The atomic structure of the bluetongue virus core

Potential of Using Capripoxvirus Vectored Vaccines Against Arboviruses in Sheep, Goats, and Cattle

The genus capripoxvirus consists of sheeppox virus, goatpox virus, and lumpy skin disease virus, which affect sheep, goats, and cattle, respectively. Together capripoxviruses cause significant economic losses to the sheep, goat, and cattle industry where these diseases are present. These diseases have spread into previously free bordering regions most recently demonstrated with the spread of lumpy skin disease virus into the Middle East, some Eastern European countries, and Russia. This recent spread has highlighted the transboundary nature of these diseases. To control lumpy skin disease virus, live attenuated viral vaccines are used in endemic countries as well as in response to an outbreak. For sheeppox and goatpox, live attenuated viral vaccines are used in endemic countries; these diseases can also be contained through slaughter of infected animals to stamp out the disease. The thermostability, narrow host range, and ability of capripoxviruses to express a wide variety of antigens make capripoxviruses ideal vectors. The ability to immunize animals against multiple diseases simultaneously increases vaccination efficiency by decreasing the number of vaccinations required. Additionally, the use of capripoxvirus vectored vaccines allows the possibility of differentiating infected from vaccinated animals. Arboviruses such as bluetongue virus and Rift Valley fever viruses are also responsible for significant economic losses in endemic countries. In the case of Rift Valley fever virus, vaccination is not routinely practiced unless there is an outbreak making vaccination not as effective, therefore, incorporating Rift Valley fever vaccination into routine capripoxvirus vaccination would be highly beneficial. This review will discuss the potential of using capripoxvirus as a vector expressing protective arboviral antigens.

Hidden symmetry of the anomalous bluetongue virus capsid and its role in the infection process

Clear understanding of the principles that control the arrangement of proteins and their self-assembly into viral shells is very important for the development of antiviral strategies. Here we consider the structural peculiarities and hidden symmetry of the anomalous bluetongue virus (BTV) capsid. Each of its three concentric shells violates the paradigmatic geometrical model of Caspar and Klug, which is otherwise well suited to describe most of the known icosahedral viral shells. As we show, three icosahedral spherical lattices, which are commensurate with each other and possess locally hexagonal (primitive or honeycomb) order, underlie the proteinaceous shells of the BTV capsid. This interpretation of the multishelled envelope allows us to discuss the so-called "symmetry mismatch" between its layers. We also analyze the structural stability of the considered spherical lattices on the basis of the classical theory of spherical packing and relate the proximity of the outer spherical lattice to destabilization with the fact that during infection of the cell VP2 trimers are detached from the surface of the BTV capsid. An electrostatic mechanism that can assist in this detachment is discussed in detail.

African Horse Sickness: A Review of Current Understanding and Vaccine Development

African horse sickness is a devastating disease that causes great suffering and many fatalities amongst horses in sub-Saharan Africa. It is caused by nine different serotypes of the orbivirus African horse sickness virus (AHSV) and it is spread by Culicoid midges. The disease has significant economic consequences for the equine industry both in southern Africa and increasingly further afield as the geographic distribution of the midge vector broadens with global warming and climate change. Live attenuated vaccines (LAV) have been used with relative success for many decades but carry the risk of reversion to virulence and/or genetic re-assortment between outbreak and vaccine strains. Furthermore, the vaccines lack DIVA capacity, the ability to distinguish between vaccine-induced immunity and that induced by natural infection. These concerns have motivated interest in the development of new, more favourable recombinant vaccines that utilize viral vectors or are based on reverse genetics or virus-like particle technologies. This review summarizes the current understanding of AHSV structure and the viral replication cycle and also evaluates existing and potential vaccine strategies that may be applied to prevent or control the disease.

In situ structures of RNA-dependent RNA polymerase inside bluetongue virus before and after uncoating

Bluetongue virus (BTV), a major threat to livestock, is a multilayered, nonturreted member of the Reoviridae, a family of segmented dsRNA viruses characterized by endogenous RNA transcription through an RNA-dependent RNA polymerase (RdRp). To date, the structure of BTV RdRp has been unknown, limiting our mechanistic understanding of BTV transcription and hindering rational drug design effort targeting this essential enzyme. Here, we report the in situ structures of BTV RdRp VP1 in both the triple-layered virion and double-layered core, as determined by cryo-electron microscopy (cryoEM) and subparticle reconstruction. BTV RdRp has 2 unique motifs not found in other viral RdRps: a fingernail, attached to the conserved fingers subdomain, and a bundle of 3 helices: 1 from the palm subdomain and 2 from the N-terminal domain. BTV RdRp VP1 is anchored to the inner surface of the capsid shell via 5 asymmetrically arranged N termini of the inner capsid shell protein VP3A around the 5-fold axis. The structural changes of RdRp VP1 and associated capsid shell proteins between BTV virions and cores suggest that the detachment of the outer capsid proteins VP2 and VP5 during viral entry induces both global movements of the inner capsid shell and local conformational changes of the N-terminal latch helix (residues 34 to 51) of 1 inner capsid shell protein VP3A, priming RdRp VP1 within the capsid for transcription. Understanding this mechanism in BTV also provides general insights into RdRp activation and regulation during viral entry of other multilayered, nonturreted dsRNA viruses.

