Top
ヘッダー

(Upload on September 11 2016) [ 日本語 | English ]

Virus (ウィルス)






Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily

1892 Iwanovsky WP (USSR): discovering that tobacco mosaic virus (TMV) was filterable
1898 Beijerinck: porposed virus (L.)
1935 Stanley M 1904-1971, USA

TMV = globulin-like protein (corrected later → protein + nucleic acid)
exstracted and crystallized the virus that was acicular-crystallied nucleic protein wiht 40 million MW, by using enzymatic chemistry

1936 Sir F Bowden & Pirie: confirmed that TMV was nucleoprotein
1939 Pfankuck et al.: emphasized the importance of morphology (phenotypic classification) after the detailed observation of TMV
1953, 1957 Lwoff: summarized the characteristics of virus

1) present either DNA or RNA
2) replicable by nucleic acids
3) not grown and not reproduced by binary division
4) absent energy-supply system
5) utilizing the ribosomes of host (obligate parasitic)

Virus groups based on the hosts
Bacterial virus
invertebrate virus
Vertebrate virus
Plant virus
索引

[classification, structure, biology]

TMV
Pathway of bacteriophage T4 morphogenesis. Genes participating in assembly are numbered. Chaperones that are not part of the final structure are presented in parentheses.
The families of virus infecting bacteria
Non-enveloped_____________________________________| Enveloped
group
The families of virus infecting plants
Non-enveloped_____________| Enveloped
group
The families of virus infecting invertebrates
Non-enveloped_____________| Enveloped
group
The families of virus infecting vertebrates
Non-enveloped_____________| Enveloped
group

Taxonomy (分類)


Table II. List of virus families and groups in order of presentation (proposed in 1980). V: vertebrates, I: invertebrates, P: plants. ds: double strand, ss: single strand. *: some members possess a cell membrane-derived envelope.
CharacterizationFamilies or groupsKinds of host
dsDNA, envelopedPoxviridae
Herpesviridae
Baculoviridae
Plasmaviridae
V, I
V
I
bacteria
dsDNA, non-enveloped





tailed phages
Iridoviridae *
Adenoviridae
Papovaviridae
Caulimovirus
Tectiviridae
Corticoviridae
Myoviridae
Styloviridae
Podoviridae
V, I
V
V
P
bacteria
bacteria
bacteria
bacteria
bacteria
ssDNA, non-envelopedParvoviridae
Geminivirus
Microviridae
Inoviridae
V, I
P
bacteria
bacteria
dsRNA, envelopedCystoviridaebacteria
dsRNA, non-enveloped
possible family

possible family

possible family

possible family
Reoviridae
Isometric dsRNA mycoviruses requiring
only one RNA segment for replication
Isometric dsRNA mycoviruses requiring
two RNA segments for replication
Isometric dsRNA mycoviruses requiring
three RNA segments for replication
Bisegmented dsRNA viruses
V, I, P
fungi

fungi

fungi

V, I
ssRNA, enveloped
Genome strategy

a. No DNA step
(i) positive-sense genome

(ii) negative-sense genome




(iii) not established
b. DNA step in replication cycle
Bipartite genomes
Isometric particles




Possible group
Rod-shaped particles
Tripartite genomes
Isometric particles


Isometric and bacilliform particles
Rod-shaped particles


Togaviridae
Coronaviridae
Paramyxoviridae
Orthomyxoviridae
Rhabdoviridae
Bunyaviridae
Arenaviridae
Tomato spotted wilt virus group
Retroviridae

Dianthovirus
Comovirus
Nepovirus
Pea enation mosaic virus group
Nodaviridae
Velvet tobacco mottle virus group
Tobravirus

Cucumovirus
Bromovirus
Ilarvirus
Alfalfa mosaic virus group
Hordeivirus


V, I
V
V
V
V, I, P
V, I
V
P
V

P
P
P
P
I
P
P

P
P
P
P
P
ssRNA, non-envelopedMonopartite genomes
Isometric particles









Rod-shaped particles

Picornaviridae
Caliciviridae
Nudaurelia β virus group
Leviviridae
Maize chlorotic dwarf virus group
Tymovirus
Luteovirus
Tombusvirus
Sobemovirus
Tobacco necrosis virus group
Closterovirus
Carlavirus
Potyvirus
Potexvirus
Tobamovirus

