Figure 1 (Left) Diagrammatic representation of an orthoreovirus particle in cross section. The locations and identities of the virus structural proteins are indicated, using the nomenclature scheme for both Mammalian orthoreovirus (MRV) and Avian orthoreovirus (ARV). The protein components of the inner and outer capsids are indicated (from Duncan, 1999 and Martin, M.L., Palmer, E.L., and Middleton, P.J., Virology, 68, 146, 1975). (Right) Electron micrograph of negatively-stained Mammalian orthoreovirus serotype 1 (MRV-1) particle (panel A). Image reconstructions from cryo-electron microscopy of MRV-1 virions (panel B), ISVPs (panel C), and core (panel D). All particles are viewed down the three-fold axis of rotational symmetry (Courtesy of M. Nibert and T. Baker).
Figure 2 Gene organization of the polycistronic genome segments of the four species of orthoreoviruses. The solid line indicates the dsRNA and the numbers refer to the first and last nucleotides of the genome segment, along with the nucleotide positions of the start and codons of the various ORFs indicated by the rectangles. The identities of the gene products encoded by the various ORFs and their sizes (in amino acid residues) are indicated within the rectangles. The virus species and the genome segment is indicated on the left (from Duncan, 1999).
Figure 3 Phylogenetic tree generated using the amino acid sequences of the sigma-class major inner capsid proteins of various orthoreovirus isolates. Neighbor-joining tree prepared using Clustal X (Thompson, Gibson, Plewniak, Jeanmougin and Higgins, 1997) and drawn with TreeView 1.5 (Page, 1996).
Figure 4 (Top) Diagram of the Bluetongue virus (BTV) particle structure, constructed using data from biochemical analyses, electron microscopy, cryo-electron microscopy and X-ray crystallography. (Courtesy of P.P.C. Mertens and S. Archibald.) (Bottom) Electron micrographs of African horse sickness virus (AHSV) serotype 9 particles stained with 2% aqueous uranyl acetate (left) virus particles, showing the relatively featureless surface structure; (Center) infectious subviral particles (ISVP), containing chymotrypsin cleaved outer capsid protein VP2 and showing some discontinuities in the outer capsid layer; (Right) core particles, from which the entire outer capsid has been removed, to reveal the structure of the VP7 (T13) core surface layer and showing the ring shaped capsomeres (Courtesy of P.P.C. Mertens.)
Figure 5 (Top left) Isosurface representation of Great Island virus (GIV), strain Broadhaven virus (BRDV) to 23Å resolution as deduced by cryoelectron microscopy, showing the arrangement of proteins in the capsid surface (view down a 5-fold axis). The four major structural proteins, with VP4 (structurally equivalent to VP2 of BTV), VP5, VP7 (T13) and VP3 (T2) are coloured in different grays. (Courtesy of G. Schoen and E. Hewat.) (Top right) Model of the core structure of Bluetongue virus (BTV) from X-ray crystallography of the native core particle. The outer core surface, composed of 260 trimers of VP7 (T13) arranged with T = 13 l symmetry. The chemically identical but structurally different trimers are named in order of increasing distance from the five fold axes of symmetry (P, Q, R, S and T situated at the three fold axes). (Bottom left) The BTV1 subcore shell composed of 120 copies of VP3 (T2), arranged with T = 2 symmetry. The chemically identical but structurally different ‘A’ and ‘B’ molecules are shown; (Bottom right) Model cross section of the BTV core showing packaging of the dsRNA as four concentric shells. (Courtesy of D.I. Stuart, J. Grimes, P. Gouet, J. Diprose, R. Malby and P.P.C. Mertens.)
Figure 6 (Top) Phylogenetic tree for the genus Orbivirus, constructed using partial genome segment 3 (1193-1661 bp), or equivalent sequences (encoding the major structural protein VP3(T2) of the subcore capsid shell). (Bottom) Phylogenetic tree for the genus Orbivirus constructed using partial VP2 sequences (aa 303-464). VP2 is the larger outer capsid protein and major neutralization antigen. Nucleotide sequences of genome segment 3 and amino acid sequences derived from the nucleotide sequence of genome segment 2 were aligned by using the CLUSTALW 1.60 program (Higgins and Sharp, 1989). The tree was prepared using Clustal X (Thompson, Gibson, Plewniak, Jeanmougin and Higgins, 1997) and drawn with TreeView 1.5 (Page, 1996).
Figure 7 Electron micrograph of Simian rotavirus A/SA11 (SiRV-A/SA11) particles viewed by negative staining. (Courtesy of B.V.V. Prasad.)
Figure 8 (Upper left) Cutaway view of the mature particle of Simian rotavirus A/SA11 (SiRV-A/SA11), illustrating the triple-layered capsid structure at 24Å. (Upper right) Cutaway view of the transcriptionally-competent double layered particle at 19Å. (Lower left) Transcription enzyme complex composed of VP1 and VP3, shown anchored to the inner surface of VP2 at the icosahedral vertex. This figure has been computationally isolated from the 22Å reconstruction of a VP1/3/2/6-VLP (virus-like particle). (Lower right) Proposed pathway of mRNA translocation through the double-layered capsid during genome transcription. The mass of density at the extremity of the mRNA represents the structurally discernible portion of nascent mRNA visible in the 25Å structure of the actively transcribing particle (from Prasad, Rothnagel, Zeng, Jakana, Lawton, Chiu and Estes, 1996).