A low-passage insect-cell isolate of bluetongue virus uses a macropinocytosis-like entry pathway to infect natural target cells derived from the bovine host

Bluetongue virus (BTV) causes an economically important disease in domestic and wildlife ruminants and is transmitted by Culicoides biting midges. In ruminants, BTV has a wide cell tropism that includes endothelial cells of vascular and lymphatic vessels as important cell targets for virus replication, and several cell types of the immune system including monocytes, macrophages and dendritic cells. Thus, cell-entry represents a particular challenge for BTV as it infects many different cell types in widely diverse vertebrate and invertebrate hosts. Improved understanding of BTV cell-entry could lead to novel antiviral approaches that can block virus transmission from cell to cell between its invertebrate and vertebrate hosts. Here, we have investigated BTV cell-entry using endothelial cells derived from the natural bovine host (BFA cells) and purified whole virus particles of a low-passage, insect-cell isolate of a virulent strain of BTV-1. Our results show that the main entry pathway for infection of BFA cells is dependent on actin and dynamin, and shares certain characteristics with macropinocytosis. The ability to use a macropinocytosis-like entry route could explain the diverse cell tropism of BTV and contribute to the efficiency of transmission between vertebrate and invertebrate hosts.

Mapping the pH Sensors Critical for Host Cell Entry by a Complex Nonenveloped Virus

Virus entry into a susceptible cell is the first step of infection and a significant point at which infection can be prevented. To enter effectively, viruses must sense the cellular environment and, when appropriate, initiate a series of changes that eventually jettison the protective shell and deposit virus genes into the cytoplasm. Many viruses sense pH, but how this happens and the events that follow are often poorly understood. Here, we address this question for a large multilayered bluetongue virus. We show key residues in outer capsid proteins, a pH-sensing histidine of a zinc finger within the receptor-binding VP2 protein, and certain histidine residues in the membrane-penetrating VP5 protein that detect cellular pH, leading to irreversible changes and propel the virus through the cell membrane. Our data reveal a novel mechanism of cell entry for a nonenveloped virus and highlight mechanisms which may also be used by other viruses.

Bluetongue virus (BTV), in the family Reoviridae, is an insect-borne, double-capsid virus causing hemorrhagic disease in livestock around the world. Here, we elucidate how outer capsid proteins VP2 and VP5 coordinate cell entry of BTV. To identify key functional residues, we used atomic-level structural data to guide mutagenesis of VP2 and VP5 and a series of biological and biochemical approaches, including site-directed mutagenesis, reverse genetics-based virus recovery, expression and characterization of individual recombinant mutant proteins, and various in vitro and in vivo assays. We demonstrate the dynamic nature of the conformational change process, revealing that a unique zinc finger (CCCH) in VP2 acts as the major low pH sensor, coordinating VP2 detachment, subsequently allowing VP5 to sense low pH via specific histidine residues at key positions. We show that single substitution of only certain histidine residues has a lethal effect, indicating that the location of histidine in VP5 is critical to inducing changes in VP5 conformation that facilitates membrane penetration. Further, we show that the VP5 anchoring domain alone recapitulates sensing of low pH. Our data reveal a novel, multiconformational process that overcomes entry barriers faced by this multicapsid nonenveloped virus.

IMPORTANCE Virus entry into a susceptible cell is the first step of infection and a significant point at which infection can be prevented. To enter effectively, viruses must sense the cellular environment and, when appropriate, initiate a series of changes that eventually jettison the protective shell and deposit virus genes into the cytoplasm. Many viruses sense pH, but how this happens and the events that follow are often poorly understood. Here, we address this question for a large multilayered bluetongue virus. We show key residues in outer capsid proteins, a pH-sensing histidine of a zinc finger within the receptor-binding VP2 protein, and certain histidine residues in the membrane-penetrating VP5 protein that detect cellular pH, leading to irreversible changes and propel the virus through the cell membrane. Our data reveal a novel mechanism of cell entry for a nonenveloped virus and highlight mechanisms which may also be used by other viruses.

Half a Century of Research on Membrane-Containing Bacteriophages: Bringing New Concepts to Modern Virology

Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of "viral lineages", postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 1031) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.

IRAM: virus capsid database and analysis resource

IRAM is an online, open access, comprehensive database and analysis resource for virus capsids. The database includes over 200 000 hierarchically organized capsid-associated nucleotide and amino acid sequences, as well as 193 capsids structures of high resolution (1-5 Å). Each capsid's structure includes a data file for capsid domain (PDB), capsid symmetry unit (PDB) and capsid structure information (PSF); these contain capsid structural information that is necessary to run further computational studies. Physicochemical properties analysis is implemented for calculating capsid total charge at given radii and for calculating charge distributions. This resource includes BLASTn and BLASTp tools, which can be applied to compare nucleotide and amino acid sequences. The diverse functionality of IRAM is valuable to researchers because it integrates different aspects of virus capsids via a user-friendly interface. Such data are critical for studying capsid evolution and patterns of conservation. The IRAM database can also provide initial necessary information for the design of synthetic capsids for various biotechnological applications.

