Supplementary Table S1 CSVd isolates and variants described in this study
No. / Variant No. a / Isolate b / Country c / Accession No. d / Synonyms e / Reference1 / UK1 / English / United Kingdom / M19506 / DEV1; JPV2; LV1; NL1 / [1, 2]
2 / UK2 / — / UK / GQ174501 f
3 / UK3 / — / UK / GQ174502 f
4 / AU1 / Adelaide / Australia / V01107 (M19505); E13156 g / [3]
5 / AU1.1 h / Adelaide / AU / JQ809252
6 / AU1.2 h / Adelaide / AU / JQ809253
7 / AU1.3 h / Adelaide / AU / JQ809254
8 / US1 / Cornell Univ. / United States / X16409 (X17313) / Ithaca / [4-6]
9 / US1.1 h / CU / US / JQ809256
10 / US1.2 h / CU / US / JQ809357
11 / US1.3 h / CU / US / JQ809258
12 / US1.4 h / CU / US / JQ809259
13 / US1.5 h / CU / US / JQ809260
14 / US1.6 h / CU / US / JQ809261
15 / US1.7 h / CU / US / JQ809262
16 / US1.8 h / CU / US / JQ809263
17 / US1.9 h / CU / US / JQ809364
18 / US1.10 h / CU / US / JQ809265
19 / US1.11 h / CU / US / JQ809266
20 / US1.12 h / CU / US / JQ809267
21 / US1.13 h / CU / US / JQ809268
22 / US2 i / Beltsville / US / X16408 / CNV1; DEV2; JPV1; KRV1 / [5, 7]
23 / CNV1 / Beijing-1;
H5-2 / China / FJ031232 f
HQ891019 / DEV2; JPV1; KRV1; US2
24 / CNV2 / H5-1 / CN / HQ891018 / KRV4
25 / CNV3 j / Beijing-2 / CN / JQ809255 / CN3
26 / JPV1 / 14 isolates / Japan / X16408 / CNV1; DEV2; KRV1; US2 / [8, 9]
27 / JPV2 / 4 isolates / JP / M19506 / DEV1; LV1; NL1; UK1 / [8]
28 / JPV3 / 2 isolates / JP / D88895; AB689032 / J1; P4-12 / [8, 10]
29 / JPV4 / 1 isolate / JP / AB279770 / Strain 6 / [8]
30 / JPV5 / 2 isolates / JP / AB279769 / Strain 4; Ok8 k / [8, 11]
31 / JPV6 / 1 isolate / JP / AB006737 / Poplar / [8,12]
32 / JPV7 / 1 isolate / JP / — / [8, 13]
33 / JPV8 / 1 isolate / JP / — / [8,14]
34 / JPV9 / 1 isolate / JP / AB055974 / J3
35 / JPV10 / 1 isolate / JP / AB255879 / Dahlia / [15]
36 / JPV11 / 1 isolate / JP / AB255880 / Dahlia
37 / JPV12 / 1 isolate / JP / AB279768 / Strain 3; KRV5
38 / JPV13 / 1 isolate / JP / AB279771 / Strain 7
39 / JPV14 / 1 isolate / JP / — / Fkc / [11]
40 / JPV15 / 1 isolate / JP / — / Mkz / [11]
41 / JPV16 / 1 isolate / JP / — / Ok2 / [11]
42 / JPV17 / 1 isolate / JP / — / Ok7 / [11]
43 / JPV18 / 1 isolate / JP / AB689031 / P4-16
44 / JPV19 / 1 isolate / JP / AB689033 / P4-1
45 / JPV20 / 1 isolate / JP / AB679034 / P4-7
46 / KRV1 / 18 isolates / S. Korea / AF394452; AB679193, -195, -196, -197, -198, -199, -200, -201, -202, -203, -204, -205, -207, -208, -209, -210, -212 / K1; SK1, -3, -4, -5, -6, -7, -8, -9, -10, -11, -12, -13, -15, -16, -17, -18, -20 / [16]
47 / KRV2 / 1 isolate / KR / AF394453 / K2 / [16]
48 / KRV3 / 1 isolate / KR / AB679194 / SK2
49 / KRV4 / 2 isolates / KR / AB679206, -211 / SK14, -19
50 / KRV5 / 1 isolate / KR / AB679213 / SK21, JPV12
51 / KRV6 / 1 isolate / KR / AB679214 / SK22
52 / INV1 / Indian / India / AJ585258
