Supplementary Table 1. Primers used to amplify genomes of Malaysian isolates.

ID
5' R GSP 1 (12)
5' R GSP 2 (12)
6F
8R
8F (12)
11R
11F
12R
12F
14R
14F
15R
15F (12)
16R
16F
17R
17F
18R
18F
19R
19F
20R
20F
21R
3' F GSP (12)
5' R GSP 1 (13)
5' R GSP 2 (13)
6F
8R
8F
11R (13)
11F (13)
12R
12F (13)
14R (13)
14F (13)
15R
15F (13)
16R
16F (13)

Gene
5' NCR
5' NCR
VP2
VP2
VP2, VP3
VP2, VP3
VP3, VP1
VP3, VP1
VP1, 2A
VP1, 2A
2A, 2B, 2C
2A, 2B, 2C
2B, 2C
2B, 2C
2C, 3A
2C, 3A
2C, 3A,3B, 3C
2C, 3A,3B, 3C
3C, 3D
3C, 3D
3C, 3D
3C, 3D
3D
3D
3' NCR
5' NCR
5' NCR
VP2
VP2
VP2, VP3
VP2, VP3
VP3, VP1
VP3, VP1
VP1, 2A
VP1, 2A
2A, 2B, 2C
2A, 2B, 2C
2B, 2C
2B, 2C
2C, 3A

Sequence 5'-3'
TCTGGTAGCTTCCACCACCAACC
AGCCTATCGGAGAACCCACATGC
GCATGTGGGTTBTCCGATAGGCTTA
GTCTTGCACCDGAGAATTCTGACTT
GCTCATAAACTTGAGGACAAACAATTC
TGTBTCATCATDGGTGTGTCACG
CCATTGTDGTACCATGGAT
ATCATADCCATCATAGAACAT
CAAATCATGTTTGTACCACC
CAAATGCATTHCCTAATTGTGT
AGACTGTGGTGGCAAGTT
TTTHAGCCADTCAATGAATTT
TGGCTAAAAAAGTTTACTGA
AGAGGACAACACTGTTTGTA
AAGTATTTTGATGGATACAAC
AAATTCGTGTTCTGGTCCTTG
ACTGCTATATTTCAGGGHTTGG
CTACCATTDCCHCCCACATGTA
AAGTTTAGAGACATAAGAAG
ATDGGTTCTGGGTTGATG
AAACTACACCCTAGTGTHTTC
CCATCATAATTGGTGTAATCAA
ACTTACTTAAAGGATGAACT
TCTTTAGTCCATCTGATTGA
TGACTGGATCGGCCATAGGCTGTGA
TCTGGAAGCTTCCACCACCATCC
AGCCTATCGGAAAACCCACATGC
GCATGTGGGTTBTCCGATAGGCTTA
GTCTTGCACCDGAGAATTCTGACTT
GATTATTAATCTTAGAACTAATAATTC
TGTBTCATCATDGGTGTGTC
ACCTTGGATATCCTCTGGTT
ATCATADCCATCATAGAACAT
CAGATAATGTATGTACCACCTGG
CAAAGGCGTTHCCTAATTGTGT
GAGATTGCGGTGGTAAATTA
TTTHAGCCADTCAATGAATTT
GGTGATTCATGGATTAAGAAATTTA
AGAGGACAACACTGTTTGTA
CCAAAATATTTTGATGGTTACG

17R (13)
17F
18R
18F (13)
19R (13)
19F (13)
20R
20F (13)
21R (17)
3' F GSP (13)
5' R GSP 1 (17)
5' R GSP 2 (17)
6F
8R
8F (17)
11R
11F (17)
12R
12F (17)
14R
14F (17)
15R
15F (17)
16R
16F (17)
17R (17)
17F
18R
18F (17)
19R (17)
19F
20R
20F (17)
21R (17)
3' F GSP (17)
5 R GSP 1 (11)
5 R GSP 2 (11)

