Table 1 Conserved terminal sequences of orthoreovirus genome segments.
|
Virus |
Conserved RNA terminal sequences (+ve strand) | |
|
Subgroup 1 |
MRV |
5-GCUA..............................UCAUC-3 |
|
Subgroup 2 |
ARV |
5-GCUU..............................UCAUC-3 |
|
NBV |
5-GCUU..............................UCAUC-3 | |
|
Subgroup 3 |
BRV |
5-GUAA..............................UCAUC-3 |
Table 2 List of the dsRNA segments of MRV-3 with their respective size (bp) and their encoded proteins for which the name, calculated size [ 103], location, copy number per virion and functions or properties are indicated.
|
dsRNA |
Size (bp) |
Proteins (§: protein structure/ function) |
Mr ( 103) |
Protein copy number per particle |
Location |
Function |
|
L1 |
3854 |
3 (Pol) |
142 |
12 |
Core |
RNA polymerase |
|
L2 |
3916 |
2 (Cap) |
144 |
60 |
Core spike |
Guanylyl transferase, methyl transferase “turret” protein |
|
L3 |
3896 |
1(Hel) |
143 |
120 |
Core |
Inner capsid structural protein, binds dsRNA and zinc, NTPase, helicase |
|
M1 |
2304 |
2 |
83 |
12 |
Core |
NTPase |
|
M2 |
2203 |
1 |
76 |
30 |
Outer capsid |
Multimerizes with 3 and cleaved to 1C and 1N which assume T = 13 symmetry in the outer capsid, 1C cleaved to and during the entry process, myristoylated N-terminus, membrane penetration |
|
1C (T13) |
72 |
600 |
||||
|
59 |
||||||
|
13 |
||||||
|
1N |
4 |
600 |
||||
|
M3 |
2235 |
NS |
8075 |
0 |
Nonstructural |
Binds ssRNA and cytoskeleton, phosphoprotein genome packaging? NSC from alternate translation start site, unknown function |
|
NSC | ||||||
|
S1 |
1416 |
1 |
49 |
36 |
Outer capsid |
Cell attachment protein, homotrimer, hemagglutinin, type-specific antigen |
|
1S |
Basic protein, function unknown | |||||
|
S2 |
1331 |
2 |
47 |
120 |
Core |
Inner capsid structural protein, weak dsRNA-binding, morphogenesis? |
|
S3 |
1189 |
NS |
41 |
0 |
Nonstructural |
ssRNA-binding, genome packaging? |
|
S4 |
1196 |
3 |
41 |
600 |
Outer capsid |
dsRNA-binding, multimerizes with 1, nuclear and cytoplasmic localization, translation control |
§ protein structure/function: RNA polymerase = “Pol”; capping enzyme (guanylyltransferase and transmethylase) = “Cap”; Virus structural protein with T = 13 symmetry = “T13”. Protein with helicase activity = “Hel”.
Table 3 Conserved terminal sequences of orbivirus genome segments.
|
Virus species |
(strain) |
Conserved RNA terminal sequences (+ve strand) |
|
BTV |
5-GUUAAA............................ACUUAC-3 | |
|
EHDV |
5-GUUAAA..........................A/GCUUAC-3 | |
|
AHSV |
5-GUUA/UAA/U.....................ACA/UUAC-3 | |
|
GIV |
(BRDV) |
5-GUAAAA........................AA/GGAUAC-3 |
|
PALV |
(CHUV) |
5-GUA/UAAA.......................A/GCUUAC-3 |
Table 4 List of the dsRNA segments of Bluetongue virus serotype 10 (BTV-10) with their respective size (bp) and their encoded proteins for which the name, calculated size ( 103) and function and/or location are indicated.