An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism

Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric protein) exhibiting icosahedral T = 13 symmetry. Here we describe the construction and structural evaluation of an assembly intermediate of the Rice dwarf virus of the family Reoviridae stalled at the second capsid layer via targeted disruption of the trimer-trimer interaction interface in the second-layer capsid protein. Structural determination was performed by conventional and Zernike/Volta phase-contrast cryoelectron microscopy. The assembly defect second-layer capsid trimers bound exclusively to the outer surface of the innermost capsid layer at the icosahedral 3-fold axis. Furthermore, the second-layer assembly could not proceed without specific inter-trimer interactions. Our results suggest that the correct assembly pathway for second-layer capsid formation is highly controlled at the inter-layer and inter-trimer interactions.

The cap-snatching reaction of yeast L-A double-stranded RNA virus is reversible and the catalytic sites on both Gag and the Gag domain of Gag-Pol are active

The yeast L-A double-stranded RNA virus synthesizes capped transcripts by a unique cap-snatching mechanism in which the m⁷ Gp moiety of host mRNA (donor) is transferred to the diphosphorylated 5' end of the viral transcript (acceptor). This reaction is activated by viral transcription. Here, we show that cap snatching can be reversible. Because only m⁷ Gp is transferred during the reaction, the resulting decapped donor, as expected, retained diphosphates at the 5' end. We also found that the 5' terminal nucleotide of the acceptor needs to be G but not A. Interestingly, the A-initiated molecule when equipped with a cap structure (m⁷ GpppA…) could work as cap donor. Because the majority of host mRNAs in yeast have A after the cap structures at the 5' ends, this finding implies that cap-snatching in vivo is virtually a one-way reaction, in favor of furnishing the viral transcript with a cap. The cap-snatching sites are located on the coat protein Gag and also the Gag domain of Gag-Pol. Here, we demonstrate that both sites are functional, indicating that activation of cap snatching by transcription is not transmitted through the peptide bonding between the Gag and Pol domains of Gag-Pol.

Phase dependent structural perturbation of a robust multicomponent assembled icosahedral array

We report on the assembly of three-fold axially compressed icosahedral arrays of the bowl shaped p-sulfonatocalix[4]arene molecules in the solid-state, intricately bound to dipicolinate and yttrium(iii) ions, with the compression reflected in Hirshfeld surface analyses. Solution studies show dissolution of the icosahedra intact, but with a geometrical rearrangement to regular icosahedra.

Capsid Structure of dsRNA Fungal Viruses

Most fungal, double-stranded (ds) RNA viruses lack an extracellular life cycle stage and are transmitted by cytoplasmic interchange. dsRNA mycovirus capsids are based on a 120-subunit T = 1 capsid, with a dimer as the asymmetric unit. These capsids, which remain structurally undisturbed throughout the viral cycle, nevertheless, are dynamic particles involved in the organization of the viral genome and the viral polymerase necessary for RNA synthesis. The atomic structure of the T = 1 capsids of four mycoviruses was resolved: the L-A virus of Saccharomyces cerevisiae (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). These capsids show structural variations of the same framework, with 60 asymmetric or symmetric homodimers for ScV-L-A and PsV-F, respectively, monomers with a duplicated similar domain for PcV, and heterodimers of two different proteins for RnQV1. Mycovirus capsid proteins (CP) share a conserved α-helical domain, although the latter may carry different peptides inserted at preferential hotspots. Insertions in the CP outer surface are likely associated with enzymatic activities. Within the capsid, fungal dsRNA viruses show a low degree of genome compaction compared to reoviruses, and contain one to two copies of the RNA-polymerase complex per virion.

Generation of infectious RNA complexes in Orbiviruses: RNA-RNA interactions of genomic segments

Viruses with segmented RNA genomes must package the correct number of segments for synthesis of infectious virus particles. Recent studies suggest that the members of the Reoviridae family with segmented double-stranded RNA genomes achieve this challenging task by forming RNA networks of segments prior to their recruitment into the assembling capsid albeit direct evidence is still lacking. Here, we investigated the capability of virus recovery by preformed complexes of ten RNA segments of H Virus (EHDV), a Reoviridae member, by transcribing exact T7 cDNA copies of genomic RNA segments in a single in vitro reaction followed by transfection of mammalian cells. The data obtained was further confirmed by RNA complexes generated from Bluetongue virus, another family member. Formation of RNA complexes was demonstrated by sucrose gradient ultracentrifugation, and RNA-RNA interactions inherent to the formation of the RNA complexes were demonstrated by electrophoretic mobility shift assay. Further, we showed that disruption of RNA complex formation inhibits virus recovery, confirming that recruitment of complete RNA networks is essential for packaging and consequently, virus recovery. This efficient reverse genetics system will allow further understanding of evolutionary relationships of Reoviridae members and may also contribute to development of antiviral molecules.

Extension of Caspar-Klug theory to higher order pentagonal polyhedra

Many viral capsids follow an icosahedral fullerene-like structure, creating a caged polyhedral arrangement built entirely from hexagons and pentagons. Viral capsids consist of capsid proteins,which group into clusters of six (hexamers) or five (pentamers). Although the number of hexamers per capsid varies depending on the capsid size, Caspar-Klug Theory dictates there are exactly twelve pentamers needed to form a closed capsid.However, for a significant number of viruses, including viruses of the Papovaviridae family, the theory doesn’t apply. The anomaly of the Caspar-Klug Theory has raised a new question:“For which Caspar and Klug models can each hexamer be replaced with a pentamer while still following icosahedral symmetry?” This paper proposes an answer to this question by examining icosahedral viral capsid-like structures composed only of pentamers, called pentagonal polyhedra. The analysis shows that pentagonal polyhedra fall in a subclass of T, defined by P ≥ 7 and T = 1( mod 3).