PV, I
V
I
bacteria
P
P
P
P
P
P
P
P
P
P
P

ICTV (International Committee on Taxonomy of Viruses) (2015)

Order Caudovirales

Family Myoviridae
Family Podoviridae
Family Siphoviridae

Order Herpesvirales

Family Alloherpesviridae
Family Herpesviridae
Family Malacoherpesviridae

Order Ligamenvirales

Family Lipothrixviridae
Family Rudiviridae

Order Mononegavirales

Family Bornaviridae
Family Filoviridae
Family Mymonaviridae
Family Nyamiviridae
Family Paramyxoviridae
Family Pneumoviridae
Family Rhabdoviridae
Family Sunviridae
Family Unassigned

Order Nidovirales

Family Arteriviridae
Family Coronaviridae
Family Mesoniviridae
Family Roniviridae

Order Picornavirales

Family Dicistroviridae
Family Iflaviridae
Family Marnaviridae
Family Picornaviridae
Family Secoviridae
Family Unassigned

Order Tymovirales

Family Alphaflexiviridae
Family Betaflexiviridae
Family Gammaflexiviridae
Family Tymoviridae

Virus families not assigned to an order

Family Adenoviridae
Family Alphatetraviridae
Family Alvernaviridae
Family Amalgaviridae
Family Ampullaviridae
Family Anelloviridae
Family Arenaviridae
Family Ascoviridae
Family Asfarviridae
Family Astroviridae
Family Avsunviroidae
Family Baculoviridae
Family Barnaviridae
Family Benyviridae
Family Bicaudaviridae
Family Bidnaviridae
Family Birnaviridae
Family Bromoviridae
Family Bunyaviridae

Hantaviruses: single-stranded, enveloped, negative sense RNA viruses that can kill humans

Family Caliciviridae
Family Carmotetraviridae
Family Caulimoviridae
Family Chrysoviridae
Family Circoviridae
Family Clavaviridae
Family Closteroviridae
Family Corticoviridae
Family Cystoviridae
Family Endornaviridae
Family Flaviviridae
Family Fuselloviridae
Family Geminiviridae
Family Genomoviridae
Family Globuloviridae
Family Guttaviridae
Family Hepadnaviridae
Family Hepeviridae
Family Hypoviridae
Family Hytrosaviridae
Family Inoviridae
Family Iridoviridae
Family Lavidaviridae
Family Leviviridae
Family Luteoviridae
Family Marseilleviridae
Family Megabirnaviridae
Family Metaviridae
Family Microviridae
Family Mimiviridae
Family Nanoviridae
Family Narnaviridae
Family Nimaviridae
Family Nodaviridae
Family Nudiviridae
Family Ophioviridae
Family Orthomyxoviridae
Family Papillomaviridae
Family Partitiviridae
Family Parvoviridae
Family Permutotetraviridae
Family Phycodnaviridae
Family Picobirnaviridae
Family Plasmaviridae
Family Pleolipoviridae
Family Polydnaviridae
Family Polyomaviridae
Family Pospiviroidae
Family Potyviridae
Family Poxviridae
Family Pseudoviridae
Family Quadriviridae
Family Reoviridae
Family Retroviridae
Family Sarthroviridae
Family Sphaerolipoviridae
Family Spiraviridae
Family Tectiviridae
Family Togaviridae
Family Tombusviridae
Family Totiviridae
Family Turriviridae
Family Unassigned
Family Virgaviridae

ICTV (2015)

Structure (構造)


TMV
TMV (タバコモザイクウィルス)
300 nm in height × 18 nm in width
rod-shaped virus → applicable this basic structure to rod-shaped and string-shaped viruses
present 2130-17500 dt of proteins
components: protein = 95% + RNA 5%