|
dsRNA Segment number |
dsRNA Segment size (bp) |
ORF (bp) |
Protein nomenclature § (protein structure/ function) |
Protein size ( 103) |
Protein copy number per particle (BTV-1) |
Function (location) |
|
1 |
3,954 |
12-3917 |
VP1(Pol) |
149,588 |
10 |
RNA dependent RNA polymerase |
|
2 |
2,926 |
20-2887 |
VP2 |
111,112 |
180 |
Outer layer of the outer capsid, controls virus serotype, cell attachment protein, involved in determination of virulence, readily cleaved by proteases. Most variable protein. Reacts with neutralizing antibodies. Trimer. |
|
3 |
2,770 |
18-2720 |
VP3(T2) |
103,304 |
120 |
Forms the innermost protein capsid shell subcore capsid layer, T = 2 symmetry, controls overall size and organization of capsid structure, RNA binding, interacts with minor internal proteins. |
|
4 |
2,011 |
9-1970 |
VP4 (Cap) |
76,433 |
20 |
Dimer, transmethylase 1 and 2, capping enzyme (guanylyl-transferase). |
|
5 |
1,769 |
35-1690 |
NS1(TuP) |
64,445 |
0 |
Forms tubules of unknown function in the cell cytoplasm. These are characteristic of orbivirus replication. |
|
6 |
1,638 |
30-1607 |
VP5 |
59,163 |
360 |
Inner layer of the outer capsid, glycosylated, helps determine virus serotype, variable protein. Trimer. |
|
7 |
1,156 |
18-1064 |
VP7 (T13) |
38,548 |
780 |
Trimer, forms outer core surface, T = 13 symmetry, in some species (AHSV) it can form flat hexagonal crystals, involved in cell entry and core particle infectivity in adults and cells of vector insects, reacts with “core neutralizing” antibodies, Immuno dominant virus species specific antigen. |
|
8 |
1,124 |
20-1090 |
NS2(ViP) |
40,999 |
0 |
Important viral inclusion body matrix protein, ssRNA binding, phosphorylated. Can be associated with outer capsid. |
|
9 |
1,046 |
16-999 |
VP6(Hel) VP6a |
35,750 |
60 |
ssRNA and dsRNA binding, Helicase, NTPase. |
|
10 |
822 |
20-706 |
NS3 |
25,572 |
0 |
Glycoproteins, membrane proteins, involved in cell exit. In some species (AHSV) these are variable proteins and are involved in determination of virulence. |
|
NS3a |
24,020 |
0 | ||||
§: protein structure/function: RNA polymerase = “Pol”; capping enzyme = “Cap”; Inner virus structural protein with T = 13 symmetry = “T13”; Inner virus structural protein with T = 2 symmetry = “T2”; viral inclusion body or viroplasm matrix protein = “ViP”; virus tubule protein = “TuP”; protein with helicase activity = “Hel”. Other species within the genus may have proteins with significant differences in sizes.
Table 5 List of the dsRNA segments of Simian rotavirus A/SA11, with their respective size (bp) and their encoded proteins, for which the name, calculated size, location, copy number per virion and functions or properties are indicated.
|
dsRNA Segment number |
dsRNA Segment size (bp) |
ORF |
Protein nomen-clature § (protein structure/ function) |
Protein size: Mr (number of aa) |
Protein copies per particle |
Function (location) |
|
1 |
3302 |
18-3285 |
VP1 (Pol) |
125,005 (1088) |
<25 |
RNA dependent RNA polymerase (subcore) |
|
2 |
2690 |
16-2662 |
VP2 (T2) |
102,431 (880) |
120 |
Binds RNA, two leucine zipper motifs, myristoylated, cleaved (innermost core shell protein) |
|
3 |
2591 |
49-2557 |
VP3 (Cap) |
98,120 (835) |
<25 |
Guanylyltransferase, basic protein (subcore) |
|
4 |
2362 |
9-2340 |
VP4 |
86,782 (776) |
120 |
Surface spike protein of outer virion shell, P-type neutralization antigen. Dimer haemagglutinin, cell attachment protein, involved in virulence. Cleavage by trypsin into VP5* and VP8* enhances infectivity. |
|
VP5* |
||||||
|
VP8* |
28,000 (247) |
|||||
|
5 |
1611 |
30-1518 |
NSP1 |
58,654 (495) |
0 |
Viral protein showing greatest intra-species diversity, conserved cysteine rich zinc finger region near amino terminus. Component of pre-core RI (nonstructural). |
|
6 |
1356 |
23-1217 |
VP6 (T13) |
44,816 (397) |
780 |
Major virion protein, making up middle shell in form of trimeric units. Carries group and sub-group antigenic determinants. Myristoylated, hydrophobic (inner capsid protein). |
|
7 |
1104 |
25-976 |
NSP3 |
34, 600 (315) |
0 |
Cytoskeleton associated, binds specifically to 3-end region of rotavirus mRNAs, oligomer. |
|
8 |
1059 |
46-1000 |
NSP2 (VIP) |
36,700 (317) |
0 |
Basic protein, possible role in RNA replication. Forms multimers, associates with VP1, involved in viroplasm formation, exhibits non-specific ssRNA binding (nonstructural: present in viroplasms). |
|
9 |
1062 |
48-1029 |
VP7 (1) |
37,368 (326) |
780 |
Cleaved signal sequence, high mannose glycosylation, RER integral membrane glycoprotein, possible cell attachment protein, G type neutralization antigen, 2 hydrophobic N terminal regions, bicistronic gene (same reading frame), putative Ca2+ binding site, (aa 127-157), (surface glycoprotein). |
|
135-1029 |
VP7 (2) |
33,919 (297) | ||||
|
mature cleaved form |
(276) | |||||
|
10 |
751 |
41-569 |
NSP4 |
20,290 (175) |
0 |
N linked high mannose, glycosylation and trimming, uncleaved signal sequence, RER trans membrane glycoprotein, 2 hydrophobic N-terminal regions, role in morphogenesis, ER budding, putative Ca2+ binding site enterotoxin, (nonstructural). |
|
11 |
667 |
20-618 |
NSP5 |
21,725 (198) |
0 |
Phosphorylated, O linked glycosylation. Slightly basic, serine threonine rich, RNA binding, kinase interacts with NSP6 (nonstructural: present in viral inclusion bodies). |
|
80-355 |
NSP6 |
11,012 (92) |
Product of 2nd ORF (different reading frame). Interacts with NSP5, (nonstructural: present in viral inclusion bodies). | |||
§: protein structure/function: RNA polymerase = “Pol”; capping enzyme = “Cap”; Inner virus structural protein with T = 13 symmetry = “T13”; Inner virus structural protein with T = 2 symmetry = “T2”; viral inclusion body or viroplasm matrix protein = “ViP”. Other species within the genus may have proteins with significant differences in sizes.
