Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54

Conserved marseilleviruses harboring diverse antibiotic resistance genes isolated from the Yangtze river Delta and the Pearl river delta, China

Marseilleviruses are a group of double-stranded DNA viruses infecting Acanthamoeba within the phylum Nucleocytoviricota and are ubiquitous in water and soil globally. Here, we report six strains of marseilleviruses isolated from environmental samples in the Yangtze River Delta and the Pearl River Delta, China. Viral particles exhibited icosahedral shaped capsids measuring about 220 ~ 240 nm in diameter. Based on stability assays, viral particles were halotolerant and acid-tolerant, but sensitive to chloroform and high temperature. Genomics and phylogenetic analyses showed that these strains were highly conserved compared with other reported marseilleviruses. Diverse members of the small multidrug resistance (SMR) family of transporter, which is a type of antibiotics resistance gene (ARG) and contribute to the feature of antibiotic resistance in bacteria, to our best knowledge, are firstly described in Marseilleviridae. The alignments of primary structures and in-silico tertiary structures reveal structural and potential functional similarity between giant viral and bacterial SMR, suggesting a possible role in viruses' interaction with antibiotics. The biological properties of marseillevirus and the discovery of viral SMR provide insight in the external and intracellular environment fitness of these large amoeba-infecting viruses.

Investigations into the Diversity and Distribution of tRNA and Phylogenetics of Translation Factors in Amoebozoa-Infecting Nucleocytoviricota

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 the genome, except in Tupanviruses and Yasmineviruses, where most tRNAs are clustered in specific genomic islands. The tRNAs in giant viruses often contain introns, with 73.1% of the genomes exhibiting at least one intronic region in these genes. Codon usage bias (CUB) analysis of various giant viruses revealed at least two distinct patterns of codon preferences among closely related viruses. We did not observe a clear correlation between the presence of tRNAs and CUB in giant viruses. Due to the limited size of these genes, we could not confidently investigate their phylogenetic relationships. However, phylogenetic analysis of TFs found in giant viruses often position these viruses as sister groups or embedded between different eukaryotic taxa with high statistical support. Overall, our findings reinforce the complexity of key components of the translation apparatus in different members of Nucleocytoviricota isolated from different regions of Earth.

20 years of research on giant viruses

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 subsequent discovery of viruses with intermediate virion and genome sizes gradually re-established a continuum between the smallest and largest viruses within the phylum Nucleocytoviricota.

A giant virus infecting the amoeboflagellate Naegleria

Giant 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 naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.

The consequences of viral infection on protists

Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.

Taxonomic update for giant viruses in the order Imitervirales (phylum Nucleocytoviricota)

Large DNA viruses in the phylum Nucleocytoviricota, sometimes referred to as "giant viruses" owing to their large genomes and virions, have been the subject of burgeoning interest over the last decade. Here, we describe recently adopted taxonomic updates for giant viruses within the order Imitervirales. The families Allomimiviridae, Mesomimiviridae, and Schizomimiviridae have been created to accommodate the increasing diversity of mimivirus relatives that have sometimes been referred to in the literature as "extended Mimiviridae". In addition, the subfamilies Aliimimivirinae, Megamimivirinae, and Klosneuvirinae have been established to refer to subgroups of the Mimiviridae. Binomial names have also been adopted for all recognized species in the order. For example, Acanthamoeba polyphaga mimivirus is now classified in the species Mimivirus bradfordmassiliense.

Novel Virus Identification through Metagenomics: A Systematic Review

Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.

Giant Viruses as a Source of Novel Enzymes for Biotechnological Application

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, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.

The Astounding World of Glycans from Giant Viruses

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.

Giant virus biology and diversity in the era of genome-resolved metagenomics

The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.

Amoebae: Hiding in Plain Sight: Unappreciated Hosts for the Very Large Viruses

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 new viruses with exciting details about novel viral biology. Through distinct isolation techniques and metagenomics, the diversity and complexity of giant viruses have astonished the scientific community. Here, we discuss the latest findings on amoeba viruses and how using these single-celled organisms as hosts has revealed entities that have remained hidden in plain sight for ages.

Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Diversity of Giant Viruses Infecting Vermamoeba vermiformis

The discovery of Acanthamoeba polyphaga mimivirus in 2003 using the free-living amoeba Acanthamoeba polyphaga caused a paradigm shift in the virology field. Twelve years later, using another amoeba as a host, i.e., Vermamoeba vermiformis, novel isolates of giant viruses have been discovered. This amoeba–virus relationship led scientists to study the evolution of giant viruses and explore the origins of eukaryotes. The purpose of this article is to review all the giant viruses that have been isolated from Vermamoeba vermiformis, compare their genomic features, and report the influence of these viruses on the cell cycle of their amoebal host. To date, viruses putatively belonging to eight different viral taxa have been described: 7 are lytic and 1 is non-lytic. The comparison of giant viruses infecting Vermamoeba vermiformis has suggested three homogenous groups according to their size, the replication time inside the host cell, and the number of encoding tRNAs. This approach is an attempt at determining the evolutionary origins and trajectories of the virus; therefore, more giant viruses infecting Vermamoeba must be discovered and studied to create a comprehensive knowledge on these intriguing biological entities.