Solubilisation and purification of recombinant bluetongue virus VP7 expressed in a bacterial system

Bluetongue virus (BTV) is an Orbivirus that has a profound economic impact due to direct loss of livestock as well as movement bans in an attempt to prevent the spread of the disease to susceptible areas. BTV VP7, along with VP3, forms the inner capsid core of the virus where it acts as the barrier between the outer layer and the inner core housing the genetic material. Purification of BTV VP7 has proven to be problematic and expensive mainly due to its insolubility is several expression systems. To overcome this, in this paper we present a protocol for the solubilisation of BTV VP7 from inclusion bodies expressed in E.coli, and subsequent purification using nickel affinity chromatography. The purified protein was then characterised using native PAGE, far ultraviolet circular dichroism (far-UV CD) and intrinsic fluorescence and found to have both secondary and tertiary structure even in the presence of 5 M urea. Both tertiary and secondary structure was further shown to be to be maintained at least to 42 °C in 5 M urea.

Hierarchical structure assembly model of rice dwarf virus particle formation

Rice dwarf virus (RDV) of the family Reoviridae and genus Phytoreovirus, is the cause of rice dwarf disease, a major negative effector of rice production throughout East Asia, including Japan. RDV has an icosahedral double-layered shell of approximately 70 nm diameter. The structural proteins constituting the capsid can self-assemble into a correct particle without requiring the help of any external factors in vitro. A total of more than 900 components assemble to make the full particle. A series of structural and functional studies of RDV, including X-ray crystallography and cryo-electron microscopy, suggest a hierarchical self-assembly mechanism involving both homologous and heterologous interactions. As such, systems for the recognition of each component should be essential for particle formation.

Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses

Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3.7 Å resolution of Rosellinia necatrix quadrivirus 1 (RnQV1), a fungal double-stranded (ds)RNA virus. RnQV1, the type species of the family Quadriviridae, has a multipartite genome consisting of four monocistronic segments. Whereas most dsRNA virus capsids are based on dimers of a single protein, the ~450-Å-diameter, T = 1 RnQV1 capsid is built of P2 and P4 protein heterodimers, each with more than 1000 residues. Despite a lack of sequence similarity between the two proteins, they have a similar α-helical domain, the structural signature shared with the lineage of the dsRNA bluetongue virus-like viruses. Domain insertions in P2 and P4 preferential sites provide additional functions at the capsid outer surface, probably related to enzyme activity. The P2 insertion has a fold similar to that of gelsolin and profilin, two actin-binding proteins with a function in cytoskeleton metabolism, whereas the P4 insertion suggests protease activity involved in cleavage of the P2 383-residue C-terminal region, absent in the mature viral particle. Our results indicate that the intimate virus-fungus partnership has altered the capsid genome-protective and/or receptor-binding functions. Fungal virus evolution has tended to allocate enzyme activities to the virus capsid outer surface.

Most fungal RNA viruses are transmitted by cytoplasmic interchange without leaving the host. We report the cryo-electron microscopy structure, at near-atomic resolution, of the double-stranded RNA Rosellinia necatrix quadrivirus 1 (RnQV1); this virus infects the fungus Rosellinia necatrix, a pathogenic ascomycete to a wide range of plants. At difference most dsRNA viruses, whose capsid is made of protein homodimers, RnQV1 is based on a single-shelled lattice built of 60 P2-P4 heterodimers. Despite a lack of sequence similarity, P2 and P4 have a similar α-helical domain, a structural signature shared with the dsRNA virus lineage. In addition to organizing the viral genome and replicative machinery, P2 and P4 have acquired new functions by inserting complex domains in preferential insertion sites. Whereas the P2 insertion domain has a fold like that of actin-binding proteins, the structure of the P4 insertion domain indicates proteolytic activity. Understanding the structure of a fungal virus capsid with enzyme activities could allow its development as nanoreactors for biotechnological application.

Assembly of silver Trigons into a buckyball-like Ag180 nanocage

Buckminsterfullerene (C60) represents a perfect combination of geometry and molecular structural chemistry. It has inspired many creative ideas for building fullerene-like nanopolyhedra. These include other fullerenes, virus capsids, polyhedra based on DNA, and synthetic polynuclear metal clusters and cages. Indeed, the regular organization of large numbers of metal atoms into one highly complex structure remains one of the foremost challenges in supramolecular chemistry. Here we describe the design, synthesis, and characterization of a Ag180 nanocage with 180 Ag atoms as 4-valent vertices (V), 360 edges (E), and 182 faces (F)--sixty 3-gons, ninety 4-gons, twelve 5-gons, and twenty 6-gons--in agreement with Euler's rule V - E + F = 2. If each 3-gon (or silver Trigon) were replaced with a carbon atom linked by edges along the 4-gons, the result would be like C60, topologically a truncated icosahedron, an Archimedean solid with icosahedral (Ih) point-group symmetry. If C60 can be described mathematically as a curling up of a 6.6.6 Platonic tiling, the Ag180 cage can be described as a curling up of a 3.4.6.4 Archimedean tiling. High-resolution electrospray ionization mass spectrometry reveals that {Ag3}n subunits coexist with the Ag180 species in the assembly system before the final crystallization of Ag180, suggesting that the silver Trigon is the smallest building block in assembly of the final cage. Thus, we assign the underlying growth mechanism of Ag180 to the Silver-Trigon Assembly Road (STAR), an assembly path that might be further employed to fabricate larger, elegant silver cages.