Table 6 Percentage amino acid differences between rotavirus VP2(T2) major core protein from rotavirus isolates of Rotavirus A, B and C.
|
RV-A |
RV-C |
RV-B | |||||||
|
BoRV-A/UK |
BoRV-A/RF |
SiRV-A/SA11 |
HuRV-A/Wa |
AvRV-A/PO-13 |
PoRV-C |
MuRV-B/IDIR |
HuRV-B/ADRV | ||
|
Accession # |
X52589 |
X14057 |
X16831 |
X14942 |
AB009630 |
M74217 |
U00673 |
M91433 | |
|
RV-A |
BoRV-A/UK |
0.0 |
2.2 |
7.4 |
9.1 |
24.9 |
55.2 |
81.6 |
82.4 |
|
BoRV-A/RF |
2.2 |
0.0 |
6.3 |
8.1 |
24.3 |
54.5 |
81.6 |
82.3 | |
|
SiRV-A/SA11 |
7.4 |
6.3 |
0.0 |
8.4 |
24.0 |
54.8 |
81.9 |
82.7 | |
|
HuRV-A/Wa |
9.1 |
8.1 |
8.4 |
0.0 |
24.3 |
54.5 |
81.9 |
82.7 | |
|
AvRV-A/PO-13 |
24.9 |
24.3 |
24.0 |
24.3 |
0.0 |
52.9 |
82.9 |
84.0 | |
|
RV-C |
PoRV-C |
55.2 |
54.5 |
54.8 |
54.5 |
52.9 |
0.0 |
84.1 |
84.3 |
|
RV-B |
MuRV-B/IDIR |
81.6 |
81.6 |
81.9 |
81.9 |
82.9 |
84.1 |
0.0 |
14.0 |
|
HuRV-B/ADRV |
82.4 |
82.3 |
82.7 |
82.7 |
84.0 |
84.3 |
14.0 |
0.0 | |
BoRV, Bovine rotavirus; SiRV, Simian rotavirus; HuRV, Human rotavirus; MuRV, Murine rotavirus; AvRV, Avian rotavirus; PoRV, Porcine rotavirus.
Table 7 Conserved terminal sequences of coltivirus genome segments
|
Virus species |
(strain) |
Conserved RNA terminal sequences (+ve strand) |
|
CTFV |
(CTFV) |
5-G/CACAUUUUGU.........................UGCAGUG/C-3 |
|
KDV |
(KDV-Ja7075) |
5-GUAGAAA/UA/UA/UU....................AA/CC/UGAC-3 |
|
BAV |
(BAV-In6423) |
5-GUAU A/UA/UAAA/UA/UU.........A/GCC/UGAC-3 |
Table 8 List of the dsRNA segments of Colorado tick fever virus (CTFV) with their respective size (bp) and their encoded proteins for which the name and calculated Mr ( 103) are shown.
|
dsRNA Segment number |
dsRNA Size (bp) |
Protein nomenclature |
Protein Mr ( 103), determined from translation products of the dsRNA ¥ |
|
1 |
4,140 |
VP1 |
125 |
|
2 |
3,890 |
VP2 |
117 |
|
3 |
3,550 |
VP3 |
113 |
|
4 |
3,050 |
VP4 |
100 |
|
5 |
2,370 |
VP5 |
90 |
|
6 |
2,100 |
VP6 |
82 |
|
7 |
2,100 |
VP7 |
75 |
|
8 |
1,990 |
VP8 |
60 |
|
9 |
1,830 |
VP9 |
55 |
|
10 |
1,884* |
VP10 |
42 (38 and 67.3) |
|
11 |
998* |
VP11 |
34 (28.5) |
|
12 |
675* |
VP12 |
25 (20.4) |
¥: Values between parenthesis represent the size of the proteins calculated from the amino-acid sequences deduced from RNA nucleotide sequences.
