0,74. 1. 0,04. 0,68. 1. 1. 0,25. 0,95. 0,29. 0,84. 0,31. 0,18. 0,54. 0,86. 0,75. 0,65 ... of human enterovirus 71 in European countries. J Gen Virol 91, 2263â2277.
FJ461785_EV71B5_NUH0085_SGP08
0,89 1 FJ461781_EV71B5_NUH0083_SGP08
Subgenogroup B5
FJ461783_EV71B5_NUH0047_SGP08 FM201330_EV71B5_34099_BRN06 1 DQ906173_EV71B5_111411_BRN06 AY258310_EV71B5_S19841_SAR_MYS03 0,97
0,15
MYS03 JPN03 BRN06 THA07 SGP00-08
0,99 0,99 DQ341362_EV71B5_SB12736_SAR_MYS03
FJ151497_EV71B5_01467_THA07
1
0,4 AY905548_EV71B5_SB12007_SAR_MYS03 0,1 AY905549_EV71B5_SB11977_SAR_MYS03 0,81
AY258304_EV71B5_S110241_SAR_MYS03 AB177816_EV71B5_2716_Yamagata_JPN03 0,86 0,65AB213650_EV71B5_2972_Yamagata_JPN03 1 1 AB213649_EV71B5_2934_Yamagata_JPN03 AB213647_EV71B5_2419_Yamagata_JPN03 AF376121_EV71B5_5511_SGP00 AF286503_EV71B4_2862_TWN98 0,980,36 0,86AY207613_EV71B4_03300_MAA_MYS97 AY207637_EV71B4_0343_MAA_MYS97 0,29 AF286490_EV71B4_1424_SGP97 0,99 0,7 0,5 AY207643_EV71B4_0898_MAA_MYS97 AF190566_EV71B4_1110_MAA_MYS97 0,32 0,99AY207646_EV71B4_0414_MAA_MYS97 AY207652_EV71B4_0615_MAA_MYS99 AB059818_EV71B4_C7_Osaka_JPN97 AB177811_EV71B4_1141_Yamagata_JPN00 1 DQ841991_EV71B4_E2003033_TWN03 0,97 DQ841992_EV71B4_AFP2003163_TWN03 0,08 DQ841984_EV71B4_AFP2001480_TWN01 0,12 1 DQ841987_EV71B4_AFP2001009_TWN01 DQ841990_EV71B4_E2002117_TWN02 1 1 DQ841989_EV71B4_E2002042_TWN02 0,21 0,96 DQ841988_EV71B4_AFP2001529_TWN01 AY940106_EV71B4_9918_SYD_AUS00 1 AY722910_EV71B4_2266_SYD_AUS00 DQ841983_EV71B4_E20001220_TWN00 0,96 0,31 1 DQ841976_EV71B4_E99217_TWN99 DQ841973_EV71B4_E99194_TWN99 AF376070_EV71B4_CN0942_SAR_MYS00 1 0,68AF376064_EV71B4_SB1191_SAR_MYS00 AF376086_EV71B4_S40201_SAR_MYS00 1 0,95 0,98 AF376065_EV71B4_SB1647_SAR_MYS00 1 AF376071_EV71B4_CN9502_SAR_MYS00 DQ341366_EV71B4_SB2864_SAR_MYS00 AF376122_EV71B4_5536_SGP00 0,84 1 DQ841974_EV71B4_E99214_TWN99 DQ841982_EV71B4_E2000120_TWN00 0,6 1 0,94 DQ841980_EV71B4_E2000260_TWN00 AF376067_EV71B4_CN04104_SAR_MYS00 AY207650_EV71B4_0919_MAA_MYS99 0,36 DQ341365_EV71B4_PP37_MYS01 0,9 AY258320_EV71B4_3742_SGP02 0,41 1 AY207624_EV71B4_0066_MAA_MYS00 0,06 0,27 AF376069_EV71B4_SB0635_SAR_MYS00 0,31 0,16 AY207623_EV71B4_0042_MAA_MYS00 AY207617_EV71B4_0778_MAA_MYS00 AY722914_EV71B4_3242_SYD_AUS01 1 1 1 AY722913_EV71B4_2999_SYD_AUS01 AY940100_EV71B4_9901_SYD_AUS01 0,12 1 AF376129_EV71B4_5926_SGP00 AF376114_EV71B4_2267_SGP01 0,17 AF376123_EV71B4_5546_SGP00 AF376095_EV71B3_18F_6_AUS99 1 0,98AF376100_EV71B3_25M_2_AUS99 0,89 AF376097_EV71B3_1M_3_AUS99 0,93 AF376089_EV71B3_11F_6_AUS99 1 EU364841_EV71B3_26M_4_AUS99 1 AF286489_EV71B3_1423_SGP98 1 0,25 AF135921_EV71B3_2322_MAA_MYS97 0,95AF190570_EV71B3_2334_MAA_MYS97 0,74 AF135918_EV71B3_2304_MAA_MYS97 AF135930_EV71B3_7208_MAA_MYS97 0,19 AF376117_EV71B3_3799_SGP98 0,54 0,12 AF135908_EV71B3_0614_A3_MAA_MYS97 0,16 AF135910_EV71B3_0632_34_MAA_MYS97 0,95 AF135912_EV71B3_0754_262D_MAA_MYS97 0,97 AF135929_EV71B3_7204_MAA_MYS97 0,39 1 AF135928_EV71B3_2337_MAA_MYS97 1 AF135923_EV71B3_2331_MAA_MYS97 AF190561_EV71B3_1105_MAA_MYS97 0,84 1 AF190563_EV71B3_1107_MAA_MYS97 