6F
8R(11)
8F (12)
11R (11)
11F
12R

2C, 3A
2C, 3A,3B, 3C
2C, 3A,3B, 3C
3C, 3D
3C, 3D
3C, 3D
3C, 3D
3D
3D
3' NCR
5' NCR
5' NCR
VP2
VP2
VP2, VP3
VP2, VP3
VP3, VP1
VP3, VP1
VP1, 2A
VP1, 2A
2A, 2B, 2C
2A, 2B, 2C
2B, 2C
2B, 2C
2C, 3A
2C, 3A
2C, 3A,3B, 3C
2C, 3A,3B, 3C
3C, 3D
3C, 3D
3C, 3D
3C, 3D
3D
3D
3' NCR
5' NCR
5' NCR
VP2
VP2
VP2, VP3
VP2, VP3
VP3, VP1
VP3, VP1

GAATTCATGTTGAGGACCCTG
ACTGCTATATTTCAGGGHTTGG
CTACCATTDCCHCCCACATGTA
CCAGAATGAGAAGTTCAGGGAC
ATDGGTTCTGGGTTGATGTC
AAATTACAGCCAAGTGCTTTC
CCATCATAATTGGTGTAATCAA
CACATATTTGAAAGATGAACTC
TGGATCTTTAGTCCATCTGAT
CTGACTGGTTCTGCGGTAGGTTGC
TCAGGTAGCTTCCACCACCATCC
AGCCTATCGGAGAACCCACATGC
GCATGTGGGTTBTCCGATAGGCTTA
GTCTTGCACCDGAGAATTCTGACTT
ACTTATAAACTTAAGAACCAACAATTC
TGTBTCATCATDGGTGTGTCACG
ATTCCATGGATTAGTTCCCATTAC
ATCATADCCATCATAGAACAT
CAGATTATGTTTGTGCCCCC
CAAATGCATTHCCTAATTGTGT
GGTGATTGTGGTGGAAAGC
TTTHAGCCADTCAATGAATTT
GATTCCTGGTTGAAAAAGTTTAC
AGAGGACAACACTGTTTGTA
CCCAAAATACTTTGATGGTTA
AAACTCGTGGTCTGGACCTTG
ACTGCTATATTTCAGGGHTTGG
CTACCATTDCCHCCCACATGTA
AAATTTAGAGATATCAGGAG
ATGGGTTCTGGGTTTATG
AAACTACACCCTAGTGTHTTC
CCATCATAATTGGTGTAATCAA
ACATACTTGAAAGATGAATT
TGGATCTTTAGTCCATCTGAT
CAGGCTCAGCAGTGGGGTGCAA
TCTGGAAGCTTCCACCACCAGCC
AGCCTATCGGAAAACCCACAGGC
GCATGTGGGTTBTCCGATAGGCTTA
CCATGGCTCCGGAAAATTCAGACTT
GCTCATAAACTTGAGGACAAACAATTC
TGCTTCATCATGGGTGTGTCTCC
CCATTGTDGTACCATGGAT

ATCATADCCATCATAGAACAT

12F (11)
14R
14F (11)
15R
15F
16R
16F (11)
17R (13)
17F (11)
18R (11)
18F (11)
19R (11)
19F (11)
20R
20F
21R
3' F GSP (11)
5 R GSP 1 (10)
5 R GSP 2 (10)

6F
8R(20)
8F (10)
11R
11F (17)
12R (10)
12F
14R (10)
14F
15R
15F (10)
16R
16F (10)
17R (10)
17F (10)
18R
18F (10)
19R (13)
19F (10)
20R (10)
20F (10)
21R
3' F GSP (10)
5 R GSP 1 (20)

VP1, 2A
VP1, 2A
2A, 2B, 2C
2A, 2B, 2C
2B, 2C
2B, 2C
2C, 3A
2C, 3A
2C, 3A,3B, 3C
2C, 3A,3B, 3C
3C, 3D
3C, 3D
3C, 3D
3C, 3D
3D
3D
3' NCR
5' NCR
5' NCR
VP2
VP2
VP2, VP3
VP2, VP3
VP3, VP1
VP3, VP1
VP1, 2A
VP1, 2A
2A, 2B, 2C
2A, 2B, 2C
2B, 2C
2B, 2C
2C, 3A
2C, 3A
2C, 3A,3B, 3C
2C, 3A,3B, 3C
3C, 3D
3C, 3D
3C, 3D
3C, 3D
3D
3D
3' NCR
5' NCR