53 / INV2 / Maharashtra / IN / AJ969017
54 / INV3 / Palampur / IN / FN646407
55 / INV4 / 11 isolates l / IN / FN669530, -31, -32, -33, -34, -35, -36, -37, -38, -39, -40
56 / INV5 / Discovery c1 / IN / FN673553
57 / INV6 / Discovery c2 / IN / FN673554
58 / LV1 / Blanka / Latvia / AJ001849 / DEV1; JPV2; NL1; UK1
59 / LV2 / r petal / LV / AJ001850 / Diplomat pink
60 / LV3 / r leaves / LV / AJ001851 / Diplomat pink
61 / LV4 / wr / LV / AJ001852 / Diplomat red
62 / LV5 / v / LV / AJ001853 / Diplomat magenta
63 / DEV1 / 3 isolates m / Germany / M19506 / K649, K653, D; K465 (NL1); JPV2; LV1; UK1 / [5]
64 / DEV2 / 2 isolates n / DE / X16408 / R, K472; K275 (US2); K655 (JP); JPV1; KRV1 / [5]
65 / DEV3 / B / DE / X16407 / [5]
66 / DEV4 / Ageratum / DE / Z68201
67 / ITV1 / 2 isolateso / Italy / JQ685734, -35 / 1,2; CNV1; DEV2; JPV1; KRV1; US2 / [17]
68 / ITV2 / 1isolate0 / IT / JQ685736 / 3 / [17]
69 / ITV3 / 2 isolateso / IT / JQ685737, -38 / 4, 5; CNV2; KRV4 / [17]
70 / ITV4 / 1 isolateo / IT / JQ685739 / 6 / [17]
71 / ITV5 / 2 isolateso / IT / JQ685740, -41 / 7, 8 / [17]
72 / ITV6 / 1 isolateo / IT / JQ685742 / 9 / [17]
73 / NL1 / K465 / The Netherlands / M19506 / DEV1; JPV2; LV1;UK1 / [5]
74 / NL2 / Petunia / NL / U82445 / [18]
75 / NL3 / —p / NL / DQ406591 / [19]
76 / AT1 / 37 p / Austria / JF414238
77 / CA1 / Vm q / Canada / DQ094298 / [20]
78 / EG1 / — / Egypt / GQ229575 f
79 / FR1 / AF164 o / France / JF938538 / [21]
80 / HU1 / — / Hungary / AJ000046
a = This is same as the isolate number (e.g., UK1) when only a single isolate from that country had the particular sequence, but is a variant number (e.g., JPV1), when more than one isolate from that country showed the same sequence; b = original name of isolate, or number of isolates, if more than one with the same sequence; c = country of isolation; d = GenBank Accession number, or given as — if not submitted; e = other names for the same isolate; f = partial sequence; g = this Accession No. deposited from Japan as part of a patent on use of primers for detecting CSVd, is not of a Japanese isolate, but a copy of the Australian isolate (deposited originally as M19595); h = cDNA clone of the isolate; i = ATCC PV105; j = nine cDNA clones with the same sequence; k = sequence of isolate Ok8 not in the GenBank, but the same as for “Strain 4”; l = isolate names different for each and are given on Accession Number data sheets; m = four new isolates were given, three of which originated from Germany and one (K645) from The Netherlands, here designated as NL1; n = four new isolates were given, two of which originated from Germany, one (K275) from the US and designated US2 here, and one (K655) from Japan, which had the same sequence as JPV1; o = isolated from Argyranthemum frutescens; p =isolated from Solanum jasminoides; q =isolated from Vinca major.