*: size determined by sequencing.
Table 9 List of the dsRNA segments of Banna virus-Indonesia 6423 (BAV-In6423) 1-12 with their respective size (bp) and their encoded proteins for which the name, calculated Mr ( 103), function and/or location are indicated.
|
dsRNA Segment number |
dsRNA Size (bp) |
Protein nomenclature |
Mr ( 103) calculated from the sequenced segments |
Structure/function |
|
1 |
3750 |
VP1 |
- |
- |
|
2 |
3000 |
VP2 |
- |
- |
|
3 |
2370 |
VP3 |
- |
- |
|
4 |
2020 |
VP4 |
- |
- |
|
5 |
1690 |
VP5 |
- |
- |
|
6 |
1660 |
VP6 |
- |
- |
|
7 |
1136* |
VP7 |
34.97 |
Contains motifs found in catalytic domains of kinases |
|
8 |
1119* |
VP8 |
32.62 |
- |
|
9 |
1101* |
VP9 |
30.52 |
- |
|
10 |
977* |
VP10 |
28.5 |
- |
|
11 |
867* |
VP11 |
20.6 |
- |
|
12 |
862* |
VP12 |
23.75 |
Contains dsRNA binding motifs |
*: size determined by sequencing.
Table 10 List of the dsRNA genome segments of Striped bass reovirus (SBRV) (ARV-A species), with their estimated size (kbp), corresponding proteins with name, size (estimated), and location.
|
Genome segment |
dsRNA Segment size (kbp) |
Protein nomenclature |
Protein size ( 103) |
Protein location |
|
Segment 1 |
3.8 |
VP1 |
130 |
Inner capsid (core) |
|
Segment 2 |
3.6 |
VP2 |
127 |
Inner capsid (core) |
|
Segment 3 |
3.3 |
VP3 |
126 |
Inner capsid (core) |
|
Segment 4 |
2.5 |
VP4 |
97 |
Nonstructural |
|
Segment 5 |
2.4 |
VP5 |
71 |
Inner capsid (core) |
|
Segment 6 |
2.2 |
VP4 |
73 |
Inner capsid (core) |
|
Segment 7 |
1.5 |
NS4 |
28 |
Nonstructural |
|
Segment 8 |
1.4 |
VP6 |
46 |
Inner capsid (core) |
|
Segment 9 |
1.2 |
NS2 |
39 |
Nonstructural |
|
Segment 10 |
0.9 |
VP7 |
34 |
Major outer capsid |
|
Segment 11 |
0.8 |
NS3 NS5 |
2915 |
Nonstructural Nonstructural |
Table 11 Conserved terminal sequences of cypovirus genome segments
|
Virus species |
Conserved RNA terminal sequences (+ve strand) |
|
CPV-1 |
5-AGUAAA . . . . . . . . . . . . . . . . . . GUUAGCC-3 |
|
CPV-5 |
5-AGUUU . . . . . . . . . . . . GAGUUUGC-3 |
|
CfCPV |
5-AGUUU . . . . . . . . . . . . . . . . . . UUUGUGC-3 |
Table 12 Cypovirus genome segment size distribution (kbp) estimated from electrophoretic comparisons of the genomic dsRNA of Cypovirus 1 to 14.