Fig. Structure of TMV. (A) Drawing to show the relationships of the RNA and the protein subunits. The DNA shown free of protein could not maintain this configuration in the absence of the protein subunits. There arc 3 nucleotides per protein subunit, or 49 per turn of the major helix spaced about 5 A apart. (B) Photograph of a model of TMV with major dimensions indicated. The structure repeats after 69 A in the axial direction, the repeat containing 49 subunits distributed over 3 turns of the helix.(Klug & Caspar 1960, and based largely on the work of R. E. Franklin) (C) Photograph of a particle of TYMV obtained by symmetrizing an electron microgrpah of a single particle. (Markham 1968)
The molecular weights of basic proteins differ between this TMV and the other TMV.

Many species have proteins of which molecular weights are approximately 18-Kd
→ attempting to apply virus classification
TMV
Rhabdovirus
Enveloped, bullet shaped. 180 nm long and 75 nm wide. Certain plant rhabdoviruses are bacilliform in shape and almost twice the length. The basic structure is comparable with the structure of TMV.

Viron
Spherical virus (球形ウィルス)
All spherical virus shells have Icosahedral symmetry = Built from 20 identical equilateral triangles.
→ enclose maximum volume → probably structurally most stable
The structures were predicted by of subunit sequences
spherical virus
The surface structures of spherical virus is estimated by the variations of the combinations of subunits and/or the relationships between variations of subunit shapes and numbers of subunits

Fig. A. Comparison of models each built of 180 units (corks) on the surface of a sphere representing in position, direction and radial extent the structure units in the outer regions of thc protein shells of A BBMV, B TYMV (Finch & King 1966). 1) Twofold view, 2) threefold view, 3) fivefold view. The structure units of BBMV protrude ca 15 A from the body of the particle and lie with their long axes approximately parallel to the nearest local sixfold or fivefold axis of the particle, forming 32 cylindrical or prismatic morphological units. The structure units of TYMV protrude further from the body of the particle than do those of BBMV and are tilted further toward the nearest local sixfold or fivefold axis to form morphological tin its shaped like frusta of cones. (Finch & King 1967)
Fig. B. Clustering patterns of subunits in icosahedra. Top left is a simple icosahedron. Its triangular faces are undivided (T = 1): each is defined by three subunits and thus there are 60 subunits in the entire icosahedron. These subunits may cluster in fives (a, pentamer clusters) at the vertices as in the particles of satellite virus. Middle left is an icosadeltahedron of 180 subunits. Each triangular face of the underlying icosahedron (broken lines) is divided into six half triangles (unbroken lines: T = 6 × 1/2 = 3). Each triangular face is defined by three subunits, and these could cluster together (trimers), or may cluster with subunits of adjacent triangles either in pairs (dimers), or in fives and sixes (pentamer/hexamers). Dimer clustering gives, in one view, a 'Star of David' pattern (b), and this is found in particles of turnip crinkle virus. Pentamer/hexamer clustering (d) is seen in particles of tymoviruses. The particles of some viruses, such as alfalfa mosaic virus are tubular variants of an icosadeltahedron (c). These particles consist of two half icosadeltahedra joined by a tubular net, which has no five-fold axes. The clustering pattern in alfalfa mosaic virus particles is not known for sure; the subunits may be clustered as pentamer/hexamers (c. top half) or trimers (c. lower half).
spherical virusA
spherical virusB

Plant virus (植物ウィルス)


Multicomponent and segmental genome

Only seen in plant virus
Information expression mechanisms on genome or gene

genome (= nucleic acids) → enzyme, protein (coat protein) = form, etc.