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Supplementary Table S2 Variation in sequence between cDNA clones of CSVd isolate AU1
Number (and position) of nucleotide differences between isolate clone numbersAU1.1 / AU1.2 / AU1.3
AU1.1 / — / 2 (214, 254) / 1 (71)
AU1.2 / 2 (214, 254) / — / 3 (71, 214, 254)
AU1.3 / 1 (71) / 3 (71, 214, 254) / —
Supplementary Table S3 Variation in sequence between Chinese CSVd variants
Number (and position) of nucleotide differences between CNV numbersCNV1 / CNV2 / CNV3
CNV1 / — / 1 (298) / 3 (64, 65, 298)
CNV2 / 1 / — / 2 (64, 65)
CNV3 / 3 (64, 65, 298) / 2 (64, 65) / —
SupplementaryTable S4 Variation in sequence between UK CSVd isolates
Number of nucleotide differences between isolate numbersUK1 / UK2 / UK3
UK1 / — / 2 / 3
UK2 / — / 5
UK3 / —
SupplementaryTable S5 Variation in sequence between Dutch CSVd isolates
Number of nucleotide differences between isolate numbersNL1 / NL2 / NL3
NL1 / — / 6 / 4
NL2 / — / 8
NL3 / —
SupplementaryTable S6 Variation in sequence between Latvian CSVd isolates
Number of nucleotide differences between isolate numbersLV1 / LV2 / LV3 / LV4 / LV5
LV1 / — / 1/2 / 0/1 / 1 / 1
LV2 / — / 1/2 / 0/1 / 2/3
LV3 / — / 1/2 / 1/2
LV4 / — / 2
LV5 / —
SupplementaryTable S7 Variation in sequence between German CSVd variants
Number of nucleotide differences between DEV numbersDEV1 / DEV2 / DEV3 / DEV4
DEV1 / — / 1 / 1 / 4
DEV2 / — / 2 / 5
DEV3 / — / 4
DEV4 / —
Supplementary Table S8 Variation in sequence between Indian CSVd variants
Number of nucleotide differences between INV numbersINV1 / INV2 / INV3 / INV4 / INV5 / INV6
INV1 / — / 8 / 8 / 6 / 6 / 7
INV2 / — / 14 / 14 / 14 / 14
INV3 / — / 9 / 8 / 8
INV4 / — / 12 / 9
INV5 / — / 6
INV6 / —
Supplementary Table S9 Variation in sequence between Italian CSVd variants
Number of nucleotide differences between ITV numbersITV1 / ITV2 / ITV3 / ITV4 / ITV5 / ITV6
ITV1 / — / 4 / 1 / 2 / 4 / 5
ITV2 / — / 3 / 4 / 2 / 3
ITV3 / — / 1 / 3 / 4
ITV4 / — / 4 / 4
ITV5 / — / 1
ITV6 / —
Supplementary Table S10 Variation in sequence between Korean CSVd variants
Number of nucleotide differences between KRV numbersKRV1 / KRV2 / KRV3 / KRV4 / KRV5 / KRV6
KRV1 / — / 2 / 1 / 1 / 1 / 1
KRV2 / — / 3 / 3 / 3 / 3
KRV3 / — / 2 / 2 / 2
KRV4 / — / 2 / 2
KRV5 / — / 2
KRV6 / —
Supplementary Table S11 Variation in sequence between Japanese CSVd variants
Number of nucleotide differences between JPV numbers1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12 / 13 / 14 / 15 / 16 / 17 / 18 / 19 / 20
1 / — / 1 / 3 / 5 / 2 / 3 / 1 / 1 / 1 / 3 / 5 / 1 / 3 / 5 / 3 / 4 / 4 / 6 / 4 / 4
2 / — / 4 / 4 / 3 / 4 / 2 / 2 / 2 / 4 / 6 / 2 / 2 / 6 / 4 / 5 / 5 / 7 / 5 / 5
3 / — / 8 / 2 / 2 / 4 / 4 / 4 / 6 / 8 / 4 / 2 / 8 / 6 / 7 / 1 / 3 / 1 / 1
4 / — / 7 / 7 / 6 / 6 / 6 / 4 / 4 / 4 / 6 / 10 / 8 / 9 / 7 / 5 / 9 / 9
5 / — / 1 / 3 / 3 / 3 / 5 / 7 / 3 / 1 / 7 / 5 / 6 / 2 / 4 / 2 / 2
6 / — / 4 / 4 / 4 / 6 / 8 / 4 / 2 / 8 / 6 / 7 / 3 / 5 / 3 / 3
7 / — / 2 / 2 / 4 / 6 / 2 / 4 / 4 / 2 / 3 / 5 / 7 / 5 / 5
8 / — / 2 / 4 / 6 / 2 / 4 / 6 / 4 / 5 / 5 / 7 / 7 / 5
9 / — / 4 / 6 / 2 / 4 / 6 / 4 / 5 / 5 / 7 / 5 / 5
10 / — / 4 / 4 / 6 / 8 / 6 / 7 / 7 / 5 / 7 / 7
11 / — / 6 / 8 / 10 / 8 / 9 / 7 / 5 / 9 / 9
12 / — / 4 / 6 / 4 / 5 / 5 / 7 / 5 / 5
13 / — / 8 / 6 / 7 / 3 / 5 / 3 / 3
14 / — / 2 / 6 / 9 / 11 / 9 / 9
15 / — / 3 / 7 / 9 / 7 / 7
16 / — / 8 / 9 / 8 / 8
17 / — / 2 / 2 / 2
18 / — / 4 / 4
19 / — / 2
20 / —