|
Genome segment number |
Cypovirus 1 to 14 | |||||||||||||
|
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
12 |
13 |
14 | |
|
Total Mr |
31.3 |
30.8 |
32.3 |
33.3 |
31.8 |
32.8 |
31.0 |
32.7 |
29.2 |
33.4 |
30.9 |
31.6 |
30.5 |
31.3 |
|
1 |
5.47 |
4.91 |
5.19 |
5.04 |
5.04 |
5.04 |
5.23 |
5.49 |
5.23 |
5.21 |
5.56 |
5.36 |
5.15 |
5.58 |
|
2 |
5.19 |
4.91 |
4.98 |
5.04 |
5.04 |
4.91 |
5.02 |
5.49 |
5.06 |
5.21 |
5.32 |
4.98 |
5.15 |
5.11 |
|
3 |
4.98 |
4.63 |
4.98 |
5.04 |
5.04 |
4.78 |
4.87 |
5.32 |
4.93 |
4.8 |
5.32 |
4.98 |
4.88 |
5.04 |
|
4 |
4.35 |
4.42 |
4.46 |
4.72 |
4.46 |
4.50 |
4.61 |
4.74 |
4.38 |
4.87 |
4.63 |
4.44 |
4.35 |
4.40 |
|
5 |
3.90 |
2.68 |
4.35 |
2.94 |
3.90 |
3.30 |
3.07 |
4.46 |
2.83 |
3.02 |
2.40 |
3.99 |
3.87 |
4.23 |
|
6 |
2.40 |
2.34 |
2.77 |
2.62 |
2.62 |
2.85 |
2.75 |
2.30 |
2.08 |
2.77 |
2.40 |
2.42 |
1.93 |
2.40 |
|
7 |
1.80 |
2.17 |
2.60 |
2.36 |
2.49 |
2.70 |
2.45 |
1.57 |
2.08 |
2.77 |
1.63 |
1.74 |
1.70 |
1.39 |
|
8 |
1.33 1.328* |
1.89 |
1.31 |
2.08 |
1.46 |
1.97 |
1.31 |
1.44 |
0.94 |
2.04 |
1.54 |
1.54 |
1.38 |
1.29 |
|
9 |
1.20 1.186* |
1.67 |
1.01 |
1.74 |
1.07 |
1.69 |
1.03 |
1.07 |
0.84 |
1.46 |
1.18 |
1.37 |
1.18 |
1.09 |
|
10 |
0.75 0.942* |
1.18 |
0.73 |
1.74 |
0.73 0.883* |
1.09 |
0.64 |
0.79 |
0.84 |
1.20 |
0.86 |
0.77 |
0.94 |
0.79 |
Previously published estimates of genome segment sizes for CPV-1 to 12 and 14 have been adjusted in line with Mr values calculated by Galinski et al., (1982). The genome segment 10 of CfCPV is 1171 bp.
*: Values calculated from analyses of the RNA sequence.
Table 13 List of dsRNA segments of Bombyx mori cypovirus 1 (BmCPV-1) and the proteins for which they code, estimated protein sizes ( 103) and function are indicated.
|
dsRNA Segment number |
Size (kbp) |
Protein nomenclature § (protein structure/function) |
Mr ( 103) |
Protein copy number per particle |
Function (location) |
|
1 |
5.47 |
V1 |
146 |
No information |
(Virion) |
|
2 |
5.19 |
V2 |
138 |
” |
(Virion) |
|
3 |
4.98 |
138 |
” |
Unknown | |
|
4 |
4.35 |
V3 |
125 |
” |
(Virion) |
|
5 |
3.9 |
NS1 |
107 |
0 |
Nonstructural |
|
NS2 |
80 |
||||
|
NS6 |
23 |
||||
|
6 |
2.4 |
V4 |
70 |
No information |
(Virion) |
|
7 |
1.8 |
NS3 |
58 |
0 |
Nonstructural |
|
NS4 |
61 |
||||
|
8 |
1.328* |
(P44) |
44* |
No information |
Unknown (shows anomalous migration during PAGE, with apparent Mr of 55 103) |
|
9 |
1.186* |
NS5 |
36* |
0 |
Nonstructural, dsRNA binding |
|
10 |
0.942* |
polyhedrin (Pod) |
28.5* |
Unknown |
Polyhedron matrix protein (Pod) |
§: Polyhedrin = “Pod”. *: Size determined by sequence analysis of the genome segment 8, 9 and 10.
Table 14 Terminally conserved oligonucleotide sequences of some Fijiviruses.
|
Virus |
Sequence |
|
MRDV |
5-AAGUUUUUU------------------UGUC-3 |
|
RBSDV |
5-AAGUUUUU---------AGCUNN(C/U)GUC-3 |
|
OSDV |
5-AACGAAAAA--------UUUUUUUUAGUC-3 |
|
NLRV |
5-AGU-----------------------GUUGUC-3 |
Table 15 Genome organization of the members of the genus Fijivirus.