Figure 9 Phylogenetic tree comparing the sequences of rotavirus VP4, the P neutralization antigen from a limited number of Rotavirus A (RV-A) isolates. Sequences were aligned and trees calculated (Neighbor-joining method) using ClustalX. The trees were drawn using TreeView v.1.5.2. The matrix was of amino acid similarities. The abbreviations used to indicate host species are: Av, avian; Bo, bovine; Ca, canine; Eq, equine; Fe, feline; Hu, human; Mu, murine; Po, porcine; Si, simian.
Figure 10 Phylogenetic tree of Rotavirus VP2(T2) (major core protein) (amino acid differences, corrected for multiple substitutions and excluding gaps). The isolates and accession numbers used are given in Table 6. Sequences were aligned and the tree calculated (Neighbor-joining method) using ClustalX. The tree was drawn using TreeView v.1.5.2. The matrix was of amino acid similarities.
Figure 11 Negative contrast electron micrograph of Colorado tick fever virus (CTFV) particles. (Courtesy of F.A. Murphy.) The bar represents 50 nm.
Figure 12 Phylogenetic tree for genome segment 12 of different coltiviruses. Unrooted neighbor-joining tree created using the program ClustalX, depicting groupings for the deduced amino acid sequence of translation products from genome segment 12 of different coltiviruses. The two subgroups (A and B) that are currently recognized are labelled. Bar marker represents the number of substitutions per site. The relationships illustrated were not corrected for multiple amino acid substitutions (from Attoui, Charrel, Billoir, Cantaloube, de Micco and de Lamballerie, 1998). The relationships between segments 7 to 11 of some isolates have also been analyzed and have provided additional support for the relationships illustrated. The percentage differences between species calculated from the amino-acid sequence of segment 12 are; CTFV/BAV-In6423: 80%; CTFV/EYAV: 45%; CTFV/KDV: 83%; EYAV/BAV-In6423: 86%; EYAV/KDV: 86%; BAV-In6423/KDV: 90%. The difference between BAV-In6423 and KDV in segment 12 is very high but in segment 7 and 9 there are conserved sequences between these two species where the difference is only 60%.
Figure 13 (Top) Surface representations of the mature aquareovirus particle viewed at (Left) the icosahedral3-fold axis and (Right) the icosahedral 5-fold axis. The scale bar represents 200Å (Courtesy of B.V.V. Prasad). (Bottom) Negative contrast electron micrograph of negatively stained Striped bass reovirus (SBRV) particles (Courtesy of S.K. Samal). The bar represents 100 nm.
Figure 14 (Left) Negative contrast electron micrograph of empty and full, occluded (purified from polyhedra) Orgyia pseudosugata cypovirus 5 (OpCPV-5) virions stained with uranyl acetate; (Right) Negative contrast electron micrograph of non occluded OpCPV-5 virion. (Courtesy of C.L. Hill.) The bars represent 20 nm.
Figure 15 (Top left) Cryo electron microscopy reconstruction of non occluded Orgyia pseudosugata cypovirus 5 (OpCPV-5) virion to 26Å resolution. (Top right) Cryo electron microscopy reconstruction of occluded OpCPV-5 virion to 26Å resolution. (Bottom left) Cross section of cryo electron microscopy reconstruction of full occluded OpCPV-5 virion to 26Å resolution. (Bottom center) Cross section of cryo electron microscopy reconstruction of full non-occluded OpCPV-5 virion to 26Å. (Bottom right) Cross section of cryo electron microscopy reconstruction of empty OpCPV-5 virion to 26Å resolution. The cross sections show evidence of dsRNA packaged as distinct layers and suggest localization of the transcriptase complexes at the 5-fold axes of symmetry. (Courtesy of C.L. Hill.)
Figure 16 (Left) Scanning electron micrograph of Bombyx mori cypovirus 1 (BmCPV-1) cubic polyhedra (Courtesy of P.P.C. Mertens); (Center) Scanning electron micrograph of Inachis io cypovirus 2 (IiCPV-2) polyhedra (Courtesy of P.P.C. Mertens). Polyhedra were purified in the presence of SDS. Surface indentations represent sites where virus particles have been lost. (Right) Cross section of OpCPV-5 polyhedra showing occluded virus particles and the crystalline polyhedrin matrix. (Courtesy of T.F. Booth.) The bars represent 100 nm.
Figure 17 Phylogenetic tree for genome segment 10 of Cypovirus 1, 5 and CfCPV. Neighbor-joining tree showing phylogenetic relationships between cypovirus isolates, as revealed by analyses of genome segment 10 RNA sequences from: CPV-1 (D37768; D37769; AB003360; AB003361; D37770; D37771); CPV-5 (J04338; U06196; U06194); CfCPV (U95954). Strain designations for the CPV-1 viruses are shown in brackets.