TMV = 5% nucleic acids + 95% proteins
TYMV = 34% nucleic acids
TNV satellite virus = 20% nucleic acids – cannot reproduce without TNV
PVX = 6% nucleic acids + 94% proteins
PVY = 5% nucleic acids

Table 1. Arrangement of elongated plant viruses accroding to normal length (NL), shape, diameter (φ), mode of transmission, and thermal inactivation point (TIP).
GroupNL (rnp)Shapeφ (μm)TransmissionTIP- (°C)ab
1130Rigid rods20Sap; soil-Barley stripe mosaic virus (1)Soil-borne wheat mosaic virus (2)
2180Rigid rods75-80Potato stem mottle virus (3)
3300Rigid rods15Sap85-95+ Tobacco mosaic virus (4)
+ Cowpea virus (5)
+ Cucumber green mottle virus (6)
Odonioglossum ring spot virus (7)
4480Flexible threads10-11Sap; (aphids?)60-75White clover mosaic virus (8)Cymbidium mosaic virus (7)
5515Flexible threadsPotato virus X (9)Cactus virus 1 (10)
6580Flexible threadsPotato aucuba mosaic virus (11)
7620Rods, rigid to slightly flexible12-13Apids; sap65-75Wisconsin pea stieak virus (12)
8650Rods, rigid to slightly flexibleRed clover vein mosaic virus (12)
* Carnation latent virus (13)
* Potato virus S (13)
* Potato virus M (13)
Cactus virus 2 (10)
"Hop virus" (14)
"Gladiolus virus"(14)
"Poplar virus" (14)
Tulip-breaking virus (15)
9700Rods, rigid to slightly flexible12-13Mites; sap-Wheat streak mosaic virus (16)
10730Flexible threads12-13Aphids; sap50-60Beet mosaic virus (17)
Potato virus A (18)
Potato virus Y (18)
Tobacco etch virus (19)
Henbane mosaic virus (19)
11750Flexible threads Bean common mosaic virus (20)
Bean yellow mosaic virus (20)
Pea mosaic virus (20)
Soybean niosaic virus (20)
Turnip mosaic virus (21)
Cockaf not streak virus (19)
Lettuce aulusaic virus (22)
Sorghum red stripe virus (23)
Sugar cane mosaic virus (24)
121250Very flexible threads10Aphids; (sap)-Beet yellows virus (25)

a, b, +, *, Indicate serological relationship within groups 3, 8, and 11, respectively. Numbers in parentheses refer to footnotes as follows: (1) Gold et al., 1954: 130 × 30 μm. Brandes (1959) gave a NL of 128 μm, but the diameter of the particles was only about 20 μm when compared with TMV and potato stem mottle virus. (2) Gold et al., 1957. (3) Paul & Bode (1955) found two frequent lengths: 70 and 180 μm. The values of Harrison & Nixon (pers comm) are in good accordance. These authors could show that the shorter particles are noninfectious. Therefore, 180 μm must be taken as NL. Potato stem mottle virus also includes tobacco rattle virus and soil-borne potato viruses found in the United States (Walkinshaw & Larson 1958, Oswald & Bowman 1958). The morphological data are apparently the same; furthermore, serological relationship has been established. (4) A great number of papers exist; 300 μm is especially the result of detailed measurements by Williams & Steers (1951). TMV often has been used as a standard in our laboratory. (5) The cowpea virus was kindly supplied by FC Bawden. (6) A detailed study on this subject is that of Knight (1955). (7) Jensen & Gold, 1951; Newton & Rosberg, 1952; Gold & Jensen, 1953; Murakishi, 1958. (8) Brandes & Quanta, 1957. (9) Bode & Paul, 1955. (10) With the aid of the dipping method we found two different viruses in several species of cactus plants (Brandes & Uachdraweit, unpublished). Cactus virus 1 possibly is identical with a virus described by Amnelunxen (1958). (11) Paul & Bode, 1956. (12) Wetter et al., 1959; Wetter & Quanta, 1953; Brandes & Quanta, 1957. (13) Brandes et al., 1959. (14) Electron microscopic studies of these viruses are going on in our laboratory. The hop virus is being studied by Nuber K (Landwirtschaftliche Hochschule, Hohenheim). (15) De Bruyn Ouboter et al., 1951. (16) Gold et al., 1957; Brandes, 1959. (17) Zimmer & Brandes, 1956. (18) Bode & Paul, 1956; Paul & Bode, 1956; Brandes & Paul, 1957. (19) Brandes, 1959. (20) These four legume viruses all have the same size (Brandes & Quanta 1955, Quanta 1959). Serological relationship has been established between bean common mosaic virus and bean yellow mosaic virus (Beenister & van der Want, 1951; Bereks, pers comm) and between bean yellow mosaic virus and pea mosaic virus (Goodchild. 1956). (21) Bode & Brandes, 1958. (22) Couch & Gold, 1954: 748 × 22 mm. Our determination of the NL revealed the same value (747 mm), but measurements in comnparison with TMV and other viruses revealed a diameter of about 12-13 μm (Brandes 1959). (23) This virus has been described and suspected of being related to sugar cane mosaic virus by Grancini (1957). It has been bee measured in our laboratory (Brandes 1959). (24) Gold et al., 1957. (25) Brandes & Zimnmer, 1955; Burghardt & Brandes, 1957.

