Oysters as hot spots for mimivirus isolation

Diversity of Surface Fibril Patterns in Mimivirus Isolates

Among the most intriguing structural features in the known virosphere are mimivirus surface fibrils, proteinaceous filaments approximately 150 nm long, covering the mimivirus capsid surface. Fibrils are important to promote particle adhesion to host cells, triggering phagocytosis and cell infection. However, although mimiviruses are one of the most abundant viral entities in a plethora of biomes worldwide, there has been no comparative analysis on fibril organization and abundance among distinct mimivirus isolates. Here, we describe the isolation and characterization of Megavirus caiporensis, a novel lineage C mimivirus with surface fibrils organized as "clumps." This intriguing feature led us to expand our analyses to other mimivirus isolates. By employing a combined approach including electron microscopy, image processing, genomic sequencing, and viral prospection, we obtained evidence of at least three main patterns of surface fibrils that can be found in mimiviruses: (i) isolates containing particles with abundant fibrils, distributed homogeneously on the capsid surface; (ii) isolates with particles almost fibrilless; and (iii) isolates with particles containing fibrils in abundance, but organized as clumps, as observed in Megavirus caiporensis. A total of 15 mimivirus isolates were analyzed by microscopy, and their DNA polymerase subunit B genes were sequenced for phylogenetic analysis. We observed a unique match between evolutionarily-related viruses and their fibril profiles. Biological assays suggested that patterns of fibrils can influence viral entry in host cells. Our data contribute to the knowledge of mimivirus fibril organization and abundance, as well as raising questions on the evolution of those intriguing structures. IMPORTANCE Mimivirus fibrils are intriguing structures that have drawn attention since their discovery. Although still under investigation, the function of fibrils may be related to host cell adhesion. In this work, we isolated and characterized a new mimivirus, called Megavirus caiporensis, and we showed that mimivirus isolates can exhibit at least three different patterns related to fibril organization and abundance. In our study, evolutionarily-related viruses presented similar fibril profiles, and such fibrils may affect how those viruses trigger phagocytosis in amoebas. These data shed light on aspects of mimivirus particle morphology, virus-host interactions, and their evolution.

A remarkably diverse and well-organized virus community in a filter-feeding oyster

BACKGROUND

Viruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that inhabit marine animals have been largely neglected. Oysters are keystone species in coastal ecosystems, yet as filter-feeding bivalves with very large roosting numbers and species co-habitation, it is not clear what role they play in marine virus transmission and coastal microbiome regulation.

RESULTS

Here, we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit contigs (≥ 800 bp) and 3473 high-quality viral genomes, enabling the first comprehensive overview of both DNA and RNA viral communities in the oyster Crassostrea hongkongensis. We discovered tremendous diversity among novel viruses that inhabit this oyster using multiple approaches, including reads recruitment, viral operational taxonomic units, and high-quality virus genomes. Our results show that these viruses are very different from viruses in the oceans or other habitats. In particular, the high diversity of novel circoviruses that we found in the oysters indicates that oysters may be potential hotspots for circoviruses. Notably, the viruses that were enriched in oysters are not random but are well-organized communities that can respond to changes in the health state of the host and the external environment at both compositional and functional levels.

CONCLUSIONS

In this study, we generated a first "knowledge landscape" of the oyster virome, which has increased the number of known oyster-related viruses by tens of thousands. Our results suggest that oysters provide a unique habitat that is different from that of seawater, and highlight the importance of filter-feeding bivalves for marine virus exploration as well as their essential but still invisible roles in regulating marine ecosystems. Video Abstract.

Tracing RNA viruses associated with Nudibranchia gastropods

Background

Nudibranchia is an under-studied taxonomic group of gastropods, including more than 3,000 species with colourful and extravagant body shapes and peculiar predatory and defensive strategies. Although symbiosis with bacteria has been reported, no data are available for the nudibranch microbiome nor regarding viruses possibly associated with these geographically widespread species.