Figure 18 (Left) Negative contrast electron micrograph of Maize rough dwarf virus (MRDV) virions stained with uranyl acetate showing A-type spikes; (Center) smooth subcores derived from MRDV on staining with neutral phosphotungstate; (Right) B-type spikes on virus-derived cores stained with uranyl acetate. (Courtesy of R.G. Milne.) The bar represents 100 nm.
Figure 19 Phylogenetic tree produced by comparison of the nucleotide sequences for genome segments that code for the Fijivirus major outer shell. (Maize rough dwarf virus, MRDV-S10 [L76560]; Rice black streaked dwarf virus, RBSDV-S10 [D00606]; Oat sterile dwarf virus, OSDV-S8 [S8:AB011025]; Nilaparvata lugens reovirus, NLRV-S8 [D26127]). Alignment and Neighbor-joining tree produced with ClustalX. Tree drawn with TreeView. Note: Core protein sequences showed a similar tree (data not shown).
Figure 20 Negative contrast electron micrograph of Rice gall dwarf virus (RGDV) particles negatively stained with phosphotungstic acid. The bar represents 50 nm.
Figure 21 Electron cryo microscopic image and 25Å resolution three-dimensional structure of the double-shelled Rice dwarf virus (RDV). (Left) Shaded surface view of the RDV reconstruction as viewed along the icosahedral 2-fold axis. ‘5’, ‘3’, and ‘2’ designate the icosahedral 5-, 3-, 2-fold axes. Highlighted in gray are a contiguous “group of 5 trimers” found in each asymmetric unit. (Center) Inner shell structure of RDV computationally extracted with 590Å diameter. It exhibits T = 1 lattice. Dashed triangle designates one triangular face of the icosahedron. (Right) Schematic diagram of fish-shaped density distribution within a triangle in a T = 1 lattice. (Courtesy of Hong Zhou and and Wah Chiu, from Lu, Zhou, Baker, Jakana, Cai, Wei, Chen, Gu and Chiu, 1998.)
Figure 22 Phylogenetic tree of phytoreoviruses constructed using the RNA sequences of genome segment 8 from the following accession numbers: Rice dwarf virus (RDV) (RDV-A; D10219), (RDV-B; D00536), (RDV-S; D13773), (RDV-China; U36565); Wound tumor virus (WTV; J04344); Rice gall dwarf virus (RGDV; D13410). Sequences were aligned and a Neighbor-joining tree was prepared using ClustalX (Thompson, Gibson, Plewniak, Jeanmougin and Higgins, 1997) and drawn with TreeView 1.5 (Page, 1996).
Figure 23 (a) Electron micrograph of Rice ragged stunt virus (RRSV). (Courtesy of R.G. Milne.) (b) Schematic of RRSV particle; (c) micrographs of the virus showing 2-, 3- and 5-fold symmetries (A1, B1 and C1, respectively) images of the same rotated by increments of 180° (A2), or 120° (B2), or 72° (C2) and proposed models of the 2-, 3- and 5-fold symmetries (A3, B3 and C3 respectively). (Courtesy of E. Shikata.) The bar represents 50 nm.
Figure 24 Phylogenetic tree for the members of the family Reoviridae. Amino acid sequences derived from the nucleotide sequence of RNA polymerase of the relevant genome segment (segment 1 in each case, except for genome segment 4 of Rice ragged stunt virus - Oryzavirus), were aligned by using the CLUSTALW 1.60 program (Higgins and Sharp, 1989). The Neighbor-joining tree was prepared using Clustal X (Thompson, Gibson, Plewniak, Jeanmougin and Higgins, 1997), allowing for multiple substitutions and ignoring gaps and drawn with TreeView 1.5 (Page, 1996). Strains of viruses and their sequences used: Orthoreovirus: Mammalian orthoreovirus, subgroup 1, serotype Dearing 3 (MRV-3) M24734; Orbivirus: African horse sickness virus, serotype 9 (AHSV-9) U94887; Bluetongue virus, serotype 2 (BTV-2) L20508; serotype 10 (BTV-10) X12819; serotype 11 (BTV-11) L20445; serotype 13 (BTV-13) L20446; serotype 17 (BTV-17) L20447. Rotavirus: Rotavirus A, Bovine rotavirus (BoRV-A) J04346; Rotavirus A, Simian rotavirus SA11 (SiRV-A/SA11) AF015955; Rotavirus B, Murine rotavirus IDIR (MuRV-B) M97203; Rotavirus C, Porcine rotavirus (PoRV-C) M74216; Fijivirus: Nilaparvata lugens reovirus, Izumo strain (NLRV) D49693; Phytoreovirus: Rice dwarf virus, Chinese strain (RDV-Ch) U73201; Rice dwarf virus, strain H (RDV-H) D10222; Rice dwarf virus, strain B (RDV-B) D90198; Rice dwarf virus, strain A (RDV-B) D90197; Oryzavirus: Rice ragged stunt virus, Thai strain (RRSV) U66714. No polymerase sequences have either been identified or are currently available for any cypoviruses, coltiviruses, aquareoviruses or any of the unclassified viruses of invertebrates.
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