CAGACAATGTATGTCCCACC
CAAATGCATTHCCTAATTGTGT
AGATTGTGGAGGGAAGTT
TTTHAGCCADTCAATGAATTT
TGGCTVAAGAAATTCACTGA

AGAGGACAACACTGTTTGTA
CCCAAATACTTTGATGGATA
GAATTCATGTTGAGGACCCTG
ACTGCCATCTTCCAAGGCTTAG
CTTCCATTCCCACCAACGTGGA
AAATTCAGAGACATTAGAAG
CAAGGGCTCTGGGTTTATA
AAGTTACAACCCAGTGTCTTT
CCATCATAATTGGTGTAATCAA
ACTTACTTAAAGGATGAACT
TCTTTAGTCCATCTGATTGA
CAGGATCAGCTGTTGGTTGCAACCC
TCAGGCAGTTTCCACCACCACCC
GAGCCTATCGGAAAACCCACAAGC
GCATGTGGGTTBTCCGATAGGCTTA
GCATTGGGCCAGAAAACTCTGATTT
GCTTATAAATTTAAGGACAAACAACTC
TGTBTCATCATDGGTGTGTCACG

ATTCCATGGATTAGTTCCCATTAC
ATCATATCCATCATAGAACAT
CAAATCATGTTTGTACCACC
CAAAAGCACTTCCCAGCTGTGT
AGACTGTGGTGGCAAGTT
TTTHAGCCADTCAATGAATTT
TGGCTGAAGAAGTTCACTGA

AGAGGACAACACTGTTTGTA
CCCAAGTACTTTGATGGTTA
AAATTCATGTTCAGGACCTTG
ACTGCTATATTCCAAGGTCTAG
CTACCATTDCCHCCCACATGTA

AAATTCAGAGACATAAGGAG

ATDGGTTCTGGGTTGATGTC
AAGTTGTACCCCAGTGTGTTC
CCGTCATAGTTTGTGTAGTCAA
ACCTACTTGAAAGATGAGCT
TCTTTAGTCCATCTGATTGA
TCACTGGTTCCGCCATAGGATGTGA
CAGTCAGGTAATTTCCACCACCATCC

5 R GSP 2 (20)

6F
8R(20)
8F (12)
11R
11F
12R
12F (20)
14R (20)
14F (20)
15R (20)
15F
16R
16F (20)
17R (20)
17F (20)
18R (20)
18F (13)
19R (20)
19F (20)
20R (20)
20F (20)
21R
3' F GSP (20)
5' R GSP 1 (14)
5' R GSP 2 (14)
6F
8R
8F (14)
11R (14)
11F
12R
12F
14R (14)
14F (14)
15R
15F (14)
16R (14)
16F (14)
17R (14)
17F (14)
18R (14)
18F

5' NCR
VP2
VP2
VP2, VP3
VP2, VP3
VP3, VP1
VP3, VP1
VP1, 2A
VP1, 2A
2A, 2B, 2C
2A, 2B, 2C
2B, 2C
2B, 2C
2C, 3A
2C, 3A
2C, 3A,3B, 3C
2C, 3A,3B, 3C
3C, 3D
3C, 3D
3C, 3D
3C, 3D
3D
3D
3' NCR
5' NCR
5' NCR
VP2
VP2
VP2, VP3
VP2, VP3
VP3, VP1
VP3, VP1
VP1, 2A
VP1, 2A
2A, 2B, 2C
2A, 2B, 2C
2B, 2C
2B, 2C
2C, 3A
2C, 3A
2C, 3A,3B, 3C
2C, 3A,3B, 3C
3C, 3D

AGCCTATCAGAGAATCCACAAGCTTCC
GCATGTGGGTTBTCCGATAGGCTTA
GCATTGGGCCAGAAAACTCTGATTT
GCTCATAAACTTGAGGACAAACAATTC
TGCTTAGTCATTGGAGTGTCACG
CCATTGTDGTACCATGGAT

