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Four distinct virions. Light microscopy images (scale bar = 2 μ m) and scanning EM images (scale bar = 100 nm) of Mimivirus ( A , C ), Mollivirus ( B , D ), Pandoravirus ( E , G ) and Pithovirus ( F , H ).
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More than a century ago, the term 'virus' was introduced to describe infectious agents that are invisible by light microscopy and capable of passing through sterilizing filters. In addition to their extremely small size, most viruses have minimal genomes and gene contents, and rely almost entirely on host cell-encoded functions to multiply. Unexpec...
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Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plastic...
35 phylogenetic trees of non-ancestral Chlorovirus protein families. Trees were reconstructed using the ML method using the WAG + G + I substitution model. Interior branch support was estimated by the approximate likelihood ratio test (aLRT). For the sake of clarity, we only show branch support for important clades. Taxon names are colorized accord...
The emergence of the eukaryotic cytoskeleton is a critical yet puzzling step of eukaryogenesis. Actin and actin-related proteins (ARPs) are ubiquitous components of this cytoskeleton. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) would have therefore harbored both actin and various ARPs. Here, we report the presence and expressi...
Contaminated surfaces in a hospital serve as reservoirs for pathogen spread. The aim of this study was to evaluate UV lights in preventing the spread of a DNA tracer in an intensive care unit (ICU) through sterilization of highly touched surfaces. In a prospective trial, a non-pathogenic DNA virus was inoculated onto surfaces in an ICU patient room...
Since 2003, various viruses from the subfamily Megavirinae in the family Mimiviridae have been isolated worldwide, including icosahedral mimiviruses and tailed tupanviruses. To date, the evolutionary relationship between tailed and non-tailed mimiviruses has not yet been elucidated. Here, we present the genomic and morphological features of a newly...
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... In addition to animal viruses, membrane fusion has been observed at the initial stage of infection by GVs of algae (e.g., chloroviruses [19]) and other microbial eukaryotes. In amoebainfecting GVs, infection typically begins with phagocytosis, followed by capsid opening and fusion of the internal membrane with the phagosome (17,20). The low endosomal pH has also been suggested to induce membrane fusion for different GVs (21), including those infecting vertebrates (22,23) and amoebozoans (24). ...
Poxviruses are known to encode a set of proteins that form an entry-fusion complex (EFC) to mediate virus entry. However, the diversity, evolution, and origin of these EFC proteins remain poorly understood. Here, we identify the EFC protein homologs in poxviruses and other giant viruses of the phylum Nucleocytoviricota. The 11 EFC genes are present in almost all poxviruses, with the two smallest, G3 and O3, being absent in Entomopoxvirinae and basal lineages of Chordopoxvirinae. Five of the EFC genes are further grouped into two families, A16/G9/J5 and F9/L1, which are widely distributed across other major lineages of Nucleocytoviricota, including metagenome-assembled genomes, but are generally absent in viruses infecting algae or nonamoebozoan heterotrophic protists. The A16/G9/J5 and F9/L1 families cooccur, mostly as single copies, in 93% of the non-Poxviridae giant viruses that have at least one of them. Distribution and phylogenetic patterns suggest that both families originated in the ancestor of Nucleocytoviricota. In addition to the Poxviridae genes, homologs from each of the other Nucleocytoviricota families are largely clustered together, suggesting their ancient presence and vertical inheritance. Despite deep sequence divergences, we observed noticeable conservation of cysteine residues and predicted structures between EFC proteins of Poxviridae and other families. Overall, our study reveals widespread distribution of these EFC protein homologs beyond poxviruses, implies the existence of a conserved membrane fusion mechanism, and sheds light on host range and ancient evolution of Nucleocytoviricota. IMPORTANCE Fusion between virus and host membranes is critical for viruses to release genetic materials and to initiate infection. Whereas most viruses use a single protein for membrane fusion, poxviruses employ a multiprotein entry-fusion complex (EFC). We report that two major families of the EFC proteins are widely distributed within the virus phylum Nucleocytoviricota, which includes poxviruses and other double-stranded (dsDNA) giant viruses that infect animals, amoebozoans, algae, and various microbial eukaryotes. Each of these two protein families is structurally conserved, traces its origin to the root of Nucleocytoviricota, was passed down to the major subclades of Nucleocytoviricota, and is retained in most giant viruses known to infect animals and amoebozoans. The EFC proteins therefore represent a potential mechanism for virus entry in diverse giant viruses. We hypothesize that they may have facilitated the infection of an animal/amoebozoan-like host by the last Nucleocytoviricota common ancestor.