Bluetongue virus structure and assembly

Bluetongue virus (BTV) is an insect-vectored emerging pathogen of wild ruminants and livestock in many parts of the world. The virion particle is a complex structure of consecutive layers of protein surrounding a genome of ten double-stranded (ds) RNA segments. BTV has been studied as a model system for large, non-enveloped dsRNA viruses. Several new techniques have been applied to define the virus-encoded enzymes required for RNA replication to provide an order for the assembly of the capsid shell and the protein sequestration required for it. Further, a reconstituted in vitro system has defined the individual steps of the assembly and packaging of the genomic RNA. These findings illuminate BTV assembly and indicate the pathways that related viruses might use to provide an informed starting point for intervention or prevention.

Engineering Recombinant Virus-like Nanoparticles from Plants for Cellular Delivery

Understanding capsid assembly following recombinant expression of viral structural proteins is critical to the design and modification of virus-like nanoparticles for biomedical and nanotechnology applications. Here, we use plant-based transient expression of the Bluetongue virus (BTV) structural proteins, VP3 and VP7, to obtain high yields of empty and green fluorescent protein (GFP)-encapsidating core-like particles (CLPs) from leaves. Single-particle cryo-electron microscopy of both types of particles revealed considerable differences in CLP structure compared to the crystal structure of infection-derived CLPs; in contrast, the two recombinant CLPs have an identical external structure. Using this insight, we exploited the unencumbered pore at the 5-fold axis of symmetry and the absence of encapsidated RNA to label the interior of empty CLPs with a fluorescent bioconjugate. CLPs containing 120 GFP molecules and those containing approximately 150 dye molecules were both shown to bind human integrin via a naturally occurring Arg-Gly-Asp motif found on an exposed loop of the VP7 trimeric spike. Furthermore, fluorescently labeled CLPs were shown to interact with a cell line overexpressing the surface receptor. Thus, BTV CLPs present themselves as a useful tool in targeted cargo delivery. These results highlight the importance of detailed structural analysis of VNPs in validating their molecular organization and the value of such analyses in aiding their design and further modification.

Genetic characterization of the non-structural protein-3 gene of bluetongue virus serotype-2 isolate from India

AIM

Sequence analysis and phylogenetic studies based on non-structural protein-3 (NS3) gene are important in understanding the evolution and epidemiology of bluetongue virus (BTV). This study was aimed at characterizing the NS3 gene sequence of Indian BTV serotype-2 (BTV2) to elucidate its genetic relationship to global BTV isolates.

MATERIALS AND METHODS

The NS3 gene of BTV2 was amplified from infected BHK-21 cell cultures, cloned and subjected to sequence analysis. The generated NS3 gene sequence was compared with the corresponding sequences of different BTV serotypes across the world, and a phylogenetic relationship was established.

RESULTS

The NS3 gene of BTV2 showed moderate levels of variability in comparison to different BTV serotypes, with nucleotide sequence identities ranging from 81% to 98%. The region showed high sequence homology of 93-99% at amino acid level with various BTV serotypes. The PPXY/PTAP late domain motifs, glycosylation sites, hydrophobic domains, and the amino acid residues critical for virus-host interactions were conserved in NS3 protein. Phylogenetic analysis revealed that BTV isolates segregate into four topotypes and that the Indian BTV2 in subclade IA is closely related to Asian and Australian origin strains.

CONCLUSION

Analysis of the NS3 gene indicated that Indian BTV2 isolate is closely related to strains from Asia and Australia, suggesting a common origin of infection. Although the pattern of evolution of BTV2 isolate is different from other global isolates, the deduced amino acid sequence of NS3 protein demonstrated high molecular stability.

Double-stranded RNA virus outer shell assembly by bona fide domain-swapping

Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution.

Double-shelled bacteriophage φ6 is a well-studied model system used to understand assembly of dsRNA viruses. Here the authors report a near-atomic resolution cryo-EM structure of φ6 and propose a model for the structural transitions occurring in the outer shell during genome packaging.

Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification

The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new additions, suggesting it could be a useful supplement to experimental approaches and to aid qualitative assessment of viral diversity in metagenome samples.

Exploiting virus-like particles as innovative vaccines against emerging viral infections

Emerging viruses pose a major threat to humans and livestock with global public health and economic burdens. Vaccination remains an effective tool to reduce this threat, and yet, the conventional cell culture often fails to produce sufficient vaccine dose. As an alternative to cell-culture based vaccine, virus-like particles (VLPs) are considered as a highpriority vaccine strategy against emerging viruses. VLPs represent highly ordered repetitive structures via macromolecular assemblies of viral proteins. The particulate nature allows efficient uptake into antigen presenting cells stimulating both innate and adaptive immune responses towards enhanced vaccine efficacy. Increasing research activity and translation opportunity necessitate the advances in the design of VLPs and new bioprocessing modalities for efficient and cost-effective production. Herein, we describe major achievements and challenges in this endeavor, with respect to designing strategies to harnessing the immunogenic potential, production platforms, downstream processes, and some exemplary cases in developing VLP-based vaccines.