AF135913_EV71B3_0770_22FC_MAA_MYS97 0,33 AY207636_EV71B3_04716_MAA_MYS97 AB433866_EV71B1_Y93_JPN08 EV71B2_BER516_GER97 EV71B2_CHE516_GER87 AF009534_EV71B2_7633_PA_USA87 0,23 0,49 AF135902_EV71B2_7235_AK_USA87 0,06 AF009535_EV71B2_7673_CT_USA87 0,09 AF135904_EV71B2_7298_AK_USA87 AF009536_EV71B2_8209_MD_USA87 0,23 0,99 AF135906_EV71B2_7635_WA_USA87 0,34 AF009532_EV71B2_7630_PA_USA87 0,75 0,2 AF009537_EV71B2_8279_PA_USA87 0,240,84AF009523_EV71B2_7962_PA_USA87 AF009530_EV71B2_7628_PA_USA87 AF009528_EV71B2_1061_TN_USA87 0,02 AF135899_EV71B_6658_COL_USA94 0,34 0,4 AF009527_EV71B2_1413_CA_USA87 AF135907_EV71B2_8149_AL_USA88 0,17 U22522___EV71B2_MS_7423_USA87 0,09 0,99 AF135905_EV71B2_7632_PA_USA87 0,75 AF009526_EV71B2_8102_WA_USA87 0,18 0,31 AF135903_EV71B2_7289_NC_USA87 AF009540_EV71B2_2222_IA_USA88 0,5 0,36 0,04AF135882_EV71B2_2260_CA_USA86 AF009525_EV71B2_1410_CA_USA86 AY079098_EV71B_FS_GER98 0,95 AF009539_EV71B2_2219_IA_USA87 0,24 AY278249_EV71B_73442_PA_BRA99 0,62 AF135897_EV71B2_4826_CT_USA83 1 AF009529_EV71B2_4827_CT_USA83 0,95 1 AF135893_EV71B2_4224_MA_USA82 AF135889_EV71B2_3663_MA_USA82 AF135896_EV71B2_4644_AR_USA83 0,86 0,24 0,98 AF135894_EV71B2_4323_UT_USA83 0,98AF135888_EV71B2_2952_SD_USA81 AF135891_EV71B2_3885_UT_USA82 1 0,63 AF135890_EV71B2_3874_ND_USA82 1 AB491215_EV71B2_12677_NLD82 AF135881_EV71B2_2259_CA_USA82 1 AF135895_EV71B2_4599_OR_USA83 AF135892_EV71B2_3982_OH_USA82 1 0,38 AF009538_EV71B2_3984_OH_USA82 AF135865_EV71B1_10181_NM_USA78 0,04 AF135864_EV71B1_1011_ND_USA79 0,31 AF135872_EV71B1_2234_NY_USA77 1 0,14 AF135870_EV71B1_2231_NY_USA77 0,29 1 AF135877_EV71B2_2239_NY_USA77 AF135874_EV71B1_2236_NY_USA77 AF135869_EV71B1_2230_NY_USA76 0,93 AF135868_EV71B1_2229_NY_USA76 AF135880_EV71B1_2258_CA_USA79 0,97 AF135866_EV71B1_2114_TN_USA80 0,78 0,44AF135873_EV71B1_2235_NY_USA77 1 AF135878_EV71B1_2241_NY_USA79 0,98 AF135876_EV71B1_2238_NY_USA77 1 1 AF135871_EV71B1_2232_NY_USA77 1 AF135879_EV71B1_2243_NY_USA79 AB059815_EV71B1_HUN78 AF135901_EV71B1_6910_OK_USA87 0,09 1 AF135900_EV71B1_6762_OK_USA86 1 0,99 AF135898_EV71B1_5115_TX_USA83 1 0,65 0,95 AB059814_EV71B1_258_BGR75 AF135886_EV71B1_2609_AUS74 AB059813_EV71B1_Nagoya_JPN73 0,07 1 AB491214_EV71B1_10866_NLD73 AF135884_EV71B1_2605_AUS74 0,98 AF135887_EV71B1_2610_AUS74 1 AF135883_EV71B1_2604_AUS74 AF135867_EV71B1_2228_NY_USA72 AB491213_EV71B0_10076_NLD66 AB491212_EV71B0_5603_NLD65
Sugenobgroup B4 MYS97-03 JPN97-00 SGP97-02 TWN98-00 AUS00-01
Subgenogroup B3 MYS97 SGP98 AUS99
Subgenogroup B2 USA81-94 NLD82 GER97-98 BRA99
Subgenogroup B1 NLD65-73 USA72-87 JPN73 AUS74 BGR75 HUN78
1
0,96
6.0
Supplementary Fig. S1. Bayesian tree topology inferred with the EV-71 1D gene sequences of genogroup B showing tip labels and posterior probabilities at nodes. Mirand, A., Schuffenecker, I., Henquell, C., Billaud, G., Jugie, G., Falcon, D., Mahul, A., Archimbaud, C., Terletskaia-Ladwig, E., Diedrich, S., Huemer, H. P., Enders, M., Lina, B., Peigue-Lafeuille, H. & Bailly, J.-L. (2010). Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries. J Gen Virol 91, 2263–2277.