ATCATADCCATCATAGAACAT
CAGATCATGTATGTACCTCC
CAAATGCATTACCAAGCTGCGT
TGGGGGAAAACTACTGTGCA
TTTAAGCCAATCAATGAACTT
TGGCTVAAGAAATTCACTGA

AGAGGACAACACTGTTTGTA
CCAAAGCACTTTGATGGATA
AAACTCATGTTCTGGCCCCTG
CATGCAATCTTCCAAGGGTTGG
CGTCCATTCCCACCAACATGAA
AAGTTCAGGGACATCAGAAG
AAAGCTTCTGTGTTGATC
AAATTGAGACCTAGTGCATTC
CCGTCATAGTTGGTGTAATCGA
ACATACCTTAAAGATGAGCT
TCTTTAGTCCATCTGATTGA
TAACTGGATCTGCTGTCGGCTGTGA

TCTGGTAGCTTCCACCACCAACC
AGCCTATCAGAAAACCCACATGC
GCATGTGGGTTBTCCGATAGGCTTA
GTCTTGCACCDGAGAATTCTGACTT
GTTAATAAACCTACGTACTAATAATTC
TGTTTCATCATAGGGCTGTCACG
CCATTGTDGTACCATGGAT
ATCATADCCATCATAGAACAT
CAAATCATGTTTGTACCACC
AAATGCACTCCCCAATTGGGT
TGATTGTGGAGGTAAATTA
TTTHAGCCADTCAATGAATTT
TGGTTACGGAAGTTCACTGA
AAGGGGCAGCATGACTTGTA
CCCAAGCATTTTGATGGGTA
AAACTCATGCTCTGGACCCTG
GCCATTTTCCAGGGHTTAG
CACCCTTCCATTGCCGCCAACA
AAGTTTAGAGACATAAGAAG

19R
3C, 3D
ATDGGTTCTGGGTTGATG
19F (14)
3C, 3D
AAGCTGCAACCAAGCATCTTT
20R
3C, 3D
CCATCATAATTGGTGTAATCAA
20F (14)
3D
TCACATACTTGAAAGATGAATTG
21R
3D
TCTTTAGTCCATCTGATTGA
3' F GSP (14)
3' NCR
AACAGGCTCTGCAATAGGGTGTGAC
* Position is according to reference sequence, HRV-C024 (accession number: EF582385)
GSP, gene specific primer; F, forward primer; R, reverse primer; NCR, non-coding region

Position*
1067
832
832
1585
1383
2285
2086
2853
2680
3595
3435
3948
3859
4691
4321
5136
4813
5618
5362
5951
5737
6383
6133
6878
6281
1067
832
832
1585
1383
2285
2087
2853
2680
3595
3434
3948
3850
4691
4318

Isolate
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1515-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10

5136
4813
5618
5352
5951
5737
6383
6132
6882
6280
1067
832
832
1585
1383
2285
2083
2853
2680
3595
3433
3948
3853
4691
4317
5136
4813
5618
5362
5951
5737
6383
6133
6882
6284
1067
832
832
1585
1383
2285
2086
2853

1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
1570-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3430-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10

2680
3595
3435
3948
3859
4691
4318
5136
4813
5618
5362
5952
5737
6383
6133
6878
6284
1067
833
832
1585
1383
2285
2083
2853
2680
3595
3435
3948
3859
4691
4318
5136
4813
5618
5362
5951
5737
6383
6133
6878
6281
1067

3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
3805-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
7383-MY-10
8097-MY-11

832
832
1585
1383
2285
2086
2853
2680
3595
3441
3948
3859
4691
4318
5136
4813
5618
5362
5951
5737
6383
6133
6878
6281
1067
832
832
1585
1383
2285
2086
2853
2680
3595
3435
3948
3859
4691
4318
5136
4816
5618
5362

8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8097-MY-11
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10

5951
5737
6383
6131
6878
6282

8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10
8713-MY-10