however, phylogenetic analysis o

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11

Bernadus, Janno Berty Bradly, Jantje Pelealu, Grace Debbie Kandou, Arthur Gehart Pinaria, Juliet Merry Eva Mamahit, and Trina Ekawati Tallei. "Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia)." Infectious Disease Reports 15, no. 5 (2023): 549–63. http://dx.doi.org/10.3390/idr15050054.

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The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the micr

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12

Lisachov, Artem P., Lada S. Lisachova, and Evgeniy Simonov. "First record of ranavirus (Ranavirus sp.) in Siberia, Russia." Herpetozoa 35, no. () (2022): 33–37. https://doi.org/10.3897/herpetozoa.35.e79490.

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Ranaviruses are a group of double-strand DNA viruses that infect fish, amphibians and reptiles. These viruses are responsible for mass fish and amphibian mortality events worldwide, both in the wild and at fish and amphibian farms. The number of detected epizootics has grown significantly in recent years. In Eastern Europe and Northern Asia, including Russia, very few ranavirus monitoring studies have been conducted, in contrast with Western Europe and America. In the present work, we used a qPCR assay to survey for the first time the amphibian populations of West Siberia (Russia) for the pres

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13

Yutin, Natalya, Pascal Mutz, Mart Krupovic, and Eugene V. Koonin. "Mriyaviruses: small relatives of giant viruses." mBio, June 4, 2024. http://dx.doi.org/10.1128/mbio.01035-24.

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ABSTRACT The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35–45 kb that appear to be related to the Nucleocytoviricota . In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCPs) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of

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14

Armen, Kotsinyan, Sahakyan Harutyun, and Zakaryan Hovakim. "Identification of the Branching Order within the Kingdom Bamfordvirae." July 2, 2022. https://doi.org/10.5281/zenodo.6790805.

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The kingdom <em>Bamfordvirae</em> comprises the majority of the realm <em>Varidnaviria</em> and, according to the 2021 release of Virus Taxonomy by the International Committee on Taxonomy of Viruses, consists of the phyla <em>Nucleocytoviricota</em> and <em>Preplasmiviricota</em>. There are several fundamental unresolved issues related to the evolution of <em>Bamfordvirae</em>. These are questions concerning <em>Bamfordvirae</em> taxonomy including the branching order of <em>Nucleocytoviricota</em> and the question of the monophyly of <em>Preplasmiviricota</em>. Here, based on the analyses of

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Armen, Kotsinyan, Sahakyan Harutyun, and Zakaryan Hovakim. "Identification of the branching order within the kingdom Bamfordvirae." July 30, 2022. https://doi.org/10.5281/zenodo.6944305.

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The kingdom <em>Bamfordvirae</em> comprises the majority of the realm <em>Varidnaviria</em> and, according to the 2021 release of Virus Taxonomy by the International Committee on Taxonomy of Viruses, consists of the phyla <em>Nucleocytoviricota</em> and <em>Preplasmiviricota</em>. There are several fundamental unresolved issues related to the evolution of <em>Bamfordvirae</em>. These are questions concerning <em>Bamfordvirae</em> taxonomy including the branching order of <em>Nucleocytoviricota</em> and the question of the monophyly of <em>Preplasmiviricota</em>. Here, based on the analyses of

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16

Guglielmini, Julien, Morgan Gaia, Violette Da Cunha, Alexis Criscuolo, Mart Krupovic, and Patrick Forterre. "Viral origin of eukaryotic type IIA DNA topoisomerases." Virus Evolution, October 8, 2022. http://dx.doi.org/10.1093/ve/veac097.

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Abstract Type II DNA topoisomerases of the family A (Topo IIA) are present in all bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologues and have no orthologues in Archaea. Interestingly, eukaryotic Topo IIA have close homologues in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasm

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17

Armen, Kotsinyan, Sahakyan Harutyun, and Zakaryan Hovakim. "Identification of branching order within the kingdom Bamfordvirae." May 25, 2022. https://doi.org/10.5281/zenodo.6579602.

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All Figures, Table 1, and Supplementary materials of the "Identification of branching order within the kingdom <em>Bamfordvirae</em>" manuscript are presented․ Supplementary materials consist of S. Figures, S. Tables, S Alignments (.fas), S. .nwk, S. .treefile, as well as ReadMe.txt files. <strong>Abstract</strong> The kingdom <em>Bamfordvirae</em> comprises the majority of the realm <em>Varidnaviria</em> and, according to the 2021 release of Virus Taxonomy by the International Committee on Taxonomy of Viruses, consists of the phyla <em>Nucleocytoviricota</em> and <em>Preplasmiv

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18

Witt, Amanda Stéphanie Arantes, João Victor Rodrigues Pessoa Carvalho, Mateus Sá Magalhães Serafim, Nidia Esther Colquehuanca Arias, Rodrigo Araújo Lima Rodrigues, and Jônatas Santos Abrahão. "The GC% landscape of the Nucleocytoviricota." Brazilian Journal of Microbiology, August 24, 2024. http://dx.doi.org/10.1007/s42770-024-01496-7.

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19

Krupovic, Mart, Natalya Yutin, and Eugene Koonin. "Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase." Virus Evolution 6, no. 2 (2020). http://dx.doi.org/10.1093/ve/veaa059.

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Abstract The diverse viruses in the phylum Nucleocytoviricota (also known as NLCDVs, Nucleo-cytoplasmic Large DNA Viruses) typically possess large icosahedral virions. However, in several families of Nucleocytoviricota, the icosahedral capsid was replaced by irregular particle shapes, most notably, the amphora-like virions of pandoraviruses and pithoviruses, the largest known virus particles in the entire virosphere. Pandoraviruses appear to be the most highly derived viruses in this phylum because their evolution involved not only the change in the virion shape, but also, the actual loss of t

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20

Truchon, Alexander R., Emily E. Chase, Eric R. Gann, et al. "Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research." Frontiers in Microbiology 14 (November 30, 2023). http://dx.doi.org/10.3389/fmicb.2023.1284617.

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Since the discovery of the first “giant virus,” particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytovi

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21

Tee, Hwee Sze, and Chuan Ku. "Host-Calibrated Time Tree Caps the Age of Giant Viruses." Molecular Biology and Evolution 42, no. 2 (2025). https://doi.org/10.1093/molbev/msaf033.

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Abstract Viruses are widespread parasites with important impacts on public health, economy, and ecosystems. However, little is known about their origins, ages, and early evolutionary relationships with hosts. Here, we infer the maximum divergence times for eukaryotic giant DNA viruses (phylum Nucleocytoviricota) with dating analyses calibrated by host taxon ages of virus lineages with specific host ranges. The last common ancestor of Nucleocytoviricota existed after 1,000 million years ago, suggesting a much later origin than that of the eukaryotes. The early evolution of Nucleocytoviricota ei

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22

Zhang, Ruixuan, Hisashi Endo, Masaharu Takemura, and Hiroyuki Ogata. "RNA Sequencing of Medusavirus Suggests Remodeling of the Host Nuclear Environment at an Early Infection Stage." Microbiology Spectrum 9, no. 2 (2021). http://dx.doi.org/10.1128/spectrum.00064-21.

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23

Queiroz, Victória F., João Victor R. P. Carvalho, Fernanda G. de Souza, et al. "Analysis of the Genomic Features and Evolutionary History of Pithovirus-Like Isolates Reveals Two Major Divergent Groups of Viruses." Journal of Virology, July 3, 2023. http://dx.doi.org/10.1128/jvi.00411-23.

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Giant viruses that infect amoebae form a monophyletic group named the phylum Nucleocytoviricota . Despite being genomically and morphologically very diverse, the taxonomic categories of some clades that form this phylum are not yet well established.

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24

Zhang, Ruixuan, Masaharu Takemura, Kazuyoshi Murata, and Hiroyuki Ogata. "“Mamonoviridae”, a proposed new family of the phylum Nucleocytoviricota." Archives of Virology 168, no. 3 (2023). http://dx.doi.org/10.1007/s00705-022-05633-1.

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25

Hosokawa, Nao, Haruna Takahashi, Keita Aoki, and Masaharu Takemura. "Draft Genome Sequence of Pandoravirus japonicus Isolated from the Sabaishi River, Niigata, Japan." Microbiology Resource Announcements 10, no. 19 (2021). http://dx.doi.org/10.1128/mra.00365-21.

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“ Pandoraviridae ” is a proposed family of the phylum Nucleocytoviricota . Its features include an amphora-shaped capsid and the largest genome among all viruses. We report the isolation and genome sequencing of a new member of this family, named Pandoravirus japonicus , the third strain discovered in Japan.

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26

Bhattacharjee, Ananda S., Frederik Schulz, Tanja Woyke, Beth N. Orcutt, and Joaquín Martínez Martínez. "Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids." ISME Communications 3, no. 1 (2023). http://dx.doi.org/10.1038/s43705-022-00210-8.

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AbstractThe oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNATyr gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), a

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27

Truchon, Alexander R., Emily E. Chase, Ashton R. Stark, and Steven W. Wilhelm. "The diel disconnect between cell growth and division in Aureococcus is interrupted by giant virus infection." Frontiers in Microbiology 15 (August 21, 2024). http://dx.doi.org/10.3389/fmicb.2024.1426193.

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Viruses of eukaryotic algae have become an important research focus due to their role(s) in nutrient cycling and top-down control of algal blooms. Omics-based studies have identified a boon of genomic and transcriptional potential among the Nucleocytoviricota, a phylum of large dsDNA viruses which have been shown to infect algal and non-algal eukaryotes. However, little is still understood regarding the infection cycle of these viruses, particularly in how they take over a metabolically active host and convert it into a virocell state. Of particular interest are the roles light and the diel cy

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Aylward, Frank O., Jonatas S. Abrahão, Corina P. D. Brussaard, et al. "Taxonomic update for giant viruses in the order Imitervirales (phylum Nucleocytoviricota)." Archives of Virology 168, no. 11 (2023). http://dx.doi.org/10.1007/s00705-023-05906-3.

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29

Wu, Junyi, Lingjie Meng, Morgan Gaïa, et al. "Gene transfer among viruses substantially contributes to gene gain of giant viruses." Molecular Biology and Evolution, August 2, 2024. http://dx.doi.org/10.1093/molbev/msae161.

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Abstract The phylum Nucleocytoviricota comprises a diverse group of double-stranded DNA viruses that display a wide range of gene repertoires. Although these gene repertoires determine the characteristics of individual viruses, the evolutionary processes that have shaped the gene repertoires of extant viruses since their common ancestor are poorly characterized. In this study, we aimed to address this gap in knowledge by using amalgamated likelihood estimation (ALE), a probabilistic tree reconciliation method that infers evolutionary scenarios by distinguishing origination, gene duplications,

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Ha, Anh D., Mohammad Moniruzzaman, and Frank O. Aylward. "Assessing the biogeography of marine giant viruses in four oceanic transects." ISME Communications 3, no. 1 (2023). http://dx.doi.org/10.1038/s43705-023-00252-6.

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AbstractViruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 m), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinovirid

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Lamb, David C., Jared V. Goldstone, Djamal Brahim Belhaouari, et al. "Cytochrome b5 occurrence in giant and other viruses belonging to the phylum Nucleocytoviricota." npj Viruses 3, no. 1 (2025). https://doi.org/10.1038/s44298-025-00091-3.

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Abstract Cytochrome b5 is an electron transport protein found in eukaryotes and bacteria, and plays roles in energy production, lipid biosynthesis and cytochrome P450 biochemistry. Here we report that genes for cytochrome b5 occur broadly among viruses in the class Megaviricetes isolated from the deep ocean, freshwater and terrestrial sources, and human patients. Transcriptional analysis showed that Mimivirus bradfordmassiliense cytochrome b5 is expressed in the host and has characteristic spectral properties. Viral cytochrome b5s have either a unique N-terminal transmembrane anchor or are pre

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Chase, E. E., T. Pitot, S. Bouchard, et al. "Viral dynamics in a high-rate algal pond reveals a burst of Phycodnaviridae diversity correlated with episodic algal mortality." mBio, November 12, 2024. http://dx.doi.org/10.1128/mbio.02803-24.

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ABSTRACT This study explores virus-host dynamics in a unique environment: an industrial high-rate algal pond (HRAP). A wealth of novel DNA algal viruses are revealed, including members of Nucleocytoviricota “giant viruses” and the enigmatic Preplasmiviricota (e.g., virophages and polinton-like viruses). Several species of single-celled eukaryotic photosynthetic algae are identified (Chlorophyta) as putative hosts, with alternating dominant populations during the year of study. We specifically observe a surprising diversity of giant viruses from the family Phycodnaviridae ( Nucleocytoviricota )

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Sheikh, Shaghayegh, Tomáš Pánek, Ondřej Gahura, et al. "A novel group of dynamin-related proteins shared by eukaryotes and giant viruses is able to remodel mitochondria from within the matrix." Molecular Biology and Evolution, June 6, 2023. http://dx.doi.org/10.1093/molbev/msad134.

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Abstract The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebo

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Ha, Anh D., and Frank O. Aylward. "Automated classification of giant virus genomes using a random forest model built on trademark protein families." npj Viruses 2, no. 1 (2024). http://dx.doi.org/10.1038/s44298-024-00021-9.

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AbstractViruses of the phylum Nucleocytoviricota, often referred to as “giant viruses,” are prevalent in various environments around the globe and play significant roles in shaping eukaryotic diversity and activities in global ecosystems. Given the extensive phylogenetic diversity within this viral group and the highly complex composition of their genomes, taxonomic classification of giant viruses, particularly incomplete metagenome-assembled genomes (MAGs) can present a considerable challenge. Here we developed TIGTOG (Taxonomic Information of Giant viruses using Trademark Orthologous Groups)

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Bosmon, Tressy, Chantal Abergel, and Jean-Michel Claverie. "20 years of research on giant viruses." npj Viruses 3, no. 1 (2025). https://doi.org/10.1038/s44298-025-00093-1.

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Abstract Some twenty years ago, the discovery of the first giant virus, Acanthamoeba polyphaga mimivirus (now mimivirus bradfordmassiliense species), paved the way for the discovery of more than 10 new families of protist-infecting DNA viruses with unexpected diversity in virion shape and size, gene content, genome topology and mode of replication. Following their brief description, we examine how the historical concepts of virology have held up in the light of this new knowledge. Although the initial emphasis was on the gigantism of the newly described viruses infecting amoebae, the subsequen

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Barth, Zachary K., Ian Hicklin, Julien Thézé, et al. "Genomic analysis of hyperparasitic viruses associated with entomopoxviruses." Virus Evolution, July 12, 2024. http://dx.doi.org/10.1093/ve/veae051.

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Abstract Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread. Here we analyze the genomes of novel PLVs associated with the occlusion bodies of entomopoxvirus (EV) infections of two separate lepidopteran hosts. The presence of these elements within EV occlusion bodies suggests that they are the first known hyperparasites of poxviruses. We find that these PLVs belong to two distinct lineages that are highly d

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Rigou, Sofia, Sébastien Santini, Chantal Abergel, Jean-Michel Claverie, and Matthieu Legendre. "Past and present giant viruses diversity explored through permafrost metagenomics." Nature Communications 13, no. 1 (2022). http://dx.doi.org/10.1038/s41467-022-33633-x.