FJ461785_EV71B5_NUH0085_SGP08 0,7 1,2 FJ461781_EV71B5_NUH0083_SGP08 FJ461783_EV71B5_NUH0047_SGP08 FM201330_EV71B5_34099_BRN06 2,78 DQ906173_EV71B5_111411_BRN06 AY258310_EV71B5_S19841_SAR_MYS03 5,53 6,18 DQ341362_EV71B5_SB12736_SAR_MYS03 FJ151497_EV71B5_01467_THA07 AY905548_EV71B5_SB12007_SAR_MYS03 AY905549_EV71B5_SB11977_SAR_MYS03 6,79 5,54 AY258304_EV71B5_S110241_SAR_MYS03 AB177816_EV71B5_2716_Yamagata_JPN03 5,54 5,77AB213650_EV71B5_2972_Yamagata_JPN03 8,96 5,97AB213649_EV71B5_2934_Yamagata_JPN03 AB213647_EV71B5_2419_Yamagata_JPN03 AF376121_EV71B5_5511_SGP00 AF286503_EV71B4_2862_TWN98 12,48 11,7AY207613_EV71B4_03300_MAA_MYS97 AY207637_EV71B4_0343_MAA_MYS97 AF286490_EV71B4_1424_SGP97 11,83 AY207643_EV71B4_0898_MAA_MYS97 13,21 AF190566_EV71B4_1110_MAA_MYS97 11,69AY207646_EV71B4_0414_MAA_MYS97 AY207652_EV71B4_0615_MAA_MYS99 AB059818_EV71B4_C7_Osaka_JPN97 AB177811_EV71B4_1141_Yamagata_JPN00 13,72 DQ841991_EV71B4_E2003033_TWN03 6,67 DQ841992_EV71B4_AFP2003163_TWN03 DQ841984_EV71B4_AFP2001480_TWN01 DQ841987_EV71B4_AFP2001009_TWN01 7,86 DQ841990_EV71B4_E2002117_TWN02 11,49 6,54 DQ841989_EV71B4_E2002042_TWN02 9,77 DQ841988_EV71B4_AFP2001529_TWN01 AY940106_EV71B4_9918_SYD_AUS00 8,58 AY722910_EV71B4_2266_SYD_AUS00 DQ841983_EV71B4_E20001220_TWN00 9,43 DQ841976_EV71B4_E99217_TWN99 9,75 DQ841973_EV71B4_E99194_TWN99 AF376070_EV71B4_CN0942_SAR_MYS00 8,27 8,67AF376064_EV71B4_SB1191_SAR_MYS00 8,82 AF376086_EV71B4_S40201_SAR_MYS00 11 9,17 AF376065_EV71B4_SB1647_SAR_MYS00 9,55 AF376071_EV71B4_CN9502_SAR_MYS00 DQ341366_EV71B4_SB2864_SAR_MYS00 AF376122_EV71B4_5536_SGP00 9,33 10,46 DQ841974_EV71B4_E99214_TWN99 DQ841982_EV71B4_E2000120_TWN00 8,92 9,739,12 DQ841980_EV71B4_E2000260_TWN00 AF376067_EV71B4_CN04104_SAR_MYS00 AY207650_EV71B4_0919_MAA_MYS99 DQ341365_EV71B4_PP37_MYS01 7,87 AY258320_EV71B4_3742_SGP02 15,92 AY207624_EV71B4_0066_MAA_MYS00 AF376069_EV71B4_SB0635_SAR_MYS00 AY207623_EV71B4_0042_MAA_MYS00 AY207617_EV71B4_0778_MAA_MYS00 AY722914_EV71B4_3242_SYD_AUS01 8,95 7,38 7,78 AY722913_EV71B4_2999_SYD_AUS01 AY940100_EV71B4_9901_SYD_AUS01 8,48AF376129_EV71B4_5926_SGP00 AF376114_EV71B4_2267_SGP01 AF376123_EV71B4_5546_SGP00 AF376095_EV71B3_18F_6_AUS99 9,49 9,82AF376100_EV71B3_25M_2_AUS99 10,08 AF376097_EV71B3_1M_3_AUS99 10,35 AF376089_EV71B3_11F_6_AUS99 10,73 EU364841_EV71B3_26M_4_AUS99 11,12 AF286489_EV71B3_1423_SGP98 18,63 AF135921_EV71B3_2322_MAA_MYS97 11,5AF190570_EV71B3_2334_MAA_MYS97 11,73AF135918_EV71B3_2304_MAA_MYS97 AF135930_EV71B3_7208_MAA_MYS97 AF376117_EV71B3_3799_SGP98 11,6 AF135908_EV71B3_0614_A3_MAA_MYS97 AF135910_EV71B3_0632_34_MAA_MYS97 12,15 AF135912_EV71B3_0754_262D_MAA_MYS97 20,69 AF135929_EV71B3_7204_MAA_MYS97 11,63AF135928_EV71B3_2337_MAA_MYS97 12,71 AF135923_EV71B3_2331_MAA_MYS97 AF190561_EV71B3_1105_MAA_MYS97 11,71 11,99AF190563_EV71B3_1107_MAA_MYS97 AF135913_EV71B3_0770_22FC_MAA_MYS97 AY207636_EV71B3_04716_MAA_MYS97 AB433866_EV71B1_Y93_JPN08 EV71B2_BER516_GER97 AF009534_EV71B2_7633_PA_USA87 AF135902_EV71B2_7235_AK_USA87 AF009535_EV71B2_7673_CT_USA87 AF135904_EV71B2_7298_AK_USA87 AF009536_EV71B2_8209_MD_USA87 25,57 AF135906_EV71B2_7635_WA_USA87 AF009532_EV71B2_7630_PA_USA87 21,69 AF009537_EV71B2_8279_PA_USA87 21,97AF009523_EV71B2_7962_PA_USA87 AF009530_EV71B2_7628_PA_USA87 AF009528_EV71B2_1061_TN_USA87 AF135899_EV71B_6658_COL_USA94 AF009527_EV71B2_1413_CA_USA87 AF135907_EV71B2_8149_AL_USA88 U22522___EV71B2_MS_7423_USA87 23,16 AF135905_EV71B2_7632_PA_USA87 