Methods

Based on 47 available RNA sequencing datasets including more than two billion reads of 35 nudibranch species, a meta-transcriptome assembly was constructed. Taxonomic searches with DIAMOND, RNA-dependent-RNA-polymerase identification with palmscan and viral hallmark genes identification by VirSorter2 in combination with CheckV were applied to identify genuine viral genomes, which were then annotated using CAT.

Results

A total of 20 viral genomes were identified as bona fide viruses, among 552 putative viral contigs resembling both RNA viruses of the Negarnaviricota, Pisuviricota, Kitrinoviricota phyla and actively transcribing DNA viruses of the Cossaviricota and Nucleocytoviricota phyla. The 20 commonly identified viruses showed similarity with RNA viruses identified in other RNA-seq experiments and can be putatively associated with bacteria, plant and arthropod hosts by co-occurence analysis. The RNA samples having the highest viral abundances showed a heterogenous and mostly sample-specific distribution of the identified viruses, suggesting that nudibranchs possess diversified and mostly unknown viral communities.

Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species

Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42-82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general.

A Brief History of Giant Viruses’ Studies in Brazilian Biomes

Almost two decades after the isolation of the first amoebal giant viruses, indubitably the discovery of these entities has deeply affected the current scientific knowledge on the virosphere. Much has been uncovered since then: viruses can now acknowledge complex genomes and huge particle sizes, integrating remarkable evolutionary relationships that date as early as the emergence of life on the planet. This year, a decade has passed since the first studies on giant viruses in the Brazilian territory, and since then biomes of rare beauty and biodiversity (Amazon, Atlantic forest, Pantanal wetlands, Cerrado savannas) have been explored in the search for giant viruses. From those unique biomes, novel viral entities were found, revealing never before seen genomes and virion structures. To celebrate this, here we bring together the context, inspirations, and the major contributions of independent Brazilian research groups to summarize the accumulated knowledge about the diversity and the exceptionality of some of the giant viruses found in Brazil.

Structural and Proteomic Characterization of the Initiation of Giant Virus Infection

Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four infection intermediates in Samba virus (Mimivirus genus, lineage A) as visualized by cryoelectron microscopy (cryo-EM), cryoelectron tomography (cryo-ET), and scanning electron microscopy (SEM). Each of these four intermediates reflects similar morphology to a stage that occurs in vivo. We show that these genome release stages are conserved in other mimiviruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved among disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.

A novel Asfarvirus-like virus identified as a potential cause of mass mortality of abalone

A novel Asfarvirus-like virus is proposed as the etiological agent responsible for mass mortality in abalone. The disease, called abalone amyotrophia, originally was recognized in the 1980s, but efforts to identify a causative agent were unsuccessful. We prepared a semi-purified fraction by nuclease treatment and ultracentrifugation of diseased abalone homogenate, and the existence of the etiological agent in the fraction was confirmed by a challenge test. Using next-generation sequencing and PCR-based epidemiological surveys, we obtained a partial sequence with similarity to a member of the family Asfarviridae. BLASTP analysis of the predicted proteins against a virus database resulted in 48 proteins encoded by the novel virus with top hits against proteins encoded by African swine fever virus (ASFV). Phylogenetic analyses of predicted proteins of the novel virus confirmed that ASFV represents the closest relative. Comparative genomic analysis revealed gene-order conservation between the novel virus and ASFV. In situ hybridization targeting the gene encoding the major capsid protein of the novel virus detected positive signals only in tissue from diseased abalone. The results of this study suggest that the putative causative agent should be considered a tentative new member of the family Asfarviridae, which we provisionally designate abalone asfa-like virus (AbALV).

A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks

Background

Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila.

Results

We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets.

Conclusions

We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1472-6) contains supplementary material, which is available to authorized users.

High-throughput isolation of giant viruses using high-content screening

The race to discover and isolate giant viruses began 15 years ago. Metagenomics is counterbalancing coculture, with the detection of giant virus genomes becoming faster as sequencing technologies develop. Since the discovery of giant viruses, many efforts have been made to improve methods for coculturing amebas and giant viruses, which remains the key engine of isolation of these microorganisms. However, these techniques still lack the proper tools for high-speed detection. In this paper, we present advances in the isolation of giant viruses. A new strategy was developed using a high-throughput microscope for real-time monitoring of cocultures using optimized algorithms targeting infected amebas. After validating the strategy, we adapted a new tabletop scanning electron microscope for high-speed identification of giant viruses directly from culture. The speed and isolation rate of this strategy has raised the coculture to almost the same level as sequencing techniques in terms of detection speed and sensitivity.