... kb (12). This approach not only allows characterization of transcripts recruited to fulllength giant virus genomes and therefore better phylogenetic resolution, but it also captures giant viruses that are missing hallmark genes (65). The genome set was dereplicated using MASH v2.0 (66) with single-linkage clustering at a MASH distance of #0.05 (corresponding to ;95% average nucleotide identity [ANI]), and the genome with the highest N 50 contig length was chosen as the representative. ...
Viruses can alter the abundance, evolution, and metabolism of microorganisms in the ocean, playing a key role in water column biogeochemistry and global carbon cycles. Large efforts to measure the contribution of eukaryotic microorganisms (e.g., protists) to the marine food web have been made, yet the in situ activities of the ecologically relevant viruses that infect these organisms are not well characterized. Viruses within the phylum Nucleocytoviricota ("giant viruses") are known to infect a diverse range of ecologically relevant marine protists, yet how these viruses are influenced by environmental conditions remains under-characterized. By employing metatranscriptomic analyses of in situ microbial communities along a temporal and depth-resolved gradient, we describe the diversity of giant viruses at the Southern Ocean Time Series (SOTS), a site within the subpolar Southern Ocean. Using a phylogeny-guided taxonomic assessment of detected giant virus genomes and metagenome-assembled genomes, we observed depth-dependent structuring of divergent giant virus families mirroring dynamic physicochemical gradients in the stratified euphotic zone. Analyses of transcribed metabolic genes from giant viruses suggest viral metabolic reprogramming of hosts from the surface to a 200-m depth. Lastly, using on-deck incubations reflecting a gradient of iron availability, we show that modulating iron regimes influences the activity of giant viruses in the field. Specifically, we show enhanced infection signatures of giant viruses under both iron-replete and iron-limited conditions. Collectively, these results expand our understanding of how the water column's vertical biogeography and chemical surroundings affect an important group of viruses within the Southern Ocean. IMPORTANCE The biology and ecology of marine microbial eukaryotes is known to be constrained by oceanic conditions. In contrast, how viruses that infect this important group of organisms respond to environmental change is less well known, despite viruses being recognized as key microbial community members. Here, we address this gap in our understanding by characterizing the diversity and activity of "giant" viruses within an important region in the sub-Antarctic Southern Ocean. Giant viruses are double-stranded DNA (dsDNA) viruses of the phylum Nucleocytoviricota and are known to infect a wide range of eukaryotic hosts. By employing a metatranscriptomics approach using both in situ samples and microcosm manipulations, we illuminated both the vertical biogeography and how changing iron availability affects this primarily uncultivated group of protist-infecting viruses. These results serve as a foundation for our understanding of how the open ocean water column structures the viral community, which can be used to guide models of the viral impact on marine and global biogeochemical cycling.
... The most relevant viruses identified on cultivated areas were species of Pseudoplusia includens, which are pathogens of the insects Chrysodeixis includen, these are parasites of the soybean crop (Alexandre et al., 2010;Craveiro et al., 2015;Harrison et al., 2019) the presence of these viruses can be considered as biopesticides and/or pest controllers in crops. Pandoraviruses, which were identified in the four sites, are giant viruses and are present in high diversity in soil and water, and can infect protozoa and amoebas (Abergel et al., 2015;Aherfi et al., 2016;Colson et al., 2017;Andradedos et al., 2018;Schulz et al., 2018;Akashi and Takemura, 2019;Tokarz-DeptułaBeata et al., 2019). Also, analysis of the composition of functional genes in these sites at levels 2 and 3 showed a greater relative abundance of genes involved in the lytic cycle, so it could be a greater abundance of prophages in the forest and phages than in the sites with culture (data not shown). ...
The tropical Amazon has a unique biodiversity that has been affected by the development of pastures and economically important crops, such as soybeans. In the Amazon soil, the communities of microorganisms are diverse and act in different biogeochemical activities relevant to their adaptation to the environment. The assessment of changes in soil microorganism communities is essential to consider the impact of agribusiness action in one of the wealthiest regions in diversity in the world. Thus, the soil microbial diversity of the Amazon forest, the north region of Brazil, was evaluated regarding the influence of soybean farming with regions with periods of two and 14 years of exploitation, with regions of pasture and forest area, through the metagenomics approach with new generation sequencing technology, in addition, it was considered chemical characteristics such as pH value, organic matter content, macronutrients, micronutrients, and cations. High microbial diversity was identified at all collection sites and, despite this, bacterial, archaeal, and virus communities were very diverse between sites, with higher identification of Enterobacter cloacae and species of Pseudomonas, Pseudoplusia includens, Methanosarcina barkeri in the farmed and pasture, whose microbial diversity is influenced by the presence of cations and the interaction of organic matter with clay. It was evident that there is a change in the communities of native microorganisms for others adapted in the areas that had their vegetal cover eliminated.