A Dual Laser Scanning Confocal and Transmission Electron Microscopy Analysis of the Intracellular Localization, Aggregation and Particle Formation of African Horse Sickness Virus Major Core Protein VP7

The bulk of the major core protein VP7 in African horse sickness virus (AHSV) self-assembles into flat, hexagonal crystalline particles in a process appearing unrelated to viral replication. Why this unique characteristic of AHSV VP7 is genetically conserved, and whether VP7 aggregation and particle formation have an effect on cellular biology or the viral life cycle, is unknown. Here we investigated how different small peptide and enhanced green fluorescent protein (eGFP) insertions into the VP7 top domain affected VP7 localization, aggregation, and particle formation. This was done using a dual laser scanning confocal and transmission electron microscopy approach in conjunction with analyses of the solubility, aggregation, and fluorescence profiles of the proteins. VP7 top domain modifications did not prevent trimerization, or intracellular trafficking, to one or two discrete sites in the cell. However, modifications that resulted in a misfolded and insoluble VP7-eGFP component blocked trafficking, and precluded protein accumulation at a single cellular site, perhaps by interfering with normal trimer-trimer interactions. Furthermore, the modifications disrupted the stable layering of the trimers into characteristic AHSV VP7 crystalline particles. It was concluded that VP7 trafficking is driven by a balance between VP7 solubility, trimer forming ability, and trimer-trimer interactions.

[A plasmid-based reverse genetics system for rotaviruses]

Rotavirus (RV), a non-enveloped icosahedral virus containing eleven gene segments of double-stranded RNA, is the leading cause of severe, acute diarrhea among infants and young children worldwide. Safe and effective rotavirus vaccines have been available since 2006, and have markedly reduced the number of deaths by severe gastroenteritis. However, rotaviruses are still responsible for approximately 200,000 deaths annually worldwide. Reverse genetics systems for the manipulation of viral genomes are a powerful approach for studying viral replication and pathogenesis, and for developing vaccines and viral vectors. The understanding of the molecular mechanisms underlying RV pathogenesis, or development of next generation vaccines, has been hampered by the lack of a complete reverse genetics system. Recently, we developed a novel reverse genetics system which enabled recovery of recombinant RVs entirely from cloned cDNAs. This new strategy requires co-expression of a small transmembrane protein that accelerates cell-to-cell fusion and vaccinia virus capping enzyme. In this review, the strategies and history of the development of reverse genetics systems for the family Reoviridae are described.

Bluetongue Virus: From BTV-1 to BTV-27

Bluetongue virus (BTV) is the type species of genus Orbivirus within family Reoviridae. Bluetongue virus is transmitted between its ruminant hosts by the bite of Culicoides spp. midges. Severe BT cases are characterized by symptoms including hemorrhagic fever, particularly in sheep, loss of productivity, and death. To date, 27 BTV serotypes have been documented. These include novel isolates of atypical BTV, which have been almost fully characterized using deep sequencing technologies and do not rely on Culicoides vectors for their transmission among hosts. Due to its high economic impact, BT is an Office International des Epizooties (OIE) listed disease that is strictly controlled in international commercial exchanges. During the 20th century, BTV has been endemic in subtropical regions. In the last 15 years, novel strains of nine "typical" BTV serotypes (1, 2, 4, 6, 8, 9, 11, 14, and 16) invaded Europe, some of which caused disease in naive sheep and unexpectedly in bovine herds (particularly serotype 8). Over the past few years, three novel "atypical" serotypes (25-27) were characterized during sequencing studies of animal samples from Switzerland, Kuwait, and France, respectively. Classical serotype-specific inactivated vaccines, although expensive, were very successful in controlling outbreaks as shown with the northern European BTV-8 outbreak which started in the summer of 2006. Technological jumps in deep sequencing methodologies made rapid full characterizations of BTV genome from isolates/tissues feasible. Next-generation sequencing (NGS) approaches are powerful tools to study the variability of BTV genomes on a fine scale. This paper provides information on how NGS impacted our knowledge of the BTV genome.

Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1

Most double-stranded RNA (dsRNA) viruses are transcribed and replicated in a specialized icosahedral capsid with a T=1 lattice consisting of 60 asymmetric capsid protein (CP) dimers. These capsids help to organize the viral genome and replicative complex(es). They also act as molecular sieves that isolate the virus genome from host defense mechanisms and allow the passage of nucleotides and viral transcripts. Rosellinia necatrix quadrivirus 1 (RnQV1), the type species of the family Quadriviridae, is a dsRNA fungal virus with a multipartite genome consisting of four monocistronic segments (segments 1 to 4). dsRNA-2 and dsRNA-4 encode two CPs (P2 and P4, respectively), which coassemble into ∼450-Å-diameter capsids. We used three-dimensional cryo-electron microscopy combined with complementary biophysical techniques to determine the structures of RnQV1 virion strains W1075 and W1118. RnQV1 has a quadripartite genome, and the capsid is based on a single-shelled T=1 lattice built of P2-P4 dimers. Whereas the RnQV1-W1118 capsid is built of full-length CP, P2 and P4 of RnQV1-W1075 are cleaved into several polypeptides, maintaining the capsid structural organization. RnQV1 heterodimers have a quaternary organization similar to that of homodimers of reoviruses and other dsRNA mycoviruses. The RnQV1 capsid is the first T=1 capsid with a heterodimer as an asymmetric unit reported to date and follows the architectural principle for dsRNA viruses that a 120-subunit capsid is a conserved assembly that supports dsRNA replication and organization.