27,92 AF009526_EV71B2_8102_WA_USA87 AF135903_EV71B2_7289_NC_USA87 AF009540_EV71B2_2222_IA_USA88 AF135882_EV71B2_2260_CA_USA86 AF009525_EV71B2_1410_CA_USA86 AY079098_EV71B_FS_GER98 22,91 AF009539_EV71B2_2219_IA_USA87 AY278249_EV71B_73442_PA_BRA99 28,43 AF135897_EV71B2_4826_CT_USA83 26,02 AF009529_EV71B2_4827_CT_USA83 26,7 AF135893_EV71B2_4224_MA_USA82 26,96 AF135889_EV71B2_3663_MA_USA82 AF135896_EV71B2_4644_AR_USA83 26,52 AF135894_EV71B2_4323_UT_USA83 27,3 AF135888_EV71B2_2952_SD_USA81 27,55 AF135891_EV71B2_3885_UT_USA82 27,16 27,94 AF135890_EV71B2_3874_ND_USA82 29,02 AB491215_EV71B2_12677_NLD82 AF135881_EV71B2_2259_CA_USA82 27,32 AF135895_EV71B2_4599_OR_USA83 AF135892_EV71B2_3982_OH_USA82 26,98 AF009538_EV71B2_3984_OH_USA82 AF135865_EV71B1_10181_NM_USA78 AF135864_EV71B1_1011_ND_USA79 AF135872_EV71B1_2234_NY_USA77 33,33 AF135870_EV71B1_2231_NY_USA77 AF135877_EV71B2_2239_NY_USA77 31,74 AF135874_EV71B1_2236_NY_USA77 AF135869_EV71B1_2230_NY_USA76 32,72 AF135868_EV71B1_2229_NY_USA76 AF135880_EV71B1_2258_CA_USA79 30,27 AF135866_EV71B1_2114_TN_USA80 31,53 AF135873_EV71B1_2235_NY_USA77 36,43 AF135878_EV71B1_2241_NY_USA79 32,03 AF135876_EV71B1_2238_NY_USA77 32,9631,44 AF135871_EV71B1_2232_NY_USA77 34,29 AF135879_EV71B1_2243_NY_USA79 AB059815_EV71B1_HUN78 AF135901_EV71B1_6910_OK_USA87 23,94 AF135900_EV71B1_6762_OK_USA86 26,59 38,99 AF135898_EV71B1_5115_TX_USA83 33,73 36,1235,28 AB059814_EV71B1_258_BGR75 AF135886_EV71B1_2609_AUS74 AB059813_EV71B1_Nagoya_JPN73 40,71 AB491214_EV71B1_10866_NLD73 AF135884_EV71B1_2605_AUS74 35,7 AF135887_EV71B1_2610_AUS74 36,26 AF135883_EV71B1_2604_AUS74 AF135867_EV71B1_2228_NY_USA72 AB491213_EV71B0_10076_NLD66 43,82 AB491212_EV71B0_5603_NLD65 4,69
47,8
6.0
Supplementary Fig. S2. Bayesian tree topology inferred with the EV-71 1D gene sequences of genogroup B showing tip labels and node age. Mirand, A., Schuffenecker, I., Henquell, C., Billaud, G., Jugie, G., Falcon, D., Mahul, A., Archimbaud, C., Terletskaia-Ladwig, E., Diedrich, S., Huemer, H. P., Enders, M., Lina, B., Peigue-Lafeuille, H. & Bailly, J.-L. (2010). Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries. J Gen Virol 91, 2263–2277.
EV71C2_BRE324_FRA07
EV71C1_GRE29_FRA07 0.24 1
FJ158600_EV71C4_DTID_ZJU_62_CHN08 0.2
0.13
EV71C1_NAN387_FRA06
EU913466_EV71C4_Fuyang22_CHN08
EV71C2_STU563062_GER07
0.24 EV71C1_CF210042_FRA06
0.07
0.02
FJ151495_EV71C1_17184_THA08
1
EU913470_EV71C4_Fuyang31_CHN08
EV71C2_ULM63_GER07 1
EV71C1_LYO10531_FRA06
0.95
0.21 0.07 EU812515_EV71C4_FY23_CHN08
EV71C1_POI777_FRA05
1
FJ461786_EV71C2_NUH0013_SGP08 0.17
EV71C1_CAE571_FRA03
0.35
EU913469_EV71C4_Fuyang44_CHN08
EV71C1_LYO06972_FRA04
0.75
EV71C2_STU543078_GER08
0.4 AM939586_EV71C1_8277_GBR01
1
FJ439769_EV71C4_Fuyang_CHN08
0.66
EV71C2_ANG261_FRA09
EV71C1_LYO16282_FRA03
0.06
0.08
0.68
FJ469158_EV71C4_CY28_BJ_CHN08
AM939577_EV71C1_2063_GBR01 0.82 0.96
0.29
EV71C2_LYO23284_FRA07
AM939579_EV71C1_2353_GBR02
FJ469152_EV71C4_CY6_BJ_CHN08 0.15
0.99
AM939589_EV71C1_11052_GBR01
EV71C2_NAN198_FRA07
EV71C1_CAE869_FRA04 0.45
FJ469154_EV71C4_CY15_BJ_CHN08 0.95 0.68
0.39
EV71C1_ANG737_FRA03 0.06
EV71C2_LMA55_FRA07
1
FJ469157_EV71C4_CY21_BJ_CHN08
0.44
EV71C1_NAN696_FRA04
0.1
0.55 0.29
EV71C1_STU565890_GER03
0.98 0.88
EV71C2_BRE537_FRA08
FJ469155_EV71C4_CY17_BJ_CHN08
0.89
EV71C1_CAE201_FRA04 0.48
EV71C1_LYO11868_FRA03
FJ360546_EV71C4_GZ0803_CHN08
AB491220_EV71C2_265_NLD08
0.16 AM939595_EV71C1_12105_GBR01 0.18