A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data

Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4% of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated with bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. Single Nucleotide Polymorphism (SNP) analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses.

The Complex Nature of Tupanviruses

The discovery of giant viruses revealed a new level of complexity in the virosphere, raising important questions about the diversity, ecology, and evolution of these viruses. The family Mimiviridae was the first group of amoebal giant viruses to be discovered (by Bernard La Scola and Didier Raoult team), containing viruses with structural and genetic features that challenged many concepts of classic virology. The tupanviruses are among the newest members of this family and exhibit structural, biological, and genetic features never previously observed in other giant viruses. The complexity of these viruses has put us one step forward toward the comprehension of giant virus biology and evolution, but also has raised important questions that still need to be addressed. In this chapter, we tell the history behind the discovery of one of the most complex viruses isolated to date, highlighting the unique features exhibited by tupanviruses, and discuss how these giant viruses have contributed to redefining limits for the virosphere.

Investigations by the Institut Hospitalo-Universitaire Méditerranée Infection of food and food-borne infections in the Mediterranean Basin and in sub-Saharan Africa

Food-borne infections are major causes of public health concern in developing and developed countries. During the past decade, the Institut Hospitalo-Universitaire Méditerranée Infection has conducted or been involved in multiple investigations that aimed at identifying the sources and strains responsible for food-borne diseases and therefore at improving the understanding, diagnosis, prevention and control of these infections. Investigations were conducted in the Mediterranean area and in sub-Saharan Africa on more than 15 food-borne agents, 17 food products and 14 antibiotic resistance-associated genes. Multiple sources, including unexpected ones, and pathogens, including emerging ones, were involved. Travelling in developing countries and zoonoses are major contributors to food-borne infections, while food-borne transmission of resistance-associated genes is increasingly reported. However, risk factors and pathogens associated with food-borne infections likely remain untapped and must be more extensively investigated, monitored and regularly reassessed. Diagnostic tests based on new technologies and real-time surveillance tools based on microbiology laboratory data are promising approaches to detect known food-borne infections and decipher new ones. Studies of the microbiota and its relationships with dietary patterns are also worth being conducted.

Ubiquitous giants: a plethora of giant viruses found in Brazil and Antarctica

BACKGROUND

Since the discovery of giant viruses infecting amoebae in 2003, many dogmas of virology have been revised and the search for these viruses has been intensified. Over the last few years, several new groups of these viruses have been discovered in various types of samples and environments.In this work, we describe the isolation of 68 giant viruses of amoeba obtained from environmental samples from Brazil and Antarctica.

METHODS

Isolated viruses were identified by hemacolor staining, PCR assays and electron microscopy (scanning and/or transmission).

RESULTS

A total of 64 viruses belonging to the Mimiviridae family were isolated (26 from lineage A, 13 from lineage B, 2 from lineage C and 23 from unidentified lineages) from different types of samples, including marine water from Antarctica, thus being the first mimiviruses isolated in this extreme environment to date. Furthermore, a marseillevirus was isolated from sewage samples along with two pandoraviruses and a cedratvirus (the third to be isolated in the world so far).

CONCLUSIONS

Considering the different type of samples, we found a higher number of viral groups in sewage samples. Our results reinforce the importance of prospective studies in different environmental samples, therefore improving our comprehension about the circulation anddiversity of these viruses in nature.