IMPORTANCE

Given their importance to health, members of the family Reoviridae are the basis of most structural and functional studies and provide much of our knowledge of dsRNA viruses. Analysis of bacterial, protozoal, and fungal dsRNA viruses has improved our understanding of their structure, function, and evolution, as well. Here, we studied a dsRNA virus that infects the fungus Rosellinia necatrix, an ascomycete that is pathogenic to a wide range of plants. Using three-dimensional cryo-electron microscopy and analytical ultracentrifugation analysis, we determined the structure and stoichiometry of Rosellinia necatrix quadrivirus 1 (RnQV1). The RnQV1 capsid is a T=1 capsid with 60 heterodimers as the asymmetric units. The large amount of genetic information used by RnQV1 to construct a simple T=1 capsid is probably related to the numerous virus-host and virus-virus interactions that it must face in its life cycle, which lacks an extracellular phase.

Genome Sequence of Bluetongue virus Serotype 17 Isolated in Brazil in 2014

The complete genome sequence of Bluetongue virus (BTV) serotype 17 strain 17/BRA/2014/73, isolated from a sheep in Brazil in 2014, is reported here. All segments clustered with western topotype strains and indicated reassortment events with other BTV from the Americas. The strain 17/BRA/2014/73 represents a novel reference strain for BTV-17 from South America.

Hidden symmetry of small spherical viruses and organization principles in "anomalous" and double-shelled capsid nanoassemblies

We propose the principles of structural organization in spherical nanoassemblies with icosahedral symmetry constituted by asymmetric protein molecules. The approach modifies the paradigmatic geometrical Caspar and Klug (CK) model of icosahedral viral capsids and demonstrates the common origin of both the "anomalous" and conventional capsid structures. In contrast to all previous models of "anomalous" viral capsids the proposed modified model conserves the basic structural principles of the CK approach and reveals the common hidden symmetry underlying all small viral shells. We demonstrate the common genesis of the "anomalous" and conventional capsids and explain their structures in the same frame. The organization principles are derived from the group theory analysis of the positional order on the spherical surface. The relationship between the modified CK geometrical model and the theory of two-dimensional spherical crystallization is discussed. We also apply the proposed approach to complex double-shelled capsids and capsids with protruding knob-like proteins. The introduced notion of commensurability for the concentric nanoshells explains the peculiarities of their organization and helps to predict analogous, but yet undiscovered, double-shelled viral capsid nanostructures.

The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes

Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short “plug” structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts.

A Greasy Aid to Capsid Assembly: Lessons from a Salty Virus

In this issue of Structure, Gil-Carton et al. (2015) use hybrid structural methods to investigate the architecture of the membrane-containing halovirus HHIV-2, a member of the PRD1-adenovirus lineage. This work sheds light on how lipid-proteins interactions guide the assembly of single β-barrel coat proteins to form an icosahedral capsid.

Diphosphates at the 5' end of the positive strand of yeast L-A double-stranded RNA virus as a molecular self-identity tag

The 5'end of RNA conveys important information on self-identity. In mammalian cells, double-stranded RNA (dsRNA) with 5'di- or triphosphates generated during virus infection is recognized as foreign and elicits the host innate immune response. Here, we analyze the 5' ends of the dsRNA genome of the yeast L-A virus. The positive strand has largely diphosphates with a minor amount of triphosphates, while the negative strand has only diphosphates. Although the virus can produce capped transcripts by cap snatching, neither strand carried a cap structure, suggesting that only non-capped transcripts serve as genomic RNA for encapsidation. We also found that the 5' diphosphates of the positive but not the negative strand within the dsRNA genome are crucial for transcription in vitro. Furthermore, the presence of a cap structure in the dsRNA abrogated its template activity. Given that the 5' diphosphates of the transcripts are also essential for cap acquisition and that host cytosolic RNAs (mRNA, rRNA, and tRNA) are uniformly devoid of 5' pp-structures, the L-A virus takes advantage of its 5' terminal diphosphates, using them as a self-identity tag to propagate in the host cytoplasm.

Recovery of data from perfectly twinned virus crystals revisited

Perfect merohedral twinning of crystals is not uncommon and complicates structural analysis. An iterative method for the deconvolution of data from perfectly merohedrally twinned crystals in the presence of noncrystallographic symmetry (NCS) has been reimplemented. It is shown that the method recovers the data effectively using test data, and an independent metric of success, based on special classes of reflections that are unaffected by the twin operator, is now provided. The method was applied to a real problem with fivefold NCS and rather poor-quality diffraction data, and it was found that even in these circumstances the method appears to recover most of the information. The software has been made available in a form that can be applied to other crystal systems.