Gemniniviruses (ジェミニウイルス)

Table 11. Geminiviruses(ssDNA) and their properties, distribution, and transmission. S: sedimentation coefficient. SCPS: Size of coat protein subunit
NameVectorGeographical distributionIn situ distributionSNucleic acidSCPS
TypeSize
Maize streakCicadulina rnbilaAfrica, India-76ssDNA7.1 × 10528000
Bean golden mosaicBemisia lubaciTropical Am.Phloem-associated parenchyma
& sieve elements
69ssDNA8.0 × 10527400
Cassava latent-Africa-76ssDNA8.0 × 10534000
Chloris striate mosaicNesoclutha pallidaAustraliaGeneral but not epidermis-ssDNA7.1 × l0528000
Curly topCirculifer tenellusNorth Am.Phloem-associated parenchyma--
Euphorbia mosaicBemisia tabaciTropical Am.Phloem-limited--
Tomato golden mosaicBemisia tabaciTropical Am.Phloem-limited--
Tomato yellow dwarfBemisia tabaciJapanPhloem-limited--
Tobacco leaf curlBernisia tabaciPantropical---
Tobacco yellow dwarfOrosius argentatusAustralia-76-27500
Bean summer deathOrosuis argentatusAustraliaPhloem-limited---
Mungbean yellow mosaicBemisia tabaciSouth Asia---
Reovirus
Table 3. dsDNA segments and polypeptides of capsid proteins in plant reoviruses. #: number of RNA segment and polypeptide. PP: polypeptide. R: RNA segment (PTE) molecular weight (× 106). MWcal = calculated molecular weight (× 106). MWobs = observed molecular weight (× 106). No: Number of capsid proteins. Loc.: location (C = core, OL = outer layer, Ca = capsomere, OC = outer capsid, B = B-spike)
#WTVRDVFDVRBSDVMRDVPSV
PPPPPP
RMWcalMWobsNoLocRMWcalMWobsNoLocRRRMWcalMWobsNoLocR
12.90170.6160.0IC3.10194.0193.0IC2.902.912.88160.0
22.40141.2131.0IIOL2.50156.0152.0IIOL2.502.502.50138.0139.0IC2.54
32.20129.4118.0IIIC2.20137.5131.0IIIC2.482.352.35130.0126.0IIC2.50
41.80105.91.80112.52.482.352.35130.0123.0IIIB2.50
51.78104.796.0IVOL1.76110.0110.0IVOL2.122.122.12117.0111.0IVOC2.12
61.1064.71.0565.61.851.751.7597.097.0VOC1.75
71.0561.858.0VC1.0263.762.0VC1.451.451.4580.01.48
80.8348.836.0VICa0.7848.846.0VIOC1.211.251.2568.0(1.25)
90.5733.535.0VIICa0.7043.845.0VIIOC1.151.181.1865.064.0VIOC
100.5532.40.6741.91.121.101.0860.0
110.5431.70.4830.0
120.3218.80.4830.0
Total16.016.619.319.018.9(19.6)