1
FJ469153_EV71C4_CY11_BJ_CHN08
EV71C2_NAN256_FRA08
EV71C1_STU563449_GER03 0.06
0.89
1
AM939581_EV71C1_2826_GBR02
0.85
EV71C2_CF078034_FRA07
EV71C1_STU554409_GER03
EU999179_EV71C4_Xinhui_9_CHN08
0.17
0.08 0.87
FJ194965_EV71C4_GDSG17_CHN08
EV71C1_VIE21_AUT03
1
0.03
AM939604_EV71C2_6332_439_GBR06
EV71C1_STU565802_GER03
EU864507_EV71C4_EV71_Zhejiang_CHN08
0.83
AM939596_EV71C1_4709_GBR01
0.05 0.25
EV71C2_CF341034_FRA06
0.15
FJ360544_EV71C4_GZ0801_CHN08
AM939591_EV71C1_12081_GBR01
0.04
AM939587_EV71C1_8300_GBR04
AM939607_EV71C2_6364_255_GBR06
EU999175_EV71C4_Zhuhai_164_CHN08
0.96
EV71C1_ANG100
0.89
DQ452074_EV71C1_804_NOR03
DQ830977_EV71C5_2006_125_TWN06
EU753378_EV71C4_521_23F_CHN07
EV71C2_STU537622_GER07
1 0.84
0.89
AM939578_EV71C1_6314_248_GBR06
0.72
0.44
EU913467_EV71C4_Fuyang5_CHN08
EV71C2_STU572078_GER08
AB115495_EV71C1_02363_THA02
0.97
EV71C1_CAE1053_FRA00
DQ846663_EV71C5_NTU1551_TWN06
0.8 0.15
0.51
FJ469159_EV71C4_Cy29_BJ_CHN08 1
FJ151492_EV71C2_01647_THA07
AB491217_EV71C1_3878_NLD02
1
0.46
EV71C1_ULM705_GER00 0.23 0.78 EV71C1_BER409_GER00 0.6
AM490146_EV71C5_1177T_VNM05
FJ713137_EV71C4_Shanghai036_CHN09
FJ151501_EV71C2_12883_THA08 1
EU753404_EV71C4_523_14T_CHN07
EV71C1_GRE454_FRA03
0.28
FJ151491_EV71C2_01644_THA07 EV71C1_HAN540_GER00
DQ868521_EV71C5_E2006249_TWN06
0.58
EU753380_EV71C4_521_27F_CHN07
0.65
EV71C1_CF605_FRA00
0.12 0.3
0.37
EV71C2_STU553555_GER07
EU753398_EV71C4_523_07T_CHN07
EV71C1_ANN1254_FRA00
0.48 0.65
1
EV71C1_CF1744_FRA00
1 0.67
EV71C2_BER180_GER06
EU753367_EV71C4_521_03T_CHN07
0.84 0.37
AM939590_EV71C1_11168_GBR00
AM490142_EV71C5_1089T_VNM05
1
EU999171_EV71C4_Zhuhai_JC455_CHN08
0.94
AM939584_EV71C1_5746_GBR01
1
1
1
0.34 0.18
0.15
AY258318_EV71C1_5026_SGP02
0.3 0.23
Subgroup C5
EV71C2_STU545774_GER07
00.72
0.77 0.08
AM939580_EV71C1_2405_GBR01
EV71C2_NAN405_FRA06
EU910861_EV71C4_0708T_NM_CHN07 0.24
AM939593_EV71C1_17728_GBR98 AY207634_EV71C1_0774_MYS00
AM490161_EV71C5_933V_VNM05
EU753368_EV71C4_521_04F_CHN07
EV71C2_LYO24365_FRA06
0.17
0.92
0.57
1
0.01
0.32
AY207635_EV71C1_05716_MYS00
1
EV71C2_MUE66_GER07
EU753363_EV71C4_518_01F_CHN07
DQ341360_EV71C1_J115_MYS01 0.89
EU999172_EV71C4_Zhuhai_JC498_CHN08
EV71C1_NAN23154_FRA00
FJ151499_EV71C5_17570_THA08 0.83
1
EV71C2_ANG544_FRA06
1
EV71C1_LYO11178_FRA00
0.09
0.72
EU999173_EV71C4_Zhuhai_213_CHN08 EV71C1_VIE94_AUT01 1
FJ469156_EV71C4_CY20_BJ_CHN08
0.63
0.96 1
1
AM939576_EV71C2_6438_418_GBR06
EV71C1_LYO26277_FRA06
0.1
FJ151493_EV71C5_01865_THA07
EV71C1_LYO05158_FRA05
0.31
AM939597_EV71C2_STH_MCN_GBR06 1
1
EV71C1_STU546711_GER08
1
0.93
AM939599_EV71C2_6486_445_GBR06
EV71C1_STU562356_GER03
0.5
EU753364_EV71C4_518_02F_CHN07
EU753403_EV71C4_523_13T_CHN07 EV71C1_CF097017_FRA03
0.46
0.07
AB491218_EV71C2_365_NLD00
0.91 AM939588_EV71C1_9027_GBR99
1 EU753370_EV71C4_521_05T_CHN07
0.27
0.99 0.84
AY258319_EV71C1_4381_SGP02 FJ151498_EV71C1_02073_THA07
0.24
0.33
0.99
AY207621_EV71C1_0937_MYS00
EU753379_EV71C4_521_25F_CHN07
0.58 0.3
0.75 AY207619_EV71C1_0836_MYS00 1
0.45
EV71C2_CF1113_FRA00
AY207620_EV71C1_0915_MYS00
1
EU753405_EV71C4_523_15F_CHN07
AM939583_EV71C2_5622_GBR99
0.04 1
0.1
EU913468_EV71C4_Fuyang26_CHN08
AM939585_EV71C2_7414_GBR99
1
AY207632_EV71C1_0832_MYS00
0.98 1
0.39
EV71C2_POI515_FRA00
AY258294_EV71C1_SB9869_MYS03 0.07
EU753365_EV71C4_518_03F_CHN07
0.98
AM939592_EV71C1_13372_GBR98
FJ828519_EV71C4_BJ08_CHN08
AF376087_EV71C1_S40221_MYS00
0.13
EV71C2_ANN1256_FRA00
0.95
1
0.45