|
dsRNA Segment |
Size (bp) |
G+C content (%) |
ORFs |
Protein size ( 103) |
§, ¥: Protein function (location) |
Equivalent genome segment from other viruses |
|
Rice black streaked dwarf virus, RBSDV | ||||||
|
Segment 7 |
2193 |
33.9 |
42-1130 1183-2112 |
41.2 36.4 |
Nonstructural Tubular structure (TuP) Nonstructural |
(MRDV-S6) (OSDV-S7) (NLRV-S10)* |
|
Segment 8 |
1927 |
34.5 |
25-1800 |
68.1 |
Core protein (¥ possible NTP-binding†) |
(MRDV-S7) (OSDV-S9) (NLRV-S7) |
|
Segment 9 |
1900 |
34.0 |
52-1095 1160-1789 |
39.9 24.2 |
Non-structural, viroplasm Viroplasm (ViP) Nonstructural |
(MRDV-S8) (OSDV-S10) (NLRV-S9) |
|
Segment 10 |
1801 |
36.2 |
22-1698 |
63.3 |
Major outer shell |
(MRDV-S10) (OSDV-S8) (NLRV-S8) |
|
Maize rough dwarf virus, MRDV | ||||||
|
Segment 6 |
2193 |
34.6 |
42-1130 1183-2112 |
41.0 36.3 |
Unknown (¥ possible, nonstructural and (TuP)) Unknown |
(RBSDV-S7) (OSDV-S7) (NLRV-S10)* |
|
Segment 7 |
1936 |
34.6 |
25-1800 |
68.1 |
Unknown (¥ possible core protein and NTP-binding†) |
(RBSDV-S8) (OSDV-S9) (NLRV-S7) |
|
Segment 8 |
1900 |
34.2 |
52-1095 |
40.0 |
Unknown (¥ possible Nonstructural and (ViP)) |
(RBSDV-S9) (OSDV-S10) (NLRV-S9) |
|
1160-1789 |
24.2 |
Unknown |
||||
|
Segment 10 |
1802 |
36.5 |
23-1699 |
62.9 |
Unknown (¥ possible major outer shell) |
(RBSDV-S10) (OSDV-S8) (NLRV-S8) |
|
Oat sterile dwarf virus, OSDV | ||||||
|
Segment 7 |
1944 |
35.6 |
42-1148 |
42.0 |
Unknown (¥ possible nonstructural and (TuP)) |
(MRDV-S6) (RBSDV-S7) |
|
1186-1863 |
30.0 |
Unknown |
(NLRV-S10)* | |||
|
Segment 8 |
1874 |
33.8 |
20-1786 |
66.2 |
Unknown (¥ possible major outer shell) |
(MRDV-S10) (RBSDV-S10) (NLRV-S8) |
|
Segment 9 |
1893 |
34.6 |
15-1766 |
68.2 |
Unknown (¥ possible core protein and NTP-binding†) |
(MRDV- S7) (RBSDV-S8) (NLRV- S7) |
|
Segment 10 |
1761 |
34.5 |
51-998 |
35.7 |
Unknown (¥ possible nonstructural and (ViP)) |
(MRDV-S8) (RBSDV-S9) |
|
1028-1612 |
22.7 |
Unknown |
(NLRV-S9) | |||
|
Nilaparvarta lugens reovirus, NLRV | ||||||
|
Segment 1 |
4391 |
33.5 |
21-4349 |
165.9 |
Core, RNA polymerase (Pol) |
|
|
Segment 2 |
3732 |
33.1 |
22-3621 |
136.6 |
Outer shell, B spike |
|
|
Segment 3 |
3753 |
34.2 |
15-3686 |
138.5 |
Major core |
|
|
Segment 4 |
3560 |
33.8 |
76-3474 |
130 |
Unknown |
|
|
Segment 5 |
3427 |
39 |
202-3120 |
106.4 |
Unknown |
|
|
Segment 6 |
2970 |
36.8 |
150-2642 |
95.1 |
Unknown |
|
|
Segment 7 |
1994 |
34.1 |
41-1930 |
73.5 |
Core protein, NTP-binding† |
(OSDV- S9) (MRDV- S7) (RBSDV-S8) |
|
Segment 8 |
1802 |
35.3 |
7-1695 |
62.4 |
Major outer shell |
(OSDV-S8) (MRDV-S10) (RBSDV-S10) |
|
Segment 9 |
1640 |
33.2 |
53-925 |
33.0 |
Nonstructural (¥ possible (ViP)) |
(OSDV-S10) (MRDV-S8) |
|
982-1602 |
23.6 |
Nonstructural |
(RBSDV-S9) | |||
|
Segment 10* |
1430 |
35.2 |
46-1341 |
49.4 |
Nonstructural (¥ possible (TuP)) |
(OSDV-S7) (MRDV-S6) (RBSDV-S7) |
*: genome segment 10 of NLRV does not contain a second open reading frame.
†: NTP binding proteins of some other genera [eg. VP4 (Cap) of BTV {Orbivirus}, or P5 (Cap) of RDV {Phytoreovirus} have guanylyltransferase and/or transmethylase activities involved in cap formation].