Transmission (伝搬)


1. Contact (接触)

2. Seed transmission (種子)

3. Soil transmission (土壌)

a. Nematode (線虫)
Transmission of nepovirus and tobravirus through nematode

Group cryptogram: [R/1:2.4/42/(1.4 – 2.2)/(27 – 40) – (2 × 1.4)/46:S/S:S/C, Ve/Ne
Type member: tobacco ring spot virus = Main characteristics: Three types of isometric particle ca 28 nm in diameter with angular outlines, sedimenting at ca 50, 90-120 and 120-130 S and containing respectively ca 0, 27-40 and 42-46% single-stranded RNA. Two RNA species, M.W. ca 2.4 × 106 and 1.4-2.2 × 106, both necessary for infection. Each particle contains 60 molecules of a single coat polypeptide. M. Wt ca 55,000. Thermal inactivation point 55-70°C: longevity in sap a few days or weeks; concentration in sap 10-50 mg/l. Wide host range, causing ring spot and mottle symptoms, often with subsequent symptomless infection. Virus particles occur in cytoplasm, some in membranous tubules. Many cells contain a vesiculated cytoplasmic inclusion body. Transmissible by inoculation of sap, by soil-inhabiting nematodes and to progeny through seed and pollen.

Table 8. Distribution of determinants for biological properties between the parts of virus genomes.
RNA-1
a. RASPBERRY RINGSPOT VIRUS

Seed transmissibility in Stellaria media
Infectivity for raspberry cv. Lloyd George
Suppression of symptoms in Petunia hybrida
Lesion type in Chenopodium quinoa
Systemic infection of Phaseolus vulgaris
Systemic symptom severity in C. quinoa
Speed of systemic symptom production in C. quinoa
Competitiveness between virus genotypes s

b. TOMATO BLACK RING VIRUS

Seed transmissibility in S. media
Speed of lesion production in C. quinoa
Speed of systemic symptom production in C. quinoa

c. TOBACCO RATTLE VIRUS

? RNA polymerase production
Lesion type
Lesion formation in P. hybrida
Systemic infection of Nicotiana spp.

RNA-2
a. RASPBERRY RINGSPOT VIRUS

Coat protein specificity
Vector specificity
Yellowing symptoms in P. hybrida
Lesion type in C. quinoa

b. TOMATO BLACK RING VIRUS

Coat protein specificity
Vector specificity
Lesion type in C. quinoa

c. TOBACCO RATTLE VIRUS

Coat protein specificity
Yellowing symptoms in Nicotiana spp.
Length of short nucleoprotein particles

b. Fungi (菌類)

4. Sap transmission (汁液)

5. Insect transmission (虫媒)

Aphid (アブラムシ)
aphid
Fig. Illustration of aphids in probing position. (A) Aphids on position to probe virus-infected tissues of the epidermis. (B) Aphids in feeding position, acquiring virus from phloem cells.
Leaf beetle (ハムシ)
= chrysomelid
Tick (ダニ)
Whitefly (コナジラミ)
Issues
1. genome masking
Table 6. General pattern of transmission (+) or non-transmission (-) of 5 isolates of barley yellow dwarf virus by 4 aphid species.

Virus isolates R. padi M. avenae R. maidis S. graminum

	PAV        +       +        -         +
	RPV        +       -        -         +
	MAV        -       +        -         -
	RMV        -       -        +         -
	SGV        -       -        -         +
→ a mechanism that the early-infected virus protects against the infection of phylogenetically-different virus ↔ this virus does not have this mechanims = simultaneous replication
genome masking
Fig. 6. The combinations of proteins and nucleic acids extracted from the strains concomitantly infected by two virus species. C, D: transcapsidation, E, F: phenotypic mixing.
2. helper component

Viroids (ウイロイド)


1971: potato spindle tuber viroid discovered
→ the smallest known pathogens, are naked, circular, single-stranded RNA molecules that do not encode protein yet replicate autonomously when introduced into host plants
≥ 30 viroids
フッター