FJ360545_EV71C4_GZ0802_CHN08
AY207626_EV71C1_0389_MYS00
AF376108_EV71C2_7F_AUS99
AF135935_EV71C1_0756_MYS97
FJ606447_EV71C4_BJ08_Z004_3_CHN08
0.2 1
AF376120_EV71C1_4575_SGP98
AF376092_EV71C2_15M_8_AUS99
AY189154_EV71C1_S18191_MYS02
0.96
FJ469160_EV71C4_CY43_BJ_CHN08
AF135937_EV71C1_2132_VA_USA95
1
AF190577_EV71C2_31214_AZ_USA99
1
FJ606450_EV71C4_BJ08_Z025_5_CHN08
AF009559_EV71C1_1873_CT_USA93
0.59
0.4
0.14 1
AF009556_EV71C1_2037_MD_USA95
0.78
AF376080_EV71C1_S10862_MYS98
0.04 0.14 0.81
AF376103_EV71C2_2M_AUS99
EU753372_EV71C4_521_09F_CHN07
AF376102_EV71C2_27M_2_AUS99
EU753401_EV71C4_523_11F_CHN07
1
EV71C1_NAN10838_FRA94 AF009544_EV71C1_2253_NY_USA94
1
0.45
AF135940_EV71C1_2263_CA_USA94
AB433877_EV71C4_2753_Yama_JPN06
AY940112_EV71C2_1181_AUS98
0.99 0.13
0.9 0.64
AF009545_EV71C1_2254_NY_USA94 AF009543_EV71C1_2251_NY_USA93 AF009555_EV71C1_2007_CT_USA94
0.28
AF135950_EV71C2_2814_MO_USA98
AF135936_EV71C1_1997_NC_USA94
0.21
AF135942_EV71C2_2355_OK_USA97
AY722909_EV71C1_1065_AUS94
FJ556875_EV71C4_33951_THA08
AF135946_EV71C1_2640_AUS95
0.71
0.18 1
AF135943_EV71C2_2381_MA_USA97
0.95
AY905616_EV71C4_ZJ_3_CHN03
AF135933_EV71C1_0443_TX_USA91
0.97
AF135944_EV71C1_2583_CAN91
AY207611_EV71C2_03907_MYS97
AF135956_EV71C1_9323_TX_USA89
AY905618_EV71C4_ZJ_5_CHN03
1
DQ841965_EV71C4_E2004912_TWN04
AY207615_EV71C2_03750_MYS97
AF135959_EV71C1_9873_NM_USA89 0.97
0.24
AF135938_EV71C1_2261_CA_USA91
0.54
0.31 1
AF286497_EV71C2_2848_TWN98 AY722907_EV71C1_5247_AUS92
0.86
DQ841964_EV71C4_E2004104_TWN04
DQ841959_EV71C2_E98551_TW98
AY722902_EV71C1_7784_AUS90
0.06
AF135958_EV71C1_9837_WA_USA89
0.28
EV71C4_STU535542_GER04
0.14 0.14
0.67
AF135953_EV71C1_8495_VA_USA88
0.22
AF286505_EV71C2_2865_TWN98
1 0.99EV71C4_ULM275_GER04
0.98
AY722886_EV71C1_7610_AUS86 AY722884_EV71C1_1058_AUS86 1
1
Subgroup C5
AF304457_EV71C2_5746_CHN98
EV71C4_VIE148_AUT04
0.3
0.98 0.24AB177814_EV71C4_100_Yama_JPN03
AF286522_EV71C2_2912_TWN98
AF009542_EV71C1_2246_NY_USA87 AF135952_EV71C1_7238_AK_USA87
AB213629_EV71C4_2779_Yama_JPN02
0.97
AF135949_EV71C2_2644_AUS95
1
AF135951_EV71C1_7237_AK_USA87
0.94
0.78
AF009546_EV71C1_2264_CA_USA94
0.91
AB213644_EV71C4_2316_Yama_JPN03
AF135947_EV71C2_2641_AUS95
1
1 0.63
AF009553_EV71C1_1924_AZ_USA94
AB213633_EV71C4_944_Yama_JPN03
0.89
AF009552_EV71C1_1919_NM_USA94
0.11
EV71C4_STU408070_GER04
1
AF119796_EV71C2_2086_TWN98
AF009549_EV71C1_0915_MA_USA87 1 0.24 AF009550_EV71C1_0916_MA_USA87 0.27 0.19 0.84
EV71C4_CF192013_FRA04 0.24
AF286492_EV71C2_2732_TWN98
AF009547_EV71C1_0925_OR_USA91 0.95
AM490159_EV71C4_900S_VNM05
1
AY722905_EV71C1_0681_AUS91
1 1 0.6
0.95
0.91
AY722908_EV71C1_2978_AUS92 1
DQ841969_EV71C4_E20051509_TWN05
AF176044_EV71C2_1245a_TWN98
AF009551_EV71C1_1411_CA_USA90 1
FJ194964_EV71C4_GDFS_3_CHN08
0.97
AF009554_EV71C1_2006_CT_USA94
0.17
1
0.68
AB213618_EV71C2_983_Yama_JPN99
AY940111_EV71C1_1232_AUS96 0.7
AB433875_EV71C4_2404_Yama_JPN06
0.58
AY940110_EV71C1_1095_AUS95 0.12 1 1
AB433871_EV71C4_2147_Yama_JPN06
1
1
1
AB433883_EV71C4_1667_Yama_JPN07
0.66 0.2
AY940113_EV71C2_0964_AUS98
1
AB213616_EV71C2_932_Yama_JPN99
0.97
AF135932_EV71C1_0390_TX_USA91
0.37
1
1
AF135939_EV71C1_2262_CA_USA92
1
0.12 0.47
AY547499_EV71C4_SHH02_6_CHN02
AB213614_EV71C2_671_Yama_JPN98 1
0.43
AF135931_EV71C1_0359_TX_USA90
AY547501_EV71C4_CQ03_1_CHN03
0.72
AB059817_EV71C2_1095_JPN97
0.62 AF135957_EV71C1_9718_TX_USA89
AY465356_EV71C4_SHZH_CHN03
AY722904_EV71C1_1182_AUS91 0.78 0.68
AB213630_EV71C2_452_Yama_JPN03