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AbstractGiant viruses are abundant in aquatic environments and ecologically important through the metabolic reprogramming of their hosts. Less is known about giant viruses from soil even though two of them, belonging to two different viral families, were reactivated from 30,000-y-old permafrost samples. This suggests an untapped diversity of Nucleocytoviricota in this environment. Through permafrost metagenomics we reveal a unique diversity pattern and a high heterogeneity in the abundance of giant viruses, representing up to 12% of the sum of sequence coverage in one sample. Pithoviridae and

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Irwin, Nicholas A. T., and Thomas A. Richards. "Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes." Nature Microbiology, May 28, 2024. http://dx.doi.org/10.1038/s41564-024-01707-9.

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AbstractNucleosomes are DNA–protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state. Here we examine the diversity of histones encoded by Nucleocytoviricota viruses. We identified 258 histones from 168 viral metagenomes with variable domain configurations including histone singlets, doublets, triplets and q

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Thomy, Julie, Frederic Sanchez, Camille Prioux, et al. "Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea." ISME Communications, August 29, 2024. http://dx.doi.org/10.1093/ismeco/ycae109.

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Abstract None declared. Conflicts of interestUnicellular green picophytoplankton from the Mamiellales order are pervasive in marine ecosystems and susceptible to infections by prasinoviruses, large double-stranded DNA (dsDNA) viruses within the Nucleocytoviricota phylum. We developed a dsDNA virus enrichment and shotgun sequencing method, successfully assembled 80 prasinovirus genomes from 43 samples in the South China Sea (SCS). Our research delivered the first direct estimation of 94% accuracy in correlating genome similarity to host range. Stirkingly, our analyses uncovered unexpected host-

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Zhao, Zhennan, Youhua Huang, Congcong Liu, et al. "Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly." Nature Communications 14, no. 1 (2023). http://dx.doi.org/10.1038/s41467-023-37681-9.

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AbstractSingapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and significantly threatens global biodiversity. In recent years, high morbidity and mortality in aquatic animals have been caused by iridovirid infections worldwide. Effective control and prevention strategies are urgently needed. Here, we present a near-atomic architecture of the SGIV capsid and identify eight types of capsid proteins. The viral inner membrane-integrated anchor protein coloc

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Homola, Miroslav, Carina R. Büttner, Tibor Füzik, et al. "Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi." Science Advances 10, no. 15 (2024). http://dx.doi.org/10.1126/sciadv.adk1954.

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The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma

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Pitot, Thomas M., Josephine Z. Rapp, Frederik Schulz, Catherine Girard, Simon Roux, and Alexander I. Culley. "Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes." ISME Communications, March 29, 2024. http://dx.doi.org/10.1093/ismeco/ycae048.

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Abstract Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remains poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel giant virus genome identification tool, we i

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Ban, Hiroki. "Infection signatures of multiple Nucleocytoviricota virus lineages in the brown algae Undaria pinnatifida revealed by population-wide genome analysis." Journal of Applied Phycology, May 3, 2025. https://doi.org/10.1007/s10811-025-03518-9.

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Queiroz, Victória Fulgêncio, Rodrigo Araújo Lima Rodrigues, Paulo Victor de Miranda Boratto, Bernard La Scola, Julien Andreani, and Jônatas Santos Abrahão. "Amoebae: Hiding in Plain Sight: Unappreciated Hosts for the Very Large Viruses." Annual Review of Virology 9, no. 1 (2022). http://dx.doi.org/10.1146/annurev-virology-100520-125832.