Identification of the Genome Segments of Bluetongue Virus Serotype 26 (Isolate KUW2010/02) that Restrict Replication in a Culicoides sonorensis Cell Line (KC Cells)

Bluetongue virus (BTV) can infect most ruminant species and is usually transmitted by adult, vector-competent biting midges (Culicoides spp.). Infection with BTV can cause severe clinical signs and can be fatal, particularly in naïve sheep and some deer species. Although 24 distinct BTV serotypes were recognized for several decades, additional 'types' have recently been identified, including BTV-25 (from Switzerland), BTV-26 (from Kuwait) and BTV-27 from France (Corsica). Although BTV-25 has failed to grow in either insect or mammalian cell cultures, BTV-26 (isolate KUW2010/02), which can be transmitted horizontally between goats in the absence of vector insects, does not replicate in a Culicoides sonorensis cell line (KC cells) but can be propagated in mammalian cells (BSR cells). The BTV genome consists of ten segments of linear dsRNA. Mono-reassortant viruses were generated by reverse-genetics, each one containing a single BTV-26 genome segment in a BTV-1 genetic-background. However, attempts to recover a mono-reassortant containing genome-segment 2 (Seg-2) of BTV-26 (encoding VP2), were unsuccessful but a triple-reassortant was successfully generated containing Seg-2, Seg-6 and Seg-7 (encoding VP5 and VP7 respectively) of BTV-26. Reassortants were recovered and most replicated well in mammalian cells (BSR cells). However, mono-reassortants containing Seg-1 or Seg-3 of BTV-26 (encoding VP1, or VP3 respectively) and the triple reassortant failed to replicate, while a mono-reassortant containing Seg-7 of BTV-26 only replicated slowly in KC cells.

Inter-segment complementarity in orbiviruses: a driver for co-ordinated genome packaging in the Reoviridae?

The process by which eukaryotic viruses with segmented genomes select a complete set of genome segments for packaging into progeny virus particles is not understood. In this study a model based on the association of genome segments through specific RNA-RNA interactions driven by base pairing was formalized and tested in the Orbivirus genus of the Reoviridae family. A strategy combining screening of the genomic sequences for inter-segment complementarity with direct functional testing of inter-segment RNA-RNA interactions using reverse genetics is described in the type species of the Orbivirus genus, Bluetongue virus (BTV). Two examples, involving four of the ten BTV genomic segments, of specific inter-segment interaction motifs whose maintenance is essential for the generation of infectious virus, were identified. Equivalent inter-segment complementarities were found between the identified regions of the orthologous genome segments of all orbiviruses, including phylogenetically distant species. Specific interaction of the participating RNA segments was confirmed in vitro using electrophoretic mobility shift assays, with the interactions inhibited using oligonucleotides complementary to the interaction motif of one of the interacting partners, and also through mutagenesis of the motifs. In each example, the base pairing rather than the absolute sequence was critical to the formation of a functional inter-segment interaction, with mutations only being tolerated in rescued virus if compensating changes were made in the interacting partner to restore uninterrupted base pairing. The absolute sequence of the complementarity motifs varied between species, indicating that this newly identified phenomenon may contribute to the observed lack of reassortment between Orbivirus species.

Atomic model of a nonenveloped virus reveals pH sensors for a coordinated process of cell entry

Viruses sense environmental cues (such as pH) to engage in membrane interactions for cell entry during infection but how non-enveloped viruses sense pH is largely undefined. Here, we report the structures — at high and low pH conditions — of bluetongue virus (BTV), which enters cells via a two-stage endosomal process. The receptor-binding protein VP2 possesses a zinc-finger and a conserved His866, which may function to maintain VP2 in a metastable state and to sense early-endosomal pH, respectively. The membrane penetration protein VP5 has three domains: dagger, unfurling, and anchoring. Notably, the β-meander motif of the anchoring domain contains a histidine cluster that could sense the late-endosomal pH and four putative membrane-interaction elements. Exposing BTV to low pH detaches VP2 and dramatically refolds the dagger and unfurling domains of VP5. Our biochemical and structure-guided mutagenesis studies support these coordinated pH-sensing mechanisms.

Isolation and Genetic Characterization of Mangshi Virus: A Newly Discovered Seadornavirus of the Reoviridae Family Found in Yunnan Province, China

BACKGROUND

Seadornavirus is a genus of viruses in the family Reoviridae, which consists of Banna virus, Kadipiro virus, and Liao ning virus. Banna virus is considered a potential pathogen for zoonotic diseases. Here, we describe a newly discovered Seadornavirus isolated from mosquitos (Culex tritaeniorhynchus) in Yunnan Province, China, which is related to Banna virus, and referred to as Mangshi virus.

METHODS AND RESULTS

The Mangshi virus was isolated by cell culture in Aedes albopictus C6/36 cells, in which it replicated and caused cytopathic effects, but not in mammalian BHK-21 or Vero cells. Polyacrylamide gel analysis revealed a genome consisting of 12 segments of double-stranded RNA, with a "6-4-2" pattern in which the migrating bands were different from those of the Banna virus. Complete genome sequencing was performed by full-length amplification of cDNAs. Sequence analysis showed that seven highly conserved nucleotides and three highly conserved nucleotides were present at the ends of the 5'- and 3'-UTRs in each of 12 genome segments. The amino acid identities of Mangshi virus shared with Balaton virus varied from 27.3% (VP11) to 72.3% (VP1) with Banna virus varying from 18.0% (VP11) to 63.9% (VP1). Phylogenetic analysis based on amino acid sequences demonstrated that Mangshi virus is a member of the genus Seadornavirus and is most closely related to, but distinct from, Balaton virus and Banna virus in the genus Seadornavirus of the family Reoviridae.

CONCLUSION

Mangshi virus isolated from mosquitoes (C. tritaeniorhynchus) was identified as a newly discovered virus in the genus Seadornavirus and is phylogenetically close to Banna virus, suggesting that there is genetic diversity of seadornaviruses in tropical and subtropical areas of Southeast Asia.