The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

Gorbalenya, Alexander E.; Krupovìč, Mart; Mushegian, Arcady; Kropinski, Andrew M.; Siddell, Stuart G.; Varsani, Arvind; Adams, Michael J.; Davison, Andrew J.; Dutilh, Bas E.; Harrach, Balázs; Harrison, Robert L.; Junglen, Sandra; King, Andrew M. Q.; Knowles, Nick J.; Lefkowitz, Elliot J.; Nibert, Max L.; Rubino, Luisa; Sabanadzovic, Sead; Sanfaçon, Hélène; Simmonds, Peter; Walker, Peter; Zerbini, F. Murilo; Kuhn, Jens H.

doi:10.1038/s41564-020-0709-x

Cited by 205 publications

(140 citation statements)

References 46 publications

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“…The Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs) are a group of double-stranded DNA viruses of eukaryotes that was established two decades ago [ 1 ]. Analyses of few widely distributed core genes suggest a monophyletic origin of NCLDVs [ 1 , 2 ], which have been formally named Nucleocytoviricota within the virus kingdom Bamfordvirae (realm Varidnaviria ) by the ICTV [ 3 , 4 ]. For their extraordinary genome size (up to 2.8 Mb [ 5 ]) and virion size (up to 2.5 μm [ 6 ]) among all viruses, NCLDVs are commonly known as giant viruses [ 7 , 8 , 9 , 10 , 11 ], which reflects their distinction from traditionally defined viruses [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Host Range and Coding Potential of Eukaryotic Giant Viruses

Sun

Yang

Kao

et al. 2020

Viruses

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Giant viruses are a group of eukaryotic double-stranded DNA viruses with large virion and genome size that challenged the traditional view of virus. Newly isolated strains and sequenced genomes in the last two decades have substantially advanced our knowledge of their host diversity, gene functions, and evolutionary history. Giant viruses are now known to infect hosts from all major supergroups in the eukaryotic tree of life, which predominantly comprises microbial organisms. The seven well-recognized viral clades (taxonomic families) have drastically different host range. Mimiviridae and Phycodnaviridae, both with notable intrafamilial genome variation and high abundance in environmental samples, have members that infect the most diverse eukaryotic lineages. Laboratory experiments and comparative genomics have shed light on the unprecedented functional potential of giant viruses, encoding proteins for genetic information flow, energy metabolism, synthesis of biomolecules, membrane transport, and sensing that allow for sophisticated control of intracellular conditions and cell-environment interactions. Evolutionary genomics can illuminate how current and past hosts shape viral gene repertoires, although it becomes more obscure with divergent sequences and deep phylogenies. Continued works to characterize giant viruses from marine and other environments will further contribute to our understanding of their host range, coding potential, and virus-host coevolution.

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Section: Introductionmentioning

confidence: 99%

Host Range and Coding Potential of Eukaryotic Giant Viruses

Sun

Yang

Kao

et al. 2020

Viruses

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“…Among these genes, some code for unexpected functions for a virus, the most surprising being homologues to cellular histones [1,2]. Viruses from this family belong to the NCLDVs (for nucleocytoplasmic large DNA viruses), i.e., the Nucleocytoviricota phylum, according to the latest International Committee on Taxonomy of Viruses (ICTV) classification [13,14]. Marseilleviruses' replication cycles start with their phagocytosis by the Acanthamoeba host.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes

Blanca

Christo-Foroux

Rigou

et al. 2020

Viruses

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Marseilleviridae members are large dsDNA viruses with icosahedral particles 250 nm in diameter infecting Acanthamoeba. Their 340 to 390 kb genomes encode 450 to 550 protein-coding genes. Since the discovery of marseillevirus (the prototype of the family) in 2009, several strains were isolated from various locations, among which 13 are now fully sequenced. This allows the organization of their genomes to be deciphered through comparative genomics. Here, we first experimentally demonstrate that the Marseilleviridae genomes are circular. We then acknowledge a strong bias in sequence conservation, revealing two distinct genomic regions. One gathers most Marseilleviridae paralogs and has undergone genomic rearrangements, while the other, enriched in core genes, exhibits the opposite pattern. Most of the genes whose protein products compose the viral particles are located in the conserved region. They are also strongly biased toward a late gene expression pattern. We finally discuss the potential advantages of Marseilleviridae having a circular genome, and the possible link between the biased distribution of their genes and the transcription as well as DNA replication mechanisms that remain to be characterized.

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“…Next, we tested whether SMALPs from both Gram-positive B. subtilis and Gram-negative E. coli bacteria inhibit the lytic activity of three model phages ( Table 1 ). As model phages, we selected one member from each of the three major International Committee on the Taxonomy of Viruses-recognized families of tailed phages ( Myo -, Podo -, and Siphoviridae ) ( 35 , 36 ), as the distinct morphologies of these families differentiates their binding mechanisms ( 1 ). The three model phages, Podoviridae Bacillus phage φ29, Siphoviridae Escherichia phage λ and Myoviridae Escherichia phage T4, each bind to distinct receptor molecules.…”

Section: Resultsmentioning

confidence: 99%

Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions

Jonge

Sibinga

Boright

et al. 2020

J Virol

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The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. As receptor-phage interactions are crucial to successful infections, they are major determinants of phage host-range and by extension of the broader effects that phages have on bacterial communities. Many receptor molecules, particularly membrane proteins, are difficult to isolate because their stability is supported by their native membrane environments. Styrene maleic acid lipid particles (SMALPs), a recent advance in membrane protein studies, are the result of membrane solubilizations by styrene maleic acid (SMA) co-polymer chains. SMALPs thereby allow for isolation of membrane proteins while maintaining their native environment. Here, we explore SMALPs as a tool to isolate and study phage-receptor interactions. We show that SMALPs produced from taxonomically distant bacterial membranes allow for receptor-specific decrease of viable phage counts of several model phages that span the three largest phage families. After characterizing the effects of incubation time and SMALP concentration on the activity of three distinct phages, we present evidence that the interaction between two model phages and SMALPs is specific to bacterial species and the phage receptor molecule. These interactions additionally lead to DNA ejection by nearly all particles at high phage titers. We conclude that SMALPs are a potentially highly useful tool for phage host-interaction studies. IMPORTANCE Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions, and furthermore show that they lead to genome ejection by the phage. Combined, the results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions.

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The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

Cited by 205 publications

References 46 publications

Host Range and Coding Potential of Eukaryotic Giant Viruses

Host Range and Coding Potential of Eukaryotic Giant Viruses

Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes

Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions

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