§: protein structure/function: RNA polymerase = “Pol”; Capping enzyme = “Cap”; Virus structural Viral inclusion body or viroplasm matrix protein = “ViP”. Virus tubule protein = “TuP”.
¥: the probable function of some of the proteins that are uncharacterized may be indicated by the equivalence of the genome segments from which they are translated, to those of other virus species.
Table 16 Genome organization of Rice dwarf virus (RDV) Akita isolate, listing the dsRNA segments, with their size (bp), and corresponding proteins with name, size (*estimated by SDS PAGE), and function and/or location.
|
Genome Segment (S) number |
dsRNA Size (bp) |
Non-coding regions (bp) 5-3 |
Protein nomenclature (§: structure/function) |
Protein Mr ( 103). *Predicted size from SDS PAGE |
Function and location (number of molecules per particle) | |
|
1 |
4423 |
35-53 |
P1 (Pol) |
164,142 |
*170 |
Core, RNA polymerase |
|
2 |
3512 |
14-147 |
P2 |
122,994 |
*130 |
Outer capsid, essential for vector transmission |
|
3 |
3195 |
38-97 |
P3 |
114,298 |
*110 |
Major core (120) |
|
4 |
2468 |
63-221 |
Pns4 |
79,836 |
*83 |
Nonstructural |
|
5 |
2570 |
26-138 |
P5 (Cap) |
90,532 |
*89 |
Core, guanylyltransferase |
|
6 |
1699 |
48-121 |
Pns6 |
57,401 |
*56 |
Nonstructural |
|
7 |
1696 |
25-150 |
P7 |
55,287 |
*58 |
Core, nucleic acid binding protein |
|
8 |
1427 |
23-138 |
P8 (T13) |
46,483 |
*43 |
Major outer capsid (780) |
|
9 |
1305 |
24-225 |
Pns9 |
38,912 |
*49 |
Nonstructural |
|
10 |
1321 |
26-233 |
Pns10 |
39,196 |
*35 |
Nonstructural |
|
11 |
1067 |
29-492 |
Pns11a |
19,988 |
*23 |
Nonstructural |
|
5-492 |
Pns11b |
20,759 |
*24 |
|||
|
12 |
1066 |
41-86 |
Pns12 |
33,916 |
*34 |
Nonstructural |
|
312-475 |
Pns12OPa |
10,551 |
*8 |
|||
|
336-475 |
Pns12OPb |
9,597 |
*7 |
|||
§: protein structure/function: RNA polymerase = “Pol”; capping enzyme = “Cap"; structural protein arranged with T = 13 icosahedral symmetry = “T13”.
Table 17 List of the segments of Rice ragged stunt virus (RRSV), with their estimated size (bp), and corresponding proteins with name, Mr (estimated), and function and/or location.
|
dsRNA Segment number |
Size (bp) |
Protein nomenclature § (protein structure/function) |
Protein Mr predicted ( 103) |
Protein Mr apparent ( 103) |
Function (location) |
|
1 |
3849 |
P1 |
137.7 |
137 |
Virus core associated (B Spike) |
|
2 |
3810 |
P2 |
133.1 |
118 |
(Inner core capsid) |
|
3 |
3699 |
P3 |
130.8 |
130 |
(Major core capsid) |
|
4 |
3823 |
P4A (Pol) |
141.4 |
145 |
RDR polymerase (Unknown) |
|
P4B |
36.9 |
||||
|
5 |
2682 |
P5 (Cap) |
91.4 |
90 |
Capping enzyme/ guanyltransferase |
|
6 |
2157 |
P6 |
65.6 |
||
|
7 |
1938 |
NS7 |
68 |
66 |
(Nonstructural) |
|
8 |
1814 |
P8 |
67.3 |
67 |
Precursor |
|
P8A |
25.6 |
Protease | |||
|
P8B |
41.7 |
47/44 |
(Major capsid) | ||
|
9 |
1132 |
P9 |
38.6 |
37 |
Vector transmission (Spike) |
|
10 |
1162 |
NS10 |
32.3 |
32 |
Nonstructural |
§: protein structure/function: RNA polymerase = “Pol”; Capping enzyme = “Cap”.
Data from Upadhyaya, Yang, Kositratana, Gosh and Waterhouse, 1995; 1996, Upadhyaya, Ramm, Gellatly, Li, Kositratana and Waterhouse, 1997; 1998; Li et al., 1996; Suga et al., 1995.