Analyses of the Kroon Virus Major Capsid Gene and Its Transcript Highlight a Distinct Pattern of Gene Evolution and Splicing among Mimiviruses

The inclusion of Mimiviridae members in the putative monophyletic nucleocytoplasmic large DNA virus (NCLDV) group is based on genomic and phylogenomic patterns. This shows that, along with other viral families, they share a set of genes known as core or "hallmark genes," including the gene for the major capsid protein (MCP). Although previous studies have suggested that the maturation of mimivirus MCP transcripts is dependent on splicing, there is little information about the processing of this transcript in other mimivirus isolates. Here we report the characterization of a new mimivirus isolate, called Kroon virus (KV) mimivirus. Analysis of the structure, synteny, and phylogenetic relationships of the MCP genes in many mimivirus isolates revealed a remarkable variation at position and types of intronic and exonic regions, even for mimiviruses belonging to the same lineage. In addition, sequencing of KV and Acanthamoeba polyphaga mimivirus (APMV) MCP transcripts has shown that inside the family, even related giant viruses may present different ways to process the MCP mRNA. These results contribute to the understanding of the genetic organization and evolution of the MCP gene in mimiviruses.IMPORTANCE Mimivirus isolates have been obtained by prospecting studies since 2003. Based on genomic and phylogenomic studies of conserved genes, these viruses have been clustered together with members of six other viral families. Although the major capsid protein (MCP) gene is an important member of the so-called "hallmark genes," there is little information about the processing and structure of this gene in many mimivirus isolates. In this work, we have analyzed the structure, synteny, and phylogenetic relationships of the MCP genes in many mimivirus isolates; these genes showed remarkable variation at position and types of intronic and exonic regions, even for mimiviruses belonging to the same lineage. These results contribute to the understanding of the genetic organization and evolution of the MCP gene in mimiviruses.

Amoebae, Giant Viruses, and Virophages Make Up a Complex, Multilayered Threesome

Viral infection had not been observed for amoebae, until the Acanthamoeba polyphaga mimivirus (APMV) was discovered in 2003. APMV belongs to the nucleocytoplasmatic large DNA virus (NCLDV) family and infects not only A. polyphaga, but also other professional phagocytes. Here, we review the Megavirales to give an overview of the current members of the Mimi- and Marseilleviridae families and their structural features during amoebal infection. We summarize the different steps of their infection cycle in A. polyphaga and Acanthamoeba castellani. Furthermore, we dive into the emerging field of virophages, which parasitize upon viral factories of the Megavirales family. The discovery of virophages in 2008 and research in recent years revealed an increasingly complex network of interactions between cell, giant virus, and virophage. Virophages seem to be highly abundant in the environment and occupy the same niches as the Mimiviridae and their hosts. Establishment of metagenomic and co-culture approaches rapidly increased the number of detected virophages over the recent years. Genetic interaction of cell and virophage might constitute a potent defense machinery against giant viruses and seems to be important for survival of the infected cell during mimivirus infections. Nonetheless, the molecular events during co-infection and the interactions of cell, giant virus, and virophage have not been elucidated, yet. However, the genetic interactions of these three, suggest an intricate, multilayered network during amoebal (co-)infections. Understanding these interactions could elucidate molecular events essential for proper viral factory activity and could implicate new ways of treating viruses that form viral factories.

Genome Characterization of the First Mimiviruses of Lineage C Isolated in Brazil

The family Mimiviridae, comprised by giant DNA viruses, has been increasingly studied since the isolation of the Acanthamoeba polyphaga mimivirus (APMV), in 2003. In this work, we describe the genome analysis of two new mimiviruses, each isolated from a distinct Brazilian environment. Furthermore, for the first time, we are reporting the genomic characterization of mimiviruses of group C in Brazil (Br-mimiC), where a predominance of mimiviruses from group A has been previously reported. The genomes of the Br-mimiC isolates Mimivirus gilmour (MVGM) and Mimivirus golden (MVGD) are composed of double-stranded DNA molecules of ∼1.2 Mb, each encoding more than 1,100 open reading frames. Genome functional annotations highlighted the presence of mimivirus group C hallmark genes, such as the set of seven aminoacyl-tRNA synthetases. However, the set of tRNA encoded by the Br-mimiC was distinct from those of other group C mimiviruses. Differences could also be observed in a genome synteny analysis, which demonstrated the presence of inversions and loci translocations at both extremities of Br-mimiC genomes. Both phylogenetic and phyletic analyses corroborate previous results, undoubtedly grouping the new Brazilian isolates into mimivirus group C. Finally, an updated pan-genome analysis of genus Mimivirus was performed including all new genomes available until the present moment. This last analysis showed a slight increase in the number of clusters of orthologous groups of proteins among mimiviruses of group A, with a larger increase after addition of sequences from mimiviruses of groups B and C, as well as a plateau tendency after the inclusion of the last four mimiviruses of group C, including the Br-mimiC isolates. Future prospective studies will help us to understand the genetic diversity among mimiviruses.