... But it is feasible to identify host contamination in phage genomes by creating and querying a distinctive bacterial gene set. Besides, it is important to note that we excluded those large DNA viruses infecting eukaryotic microorganisms, due to their extraordinarily large and complicated genomes and the lack of evidence that they cause diseases in vertebrates (51)(52)(53). Though we have deleted hundreds of PVSs of vertebrate-infecting large DNA viruses from families like Herpesviridae and Poxviridae, there are still some ambiguous sequences that can be treated as host PVSs if using loose criteria. ...
High-throughput sequencing-based viromics highly depends on reference databases, but foreign contamination is widespread in public databases and often leads to confusing and even wrong conclusions in genomic analysis and viromic profiling. To address this issue, we systematically detected and identified the contamination in the largest viral sequence collections of GenBank and UniProt based on a stringent scrutiny pipeline.
... At the time of these analyses, only six Topo IIAs from four families (Asfarviridae, Mimiviridae, Iridoviridae, and Phycodnaviridae) within Nucleocytoviricota were known (Forterre et al. 2007). During the last decade, a great number of new Nucleocytoviricota genomes became available, including those of giant viruses from the families Mimiviridae, Marseilleviridae, and Pandoraviridae, which encode Topo IIA (Abergel, Legendre, and Claverie 2015;Colson et al. 2017). Notably, it was shown that the Topo IIA encoded by Marseilleviridae branched as a sister clade to Eukarya (Erives 2017). ...
Type II DNA topoisomerases of the family A (Topo IIAs) 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 homologs and have no orthologs in Archaea. Interestingly, eukaryotic Topo IIAs have close homologs in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses. Topo IIAs are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses on a dataset combining viral and cellular Topo IIA homologs. Topo IIAs encoded by Bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both Bacteria and Caudoviricetes from the data set, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long-branch attraction artifact. The topologies of our trees suggest that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.
... Poxviruses do not replicate or express their genomes in the nucleus, relying instead on cellular proteins. Poxviruses rely on virally encoded proteins for cytoplasmic replication [14][15][16][17][18][19] . Replication and transcription genes are in the middle of the genome, while host interaction genes are at the ends. ...
Monkeypox is an orthopoxvirus-based zoonotic illness that causes symptoms similar to smallpox in humans. Health care workers around the world are making it a priority to educate themselves on the many clinical manifestations and treatment options for this virus as public health agencies strive to stop the current outbreak. The infected do not have access to any treatment at this time. However, information obtained from the smallpox pandemic has led researchers to examine vaccinia immune globulin (IVG), tecovirimat, and cidofovir as viable treatments for monkeypox. Moreover, medication like tecovirimat may be given in extreme circumstances, and supportive therapy can help with symptom relief. The European Medicines Agency (EMA) certified tecovirimat as safe and effective against monkeypox in 2022, per the World Health Organization (WHO). As there are now no established guidelines for alleviating these symptoms, the efficacy of these treatments is highly questionable. Some high-profile cases in recent years have cast doubt on the long-held belief that this illness is rare and always resolves itself without treatment. We aimed to conduct this review to get a deeper comprehension of the evolving epidemiology of monkeypox by analysing such factors as the number of confirmed, probable, and potential cases, the median age at presentation, the mortality rate, and the geographic distribution of the disease. This study offers an updated review of monkeypox and the clinical treatments that are currently available as a result of the worldwide epidemics.
... Since we analyzed sequences from DNA, our methodology excluded RNA viruses, which have a role in infecting eukaryotes in marine environments (42), while our analytical pipeline is biased toward Caudovirales bacteriophages and excludes singlestranded DNA (ssDNA) viruses (43), which predominate in some freshwater polar environments (44). Prefiltration of our water samples at 0.22 mm also causes us to miss a portion of the viral diversity (45), in particular by removing some nucleocytoplasmic large DNA viruses (NCLDVs), including Mimiviridae, and larger Phycodnaviridae (46). Prefiltration can result in underrepresentation of lysogenic viruses, which may be found as prophages within host cells; however, given that a previous study in a polar lake in summer found a lytic lifestyle predominated (16), we consider that the majority of the dsDNA viral diversity was likely present as free virions. ...