Table 18 Comparison of sequences around the conserved RDRP motifs of reoviruses.
|
BTV (515) |
PIKATRTI 72 |
DYSEYDTH 119 |
SGENSTLIANSMHNMA 21 |
EQYVGDDTLFYTKLD 22 |
HEASPSKTM (804) |
|
Rotavirus (455) |
PGRRTRII 57 |
DVSQWDSS 63 |
SGEKQTKAANSIANLA 19 |
IRVDGDDNYAVLQFN 20 |
RMNAKVKAL (669) |
|
RDV (643) |
AWRPVRPI 73 |
DCTSWDQT 76 |
SGRLDTFFMNSVQNLI 20 |
FQVAGDDAIM.VYDG 24 |
HIINPQKTV (890) |
|
Reovirus S3 (521) |
VQRRPRSI 56 |
DISACDAS 89 |
SGSTATSTEHTANNST 31 |
YVCQGDDGLM.IIDG 21 |
GEEFGWKYD (772) |
|
NLRV (646) |
IDRRGRII 60 |
DMSGMDAH 90 |
SGLFATSGQHT.MFLV 20 |
NYVMGDDIFQNIKNG 24 |
IDGNYSKYS (894) |
|
RRSV (500) |
IGRRQRAI 62 |
DASVQASV 83 |
SGQPFTTVHHTFTLSN 1 |
LTVQGDDTRT.INYG 15 |
VSDWGFKVS (735) |
|
Consensus |
.grrtRiI |
D.s.wd.. |
SGe.aTs.a. . . . nla |
.qvqGDDtlm.ikdg |
he.n.sK.s |
|
Motifs |
I |
IV,1,A |
V,2,B |
VI,3,C |
D |
The regions covering the putative polymerase module in RRSV P4 (aa 500 to 735) and other reoviruses were analyzed using the GCG program PILEUP and further aligned manually taking into account the polymerase motifs presented and aligned by Poch et al., (1989) (A-D), Bruenn (1993) (1-3) and Koonin (1992) (I, IV-VI).
Table 19 Unassigned and incompletely characterized members of the family Reoviridae
|
Virus |
Source or host species |
Abbreviation |
Characteristics |
|
Insect viruses | |||
|
Cimex lactularius reovirus |
Cimex lactularius (Hemiptera: bed bug) |
(ClRV) |
Eleven genome segments, icosahedral double shelled ca. 50 nm in diameter |
|
Dacus oleae reovirus |
Dacus oleae (Diptera olive fly) |
(DoRV) |
Non-occluded, double shelled capsid, spiked core, ten genome segments |
|
Diadromus pulchellus reovirus |
Diadromus pulchellus (Hymenoptera: wasp) |
(DpRV) |
Sequence data for 7 segments [X80481; X80480; X82045; X82046; X82047; X82048; X82049] indicates no close relationships to members of established genera. |
|
Terminal sequences (5A/GCAAUUUUnnACU . . . . . . AGUAAAAAAAUn A/GG3) are different from species in other genera. Usually 10 segments, plus eleventh non-equimolar segment depending on sex and ploidy of wasp. | |||
|
Drosophila reoviruses including several distinct strains: |
Non-occluded, double shelled capsid, spiked core, ten genome segments. | ||
|
Drosophila F virus |
Drosophila melanogaster (Diptera: fruit fly) and D. melanogaster cell lines. |
(DFV) |
CIV has a distinct genome segment electrophoretic migration pattern (only 9 bands) and is serologically distinct from DFV. |
|
Drosophila S virus |
D. simulans |
(DSV) | |
|
Ceratitis capitata reovirus Ceratitis I virus |
Ceratitis capitata (Diptera) |
(CIV) |
|
|
Hyposoter exiguae reovirus |
Hyposoter exiguae |
(HeRV) |
Non-occluded, Buds from cell, transient envelope, non-enveloped particle is 65 nm diameter, 10 segments dsRNA-4 large and 6 small, infects all wasps in colony, both ovaries and testes infected. Does not affect and is not affected by sex of host. |
|
Musca domestica reovirus (housefly virus) |
Musca domestica (Diptera: housefly) |
(MdRV) |
Non-occluded, icosahedral particles ca. 70 nm in diameter |
|
Crustacean viruses | |||
|
Macropipus depurator P virus |
Macropipus depurator (Decapoda: crab) |
(MdRV-P) |
12 genome segments double layered capsid ca 65 nm in diameter |
|
Carcinus mediterraneus W2 virus |
(Decapoda: crab) |
(CcRV-W2) |
12 genome segments |
|
Porcelio dilatatus reovirus |
Porcellio dilatatus (Isopoda: terrestrial crustacean) |
(PdRV) |
uncharacterized |
|
Arachnid viruses | |||
|
Buthus occitanus reovirus |
Buthus occitanus (Scorpionidae: scorpion) |
(BoRV) |
uncharacterized |
|
|