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For decades, viruses have been isolated primarily from humans and other organisms. Interestingly, one of the most complex sides of the virosphere was discovered using free-living amoebae as hosts. The discovery of giant viruses in the early twenty-first century opened a new chapter in the field of virology. Giant viruses are included in the phylum Nucleocytoviricota and harbor large and complex DNA genomes (up to 2.7 Mb) encoding genes never before seen in the virosphere and presenting gigantic particles (up to 1.5 μm). Different amoebae have been used to isolate and characterize a plethora of

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Prodinger, Florian, Hisashi Endo, Yoshihito Takano, et al. "Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Imitervirales and prokaryotes in a coastal ecosystem." FEMS Microbiology Ecology 97, no. 12 (2021). http://dx.doi.org/10.1093/femsec/fiab167.

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ABSTRACT Coastal microbial communities are affected by seasonal environmental change, biotic interactions and fluctuating nutrient availability. We investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses that infect eukaryotes (order Imitervirales; phylum Nucleocytoviricota), and prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and viral polB genes as markers in 43 seawater samples collected over 20 months. Eukaryotes, prokaryotes and Imitervirales communities characterized by the compos

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Farzad, Roxanna, Anh D. Ha, and Frank O. Aylward. "Diversity and genomics of giant viruses in the North Pacific Subtropical Gyre." Frontiers in Microbiology 13 (November 25, 2022). http://dx.doi.org/10.3389/fmicb.2022.1021923.

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Large double-stranded DNA viruses of the phylum Nucleocytoviricota, often referred to as “giant viruses,” are ubiquitous members of marine ecosystems that are important agents of mortality for eukaryotic plankton. Although giant viruses are known to be prevalent in marine systems, their activities in oligotrophic ocean waters remain unclear. Oligotrophic gyres constitute the majority of the ocean and assessing viral activities in these regions is therefore critical for understanding overall marine microbial processes. In this study, we generated 11 metagenome-assembled genomes (MAGs) of giant

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Arthofer, Patrick, Florian Panhölzl, Vincent Delafont, et al. "A giant virus infecting the amoeboflagellate Naegleria." Nature Communications 15, no. 1 (2024). http://dx.doi.org/10.1038/s41467-024-47308-2.

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AbstractGiant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naeglerien

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Zhao, Hongda, Ruixuan Zhang, Junyi Wu, et al. "A 1.5 Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis." Virus Evolution, October 31, 2023. http://dx.doi.org/10.1093/ve/vead064.

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Abstract Most fungal viruses are RNA viruses and no double-stranded DNA virus that infects fungi is known to date. A recent study detected DNA polymerase genes that originated from large dsDNA viruses in the genomes of basal fungi, suggestive of the existence of dsDNA viruses capable of infecting fungi. In this study, we searched for viral infection signatures in chromosome-level genome assemblies of the arbuscular mycorrhizal fungus Rhizophagus irregularis. We identified a continuous 1.5 Mb putative viral region on a chromosome in R. irregularis strain 4401. Phylogenetic analyses revealed tha

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Karki, Sangita, Zachary K. Barth, and Frank O. Aylward. "Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere." Journal of Molecular Evolution, April 29, 2025. https://doi.org/10.1007/s00239-025-10246-8.

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Abstract The details surrounding the early evolution of eukaryotes and their viruses are largely unknown. Several key enzymes involved in DNA synthesis and transcription are shared between eukaryotes and large DNA viruses in the phylum Nucleocytoviricota, but the evolutionary relationships between these genes remain unclear. In particular, previous studies of eukaryotic DNA and RNA polymerases often show deep-branching clades of eukaryotes and viruses indicative of ancient gene exchange. Here, we performed updated phylogenetic analysis of eukaryotic and viral family B DNA polymerases, multimer

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Meng, Lingjie, Tom O. Delmont, Morgan Gaïa, et al. "Genomic adaptation of giant viruses in polar oceans." Nature Communications 14, no. 1 (2023). http://dx.doi.org/10.1038/s41467-023-41910-6.

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AbstractDespite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an

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