Milne Fiord, located on the coastal margin of the Last Ice Area (LIA) in the High Arctic (82°N, Canada), harbors an epishelf lake, a rare type of ice-dependent ecosystem in which a layer of freshwater overlies marine water connected to the open ocean. This microbe-dominated ecosystem faces catastrophic change due to the deterioration of its ice environment related to warming temperatures. We produced the first assessment of viral abundance, diversity, and distribution in this vulnerable ecosystem and explored the niches available for viral taxa and the functional genes underlying their distribution. We found that the viral community in the freshwater layer was distinct from, and more diverse than, the community in the underlying seawater and contained a different set of putative auxiliary metabolic genes, including the sulfur starvation-linked gene tauD and the gene coding for patatin-like phospholipase. The halocline community resembled the freshwater more than the marine community, but harbored viral taxa unique to this layer. We observed distinct viral assemblages immediately below the halocline, at a depth that was associated with a peak of prasinophyte algae and the viral family Phycodnaviridae. We also assembled 15 complete circular genomes, including a putative Pelagibacter phage with a marine distribution. It appears that despite its isolated and precarious situation, the varied niches in this epishelf lake support a diverse viral community, highlighting the importance of characterizing underexplored microbiota in the Last Ice Area before these ecosystems undergo irreversible change.
... Further, detailed molecular experimentation has revealed that the infection strategies of these viruses can differ markedly, underscoring the varied virus-host interactions that have evolved in this group. For example, while some strictly replicate in the cytoplasm, others have infection stages that take place in the nucleus [60]. ...
Although traditionally viewed as streamlined and simple, discoveries over the last century have revealed that viruses can exhibit surprisingly complex physical structures, genomic organization, ecological interactions, and evolutionary histories. Viruses can have physical dimensions and genome lengths that exceed many cellular lineages, and their infection strategies can involve a remarkable level of physiological remodeling of their host cells. Virus–virus communication and widespread forms of hyperparasitism have been shown to be common in the virosphere, demonstrating that dynamic ecological interactions often shape their success. And the evolutionary histories of viruses are often fraught with complexities, with chimeric genomes including genes derived from numerous distinct sources or evolved de novo. Here we will discuss many aspects of this viral complexity, with particular emphasis on large DNA viruses, and provide an outlook for future research.
... T. magnifica nos hace cuestionar algunos de los conceptos y definiciones que usamos para describir el mundo microbiológico. Además de estas bacterias, existen también virus eucariotas gigantes, cuyo tamaño puede incluso ser mayor al de algunos microbios (Abergel et al., 2015). En contraste, algunos animales que se consideran más complejos son invisibles al ojo y pueden ser más pequeños que las LSB. ...
... The infectious cycle of these two proposed virus genera proceeds like other amoeba infecting viruses, namely by phagocytosis followed by capsid opening and membrane fusion with the phagosome. 47 For the pithoviruses and cedratviruses, the viral encoded RNA polymerase is packaged in the virion, which initiates early transcription in the cytoplasm and the host nucleus remains intact throughout the replication cycle. The virions are assembled starting from one apex of the future virion, leading to a rectangular uncoated virion, then the tegument is built by patches from a reservoir in the cytoplasm and the virus morphology changes to amphora-shaped. ...
... Four glycosylation sites were detected in chlorovirus CVM-1, 47 NGSV, 279 NLTA, 285 NVGY, and 293 NTAV, making this virus the only one with a N-glycan attached to the canonical NX(T/S) consensus sequon. Of note: 47 Asn is conserved in PBCV-1 and other MCPs, but it was only glycosylated in CVM-1. ...
... Four glycosylation sites were detected in chlorovirus CVM-1, 47 NGSV, 279 NLTA, 285 NVGY, and 293 NTAV, making this virus the only one with a N-glycan attached to the canonical NX(T/S) consensus sequon. Of note: 47 Asn is conserved in PBCV-1 and other MCPs, but it was only glycosylated in CVM-1. 179 PBCV-1 is the only chlorovirus for which the structure of the capsid, along with the structure of the glycans has been determined. ...
Viruses are a heterogeneous ensemble of entities, all sharing the need for a suitable host to replicate. They are extremely diverse, varying in morphology, size, nature, and complexity of their genomic content. Typically, viruses use host-encoded glycosyltransferases and glycosidases to add and remove sugar residues from their glycoproteins. Thus, the structure of the glycans on the viral proteins have, to date, typically been considered to mimick those of the host. However, the more recently discovered large and giant viruses differ from this paradigm. At least some of these viruses code for an (almost) autonomous glycosylation pathway. These viral genes include those that encode the production of activated sugars, glycosyltransferases, and other enzymes able to manipulate sugars at various levels. This review focuses on large and giant viruses that produce carbohydrate-processing enzymes. A brief description of those harboring these features at the genomic level will be discussed, followed by the achievements reached with regard to the elucidation of the glycan structures, the activity of the proteins able to manipulate sugars, and the organic synthesis of some of these virus-encoded glycans. During this progression, we will also comment on many of the challenging questions on this subject that remain to be addressed.