AB491216_EV71C1_1134_NLD91
AB115490_EV71C4_F1_CHN00
1
0.2
0.93
AF135955_EV71C1_9243_OK_USA89
AB177810_EV71C2_1116_Yama_JPN00
FJ556874_EV71C4_29961_THA08
0.84
AY722895_EV71C1_3032_AUS86
1
AY722894_EV71C1_7870_AUS86
FJ556873_EV71C4_29778_THA08
AF135941_EV71C2_2286_TX_USA97
0.21 0.29 AF135945_EV71C1_2623_AUS86 0.26
1
FJ151494_EV71C4_12242_THA08
AY722888_EV71C1_6955_AUS86 0.14
0.66
AY722897_EV71C1_0863_AUS87
0.81
FJ151496_EV71C4_17462_THA08 AY722890_EV71C1_6560_AUS86
0.7
0.37
1
AY722893_EV71C1_5408_AUS86
AB115492_EV71C4_H25_CHN00
0.97
AY722891_EV71C1_5409_AUS86 0.86
0.96
AY722889_EV71C1_2197_AUS86
0.98
0.99
EU131776_EV71C4_N3340_TWN02 0.39
AY722887_EV71C1_6887_AUS86
AY547500_EV71C4_SHH02_17_CHN02 AY722898_EV71C1_4812_AUS89 0.93 0.23
AY722900_EV71C1_5088_AUS90
AF302996_EV71C4_SHZH_CHN98
0.95 AY722903_EV71C1_4615_AUS90 0.75
AF286531_EV71C4_3254_TWN98
AY722906_EV71C1_9855_AUS91
1
AY722899_EV71C1_5596_AUS89 0.97
AY722901_EV71C1_0649_AUS90 1
Subgroup C2
AY125966_EV71C3_01_KOR00 0.74
1
1
AY125971_EV71C3_07_KOR00 1
DQ341356_EV71C3_03_KOR00 0.38
0.93
DQ341355_EV71C3_06_KOR00
1
AB115494_EV71C3_97_56_CHN97 1 0.49
Subgroup C4
AF135934_EV71C_0667_CHN87 AB059816_EV71C_Yamanashi_JPN80 1
DQ841973_EV71B4_E99194_TWN99 1 1
AF376121_EV71B5_5511_SGP00 AY207636_EV71B3_04716_MYS97
1
AF135888_EV71B2_2952_SD_USA81
1
AF135868_EV71B1_2229_NY_USA76
1
AB491212_EV71B0_5603_NLD65
Outgroup (genogroup B sequences)
6.0
Supplementary Fig. S3. Bayesian tree topology inferred with the 1D gene sequences of genogroup C, showing posterior probability and tip labels. Mirand, A., Schuffenecker, I., Henquell, C., Billaud, G., Jugie, G., Falcon, D., Mahul, A., Archimbaud, C., Terletskaia-Ladwig, E., Diedrich, S., Huemer, H. P., Enders, M., Lina, B., Peigue-Lafeuille, H. & Bailly, J.-L. (2010). Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries. J Gen Virol 91, 2263–2277.
EV71C1_GRE29_FRA07 FJ158600_EV71C4_DTID_ZJU_62_CHN08
EV71C2_BRE324_FRA07
EV71C1_NAN387_FRA06 3.47 EV71C1_CF210042_FRA06
EU913466_EV71C4_Fuyang22_CHN08 EV71C2_STU563062_GER07
FJ151495_EV71C1_17184_THA08
4.08
EV71C1_LYO10531_FRA06
6.56
EU913470_EV71C4_Fuyang31_CHN08 EV71C2_ULM63_GER07
EV71C1_POI777_FRA05
7.26
1.64 EU812515_EV71C4_FY23_CHN08
EV71C1_CAE571_FRA03 FJ461786_EV71C2_NUH0013_SGP08 EV71C1_LYO06972_FRA04
8.43
EU913469_EV71C4_Fuyang44_CHN08
AM939586_EV71C1_8277_GBR01 EV71C1_LYO16282_FRA03 8.94 AM939577_EV71C1_2063_GBR01 8.3 AM939579_EV71C1_2353_GBR02 8.53
FJ439769_EV71C4_Fuyang_CHN08
2.19 EV71C2_ANG261_FRA09
FJ469158_EV71C4_CY28_BJ_CHN08
EV71C2_LYO23284_FRA07
AM939589_EV71C1_11052_GBR01 EV71C1_CAE869_FRA04
FJ469152_EV71C4_CY6_BJ_CHN08
3.41 FJ469154_EV71C4_CY15_BJ_CHN08
EV71C2_NAN198_FRA07
EV71C1_ANG737_FRA03 6.82 EV71C1_NAN696_FRA04 6.54 EV71C1_STU565890_GER03 7.65
1.75
EV71C2_STU543078_GER08
2.67 2.43 FJ469157_EV71C4_CY21_BJ_CHN08
EV71C2_LMA55_FRA07
EV71C1_CAE201_FRA04
FJ469155_EV71C4_CY17_BJ_CHN08
2.85
EV71C2_BRE537_FRA08 8.28
EV71C1_LYO11868_FRA03 FJ360546_EV71C4_GZ0803_CHN08
AM939595_EV71C1_12105_GBR01
AB491220_EV71C2_265_NLD08
EV71C1_STU563449_GER03
1.61
AM939581_EV71C1_2826_GBR02
FJ469153_EV71C4_CY11_BJ_CHN08
EV71C2_NAN256_FRA08 4.32
EV71C1_STU554409_GER03
2.68
3.13
EU999179_EV71C4_Xinhui_9_CHN08
7.09 7.63
EV71C1_VIE21_AUT03
EV71C2_CF078034_FRA07 FJ194965_EV71C4_GDSG17_CHN08
EV71C1_STU565802_GER03 AM939604_EV71C2_6332_439_GBR06
AM939596_EV71C1_4709_GBR01
EU864507_EV71C4_EV71_Zhejiang_CHN08
3.26
AY258318_EV71C1_5026_SGP02