Giant Viruses of Amoebae: A Journey Through Innovative Research and Paradigm Changes

Giant viruses of amoebae were discovered serendipitously in 2003; they are visible via optical microscopy, making them bona fide microbes. Their lifestyle, structure, and genomes break the mold of classical viruses. Giant viruses of amoebae are complex microorganisms. Their genomes harbor between 444 and 2,544 genes, including many that are unique to viruses, and encode translation components; their virions contain >100 proteins as well as mRNAs. Mimiviruses have a specific mobilome, including virophages, provirophages, and transpovirons, and can resist virophages through a system known as MIMIVIRE (mimivirus virophage resistance element). Giant viruses of amoebae bring upheaval to the definition of viruses and tend to separate the current virosphere into two categories: very simple viruses and viruses with complexity similar to that of other microbes. This new paradigm is propitious for enhanced detection and characterization of giant viruses of amoebae, and a particular focus on their role in humans is warranted.

Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms

The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses. This review provides a synopsis on the contribution of viral metagenomics to the discovery of viruses infecting different aquatic organisms as well as its potential role in viral diagnostics. High throughput Next Generation sequencing (NGS) and library construction used in metagenomic projects have simplified the task of generating complete viral genomes unlike the challenge faced in traditional methods that use multiple primers targeted at different segments and VPs to generate the entire genome of a novel virus. In terms of diagnostics, studies carried out this far show that viral metagenomics has the potential to serve as a multifaceted tool able to study and identify etiological agents of single infections, co-infections, tissue tropism, profiling viral infections of different aquatic organisms, epidemiological monitoring of disease prevalence, evolutionary phylogenetic analyses, and the study of genomic diversity in quasispecies viruses. With sequencing technologies and bioinformatics analytical tools becoming cheaper and easier, we anticipate that metagenomics will soon become a routine tool for the discovery, study, and identification of novel pathogens including viruses to enable timely disease control for emerging diseases in aquaculture.

Mimivirus: leading the way in the discovery of giant viruses of amoebae

Acanthamoeba polyphaga mimivirus (APMV) and subsequently discovered giant viruses of amoebae challenge the previous definition of viruses and their classification.

The replication cycle, structure, genomic make-up and plasticity of giant viruses differ from those of traditional viruses. They extend the definition of viruses into a broader range of biological entities, some of which are very simple and others of which have a complexity that is comparable to that of other microorganisms.

Giant viruses of amoebae have virus particles as large as some microorganisms that are visible by light microscopy and that have a stunning level of complexity. Their genomes are mosaics and contain large repertoires of genes, some of which are hallmarks of cellular organisms, although the majority of which have unknown functions.

Mimiviruses are associated with a specific mobilome and are parasitized by viruses that they can defend against.

Several hypotheses on the ancient origin and evolutionary relationship between cellular organisms and giant viruses of amoebae have been proposed, and these topics continue to be debated.

The detection of giant viruses of amoebae in humans and the study of their potential pathogenicity are emerging fields.

The discovery of the giant amoebal virus mimivirus, in 2003, opened up a new area of virology. Extended studies, including those of mimiviruses, have since revealed that these viruses have genetic, proteomic and structural features that are more complex than those of conventional viruses.

The accidental discovery of the giant virus of amoeba — Acanthamoeba polyphaga mimivirus (APMV; more commonly known as mimivirus) — in 2003 changed the field of virology. Viruses were previously defined by their submicroscopic size, which probably prevented the search for giant viruses, which are visible by light microscopy. Extended studies of giant viruses of amoebae revealed that they have genetic, proteomic and structural complexities that were not thought to exist among viruses and that are comparable to those of bacteria, archaea and small eukaryotes. The giant virus particles contain mRNA and more than 100 proteins, they have gene repertoires that are broader than those of other viruses and, notably, some encode translation components. The infection cycles of giant viruses of amoebae involve virus entry by amoebal phagocytosis and replication in viral factories. In addition, mimiviruses are infected by virophages, defend against them through the mimivirus virophage resistance element (MIMIVIRE) system and have a unique mobilome. Overall, giant viruses of amoebae, including mimiviruses, marseilleviruses, pandoraviruses, pithoviruses, faustoviruses and molliviruses, challenge the definition and classification of viruses, and have increasingly been detected in humans.

A bioinformatics approach reveals seven nearly-complete RNA-virus genomes in bivalve RNA-seq data

Viral metagenomics (viromics) can provide a great contribution in expanding the knowledge of viruses and the relationship with their hosts. Viromic studies on marine organisms are still at a very early stage and only little efforts have been spent in the identification of viruses associated to marine invertebrates to date, leaving the complexity of marine viromes associated to bivalve hosts almost completely unexplored. However, the potential use of viromic approaches in the management of viral diseases affecting aquacultured species has been recently evidenced by the flourishing of studies on the Ostreid herpesvirus type-1, which has been associated with bivalve mortality events. Herein we discuss an effective pipeline to retrieve and reconstruct nearly complete and previously unreported viral genomes from existing host RNA-seq data. As a case study, we report the identification of seven RNA-virus genomes within the frame of a highly diversified viral community that characterizes both Crassostrea gigas and Mytilus galloprovincialis samples collected from the lagoon of Goro (Italy).

A new marseillevirus isolated in Southern Brazil from Limnoperna fortunei

Members of the family Marseilleviridae are giant viruses that have the ability to infect amoebas. Such viruses were initially described in 2009. Since then, this family has grown, and diverse members have been found in different environments and geographic locations. Previous phylogenetic analyses suggested the existence of four marseillevirus lineages. A fourth lineage was described with the discovery of the Brazilian marseillevirus (BrMr), isolated from Pampulha Lake, Brazil. Here we describe the isolation and characterization of the Golden marseillevirus (GMar), a new marseillevirus isolated from golden mussels (Limnoperna fortunei) in South of Brazil. This new representative of Marseilleviridae has circular, double-stranded (dsDNA) that contains 360, 610 base pairs and encodes 483 open read frames (ORFs). The complete virus genome was sequenced and phylogenic analyses indicated clear differences between this virus and other marseilleviruses. In addition, this is the only marseillevirus so far that has been isolated from mussels, and this report expands the diversity of environments from which giant viruses could be recovered.

Mimiviruses: Replication, Purification, and Quantification

The aim of this protocol is to describe the replication, purification, and titration of mimiviruses. These viruses belong to the Mimiviridae family, the first member of which was isolated in 1992 from a cooling tower water sample collected during an outbreak of pneumonia in a hospital in Bradford, England. In recent years, several new mimiviruses have been isolated from different environmental conditions. These giant viruses are easily replicated in amoeba of the Acanthamoeba genus, its natural host. Mimiviruses present peculiar features that make them unique viruses, such as the particle and genome size and the genome's complexity. The discovery of these viruses rekindled discussions about their origin and evolution, and the genetic and structural complexity opened up a new field of study. Here, we describe some methods utilized for mimiviruses replication, purification, and titration. © 2016 by John Wiley & Sons, Inc.

The role of giant viruses of amoebas in humans

Since 2003, dozens of giant viruses that infect amoebas (GVA), including mimiviruses and marseilleviruses, have been discovered. These giants appear to be common in our biosphere. From the onset, their presence and possible pathogenic role in humans have been serendipitously observed or investigated using a broad range of technological approaches, including culture, electron microscopy, serology and various techniques based on molecular biology. The link between amoebal mimiviruses and pneumonia has been the most documented, with findings that fulfill several of the criteria considered as proof of viral disease causation. Regarding marseilleviruses, they have been mostly described in asymptomatic persons, and in a lymph node adenitis. The presence and impact of GVA in humans undoubtedly deserve further investigation in medicine.

Persistent virus and addiction modules: an engine of symbiosis

The giant DNA viruses are highly prevalent and have a particular affinity for the lytic infection of unicellular eukaryotic host. The giant viruses can also be infected by inhibitory virophage which can provide lysis protection to their host. The combined protective and destructive action of such viruses can define a general model (PD) of virus-mediated host survival. Here, I present a general model for role such viruses play in the evolution of host symbiosis. By considering how virus mixtures can participate in addiction modules, I provide a functional explanation for persistence of virus derived genetic 'junk' in their host genomic habitats.

Infection and Proliferation of Giant Viruses in Amoeba Cells

Acanthamoeba polyphaga mimivirus, the first discovered giant virus with genome size and particle size much larger than previously discovered viruses, possesses several genes for translation and CRISPER Cas system-like defense mechanism against virophages, which co-infect amoeba cells with the giant virus and which inhibit giant virus proliferation. Mimiviruses infect amoeba cells by phagocytosis and release their DNA into amoeba cytoplasm through their stargate structure. After infection, giant virion factories (VFs) form in amoeba cytoplasm, followed by DNA replication and particle formation at peripheral regions of VF. Marseilleviruses, the smallest giant viruses, infect amoeba cells by phagocytosis or endocytosis, form larger VF than Mimivirus's VF in amoeba cytoplasm, and replicate their particles. Pandoraviruses found in 2013 have the largest genome size and particle size among all viruses ever found. Pandoraviruses infect amoeba cells by phagocytosis and release their DNA into amoeba cytoplasm through their mouth-like apical pores. The proliferation of Pandoraviruses occurs along with nucleus disruption. New virions form at the periphery of the region formerly occupied by the amoeba cell nucleus.

The Autonomous Glycosylation of Large DNA Viruses

Glycosylation of surface molecules is a key feature of several eukaryotic viruses, which use the host endoplasmic reticulum/Golgi apparatus to add carbohydrates to their nascent glycoproteins. In recent years, a newly discovered group of eukaryotic viruses, belonging to the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) group, was shown to have several features that are typical of cellular organisms, including the presence of components of the glycosylation machinery. Starting from initial observations with the chlorovirus PBCV-1, enzymes for glycan biosynthesis have been later identified in other viruses; in particular in members of the Mimiviridae family. They include both the glycosyltransferases and other carbohydrate-modifying enzymes and the pathways for the biosynthesis of the rare monosaccharides that are found in the viral glycan structures. These findings, together with genome analysis of the newly-identified giant DNA viruses, indicate that the presence of glycogenes is widespread in several NCLDV families. The identification of autonomous viral glycosylation machinery leads to many questions about the origin of these pathways, the mechanisms of glycan production, and eventually their function in the viral replication cycle. The scope of this review is to highlight some of the recent results that have been obtained on the glycosylation systems of the large DNA viruses, with a special focus on the enzymes involved in nucleotide-sugar production.

Isolation of new Brazilian giant viruses from environmental samples using a panel of protozoa

The Megavirales are a newly described order capable of infecting different types of eukaryotic hosts. For the most part, the natural host is unknown. Several methods have been used to detect these viruses, with large discrepancies between molecular methods and co-cultures. To isolate giant viruses, we propose the use of different species of amoeba as a cellular support. The aim of this work was to isolate new Brazilian giant viruses by comparing the protozoa Acanthamoeba castellanii, A. polyphaga, A. griffini, and Vermamoeba vermiformis (VV) as a platform for cellular isolation using environmental samples. One hundred samples were collected from 3 different areas in September 2014 in the Pampulha lagoon of Belo Horizonte city, Minas Gerais, Brazil. PCR was used to identify the isolated viruses, along with hemacolor staining, labelling fluorescence and electron microscopy. A total of 69 viruses were isolated. The highest ratio of isolation was found in A. polyphaga (46.38%) and the lowest in VV (0%). Mimiviruses were the most frequently isolated. One Marseillevirus and one Pandoravirus were also isolated. With Brazilian environmental samples, we demonstrated the high rate of lineage A mimiviruses. This work demonstrates how these viruses survive and circulate in nature as well the differences between protozoa as a platform for cellular isolation.

Mimivirus Fibrils Are Important for Viral Attachment to the Microbial World by a Diverse Glycoside Interaction Repertoire

Acanthamoeba polyphaga mimivirus (APMV) is a giant virus from the Mimiviridae family. It has many unusual features, such as a pseudoicosahedral capsid that presents a starfish shape in one of its vertices, through which the ∼ 1.2-Mb double-stranded DNA is released. It also has a dense glycoprotein fibril layer covering the capsid that has not yet been functionally characterized. Here, we verified that although these structures are not essential for viral replication, they are truly necessary for viral adhesion to amoebae, its natural host. In the absence of fibrils, APMV had a significantly lower level of attachment to the Acanthamoeba castellanii surface. This adhesion is mediated by glycans, specifically, mannose and N-acetylglucosamine (a monomer of chitin and peptidoglycan), both of which are largely distributed in nature as structural components of several organisms. Indeed, APMV was able to attach to different organisms, such as Gram-positive bacteria, fungi, and arthropods, but not to Gram-negative bacteria. This prompted us to predict that (i) arthropods, mainly insects, might act as mimivirus dispersers and (ii) by attaching to other microorganisms, APMV could be ingested by amoebae, leading to the successful production of viral progeny. To date, this mechanism has never been described in the virosphere.

IMPORTANCE

APMV is a giant virus that is both genetically and structurally complex. Its size is similar to that of small bacteria, and it replicates inside amoebae. The viral capsid is covered by a dense glycoprotein fibril layer, but its function has remained unknown, until now. We found that the fibrils are not essential for mimivirus replication but that they are truly necessary for viral adhesion to the cell surface. This interaction is mediated by glycans, mainly N-acetylglucosamine. We also verified that APMV is able to attach to bacteria, fungi, and arthropods. This indicates that insects might act as mimivirus dispersers and that adhesion to other microorganisms could facilitate viral ingestion by amoebae, a mechanism never before described in the virosphere.

Pan-Genome Analysis of Brazilian Lineage A Amoebal Mimiviruses

Since the recent discovery of Samba virus, the first representative of the family Mimiviridae from Brazil, prospecting for mimiviruses has been conducted in different environmental conditions in Brazil. Recently, we isolated using Acanthamoeba sp. three new mimiviruses, all of lineage A of amoebal mimiviruses: Kroon virus from urban lake water; Amazonia virus from the Brazilian Amazon river; and Oyster virus from farmed oysters. The aims of this work were to sequence and analyze the genome of these new Brazilian mimiviruses (mimi-BR) and update the analysis of the Samba virus genome. The genomes of Samba virus, Amazonia virus and Oyster virus were 97%–99% similar, whereas Kroon virus had a low similarity (90%–91%) with other mimi-BR. A total of 3877 proteins encoded by mimi-BR were grouped into 974 orthologous clusters. In addition, we identified three new ORFans in the Kroon virus genome. Additional work is needed to expand our knowledge of the diversity of mimiviruses from Brazil, including if and why among amoebal mimiviruses those of lineage A predominate in the Brazilian environment.

A Mimivirus Enzyme that Participates in Viral Entry

Mimivirus was initially identified as a bacterium because its dense, 125-nm-long fibers stained Gram-positively. These fibers probably play a role during the infection of some host cells. The normal hosts of Mimivirus are unknown, but in the laboratory Mimivirus is usually propagated in amoeba. The structure of R135, a major component of the fibrous outer layer of Mimivirus, has been determined to 2-Å resolution. The protein's structure is similar to that of members of the glucose-methanol-choline oxidoreductase family, which have an N-terminal FAD binding domain and a C-terminal substrate recognition domain. The closest homolog to R135 is an aryl-alcohol oxidase that participates in lignin biodegradation of plant cell walls. Thus R135 might participate in the degradation of their normal hosts, including some lignin-containing algae.