EV71C2_STU545774_GER07
AM939584_EV71C1_5746_GBR01
EU999171_EV71C4_Zhuhai_JC455_CHN08 2.44
AM939591_EV71C1_12081_GBR01
FJ360544_EV71C4_GZ0801_CHN08
EV71C2_CF341034_FRA06 AM939587_EV71C1_8300_GBR04 9.41 10.15 EV71C1_ANG100
EU999175_EV71C4_Zhuhai_164_CHN08
AM939607_EV71C2_6364_255_GBR06 3.73
DQ452074_EV71C1_804_NOR03 7.55 AM939578_EV71C1_6314_248_GBR06 10.71 8.73
3.44 EU753378_EV71C4_521_23F_CHN07
EV71C2_STU537622_GER07
AB115495_EV71C1_02363_THA02
2.96
EV71C1_CAE1053_FRA00 9.94 AB491217_EV71C1_3878_NLD02
EU913467_EV71C4_Fuyang5_CHN08 EV71C2_STU572078_GER08
1.68 FJ469159_EV71C4_Cy29_BJ_CHN08 2.26
FJ151492_EV71C2_01647_THA07
EV71C1_ULM705_GER00 6.24
11.2 EV71C1_BER409_GER00 10.24
FJ713137_EV71C4_Shanghai036_CHN09 FJ151501_EV71C2_12883_THA08
EV71C1_GRE454_FRA03
3.53
EU753404_EV71C4_523_14T_CHN07
EV71C1_HAN540_GER00 FJ151491_EV71C2_01644_THA07 EV71C1_CF605_FRA00
11.5
EU753380_EV71C4_521_27F_CHN07
4.46
EV71C1_ANN1254_FRA00 10.21 EV71C1_CF1744_FRA00 9.69 AM939590_EV71C1_11168_GBR00
EV71C2_STU553555_GER07
EU753398_EV71C4_523_07T_CHN07 2.72 3.76
4.72 EV71C2_BER180_GER06
EU753367_EV71C4_521_03T_CHN07 3.15
AM939580_EV71C1_2405_GBR01
AM939593_EV71C1_17728_GBR98
EU910861_EV71C4_0708T_NM_CHN07
EV71C2_NAN405_FRA06
AY207634_EV71C1_0774_MYS00 10.26 AY207635_EV71C1_05716_MYS00 10.56
EU753368_EV71C4_521_04F_CHN07 2.82
EV71C2_LYO24365_FRA06
DQ341360_EV71C1_J115_MYS01
EU753363_EV71C4_518_01F_CHN07 EV71C2_MUE66_GER07
EV71C1_NAN23154_FRA00 11.05 EV71C1_LYO11178_FRA00
4.37
1.88 EU999173_EV71C4_Zhuhai_213_CHN08 2.42
EV71C1_LYO26277_FRA06 4.4 EV71C1_LYO05158_FRA05 5.18
AM939576_EV71C2_6438_418_GBR06 12.01
FJ469156_EV71C4_CY20_BJ_CHN08
3.69
EV71C1_STU546711_GER08
8.47
EU999172_EV71C4_Zhuhai_JC498_CHN08 EV71C2_ANG544_FRA06
5.3
EV71C1_VIE94_AUT01
AM939597_EV71C2_STH_MCN_GBR06 3.98
EV71C1_STU562356_GER03
4.44
EU753364_EV71C4_518_02F_CHN07 2.34
EV71C1_CF097017_FRA03
AM939599_EV71C2_6486_445_GBR06
EU753403_EV71C4_523_13T_CHN07
AM939588_EV71C1_9027_GBR99 11.56 AB491218_EV71C2_365_NLD00
AM939592_EV71C1_13372_GBR98
EU753365_EV71C4_518_03F_CHN07
10.32
AY258294_EV71C1_SB9869_MYS03 7.56 AY258319_EV71C1_4381_SGP02 8.76
3.01 EU753370_EV71C4_521_05T_CHN07
EV71C2_POI515_FRA00
FJ151498_EV71C1_02073_THA07 11.08
EU753379_EV71C4_521_25F_CHN07 EV71C2_CF1113_FRA00
10.18 AY207619_EV71C1_0836_MYS00
10.72
10.43 AY207632_EV71C1_0832_MYS00 11.45
EU753405_EV71C4_523_15F_CHN07
AM939583_EV71C2_5622_GBR99
AY207621_EV71C1_0937_MYS00 9.78 AY207620_EV71C1_0915_MYS00 12.63
EU913468_EV71C4_Fuyang26_CHN08
AM939585_EV71C2_7414_GBR99
2.04
AF376087_EV71C1_S40221_MYS00
FJ828519_EV71C4_BJ08_CHN08 2.89
AY207626_EV71C1_0389_MYS00
14.66
11.51 EV71C2_ANN1256_FRA00 FJ360545_EV71C4_GZ0802_CHN08
AF135935_EV71C1_0756_MYS97 AF376108_EV71C2_7F_AUS99
AF376120_EV71C1_4575_SGP98
FJ606447_EV71C4_BJ08_Z004_3_CHN08 10.7
AY189154_EV71C1_S18191_MYS02
17.2
5.86
AF376092_EV71C2_15M_8_AUS99
AF135937_EV71C1_2132_VA_USA95 16.61 AF009559_EV71C1_1873_CT_USA93 17.04
FJ469160_EV71C4_CY43_BJ_CHN08 1.84
AF190577_EV71C2_31214_AZ_USA99
AF009556_EV71C1_2037_MD_USA95 AF376080_EV71C1_S10862_MYS98
FJ606450_EV71C4_BJ08_Z025_5_CHN08
12.95
EU753372_EV71C4_521_09F_CHN07
AF376103_EV71C2_2M_AUS99 EV71C1_NAN10838_FRA94
10.88
17.76 AF009544_EV71C1_2253_NY_USA94
EU753401_EV71C4_523_11F_CHN07
AF376102_EV71C2_27M_2_AUS99
AF135940_EV71C1_2263_CA_USA94
12.07
18.11 AF009545_EV71C1_2254_NY_USA94
AB433877_EV71C4_2753_Yama_JPN06
AY940112_EV71C2_1181_AUS98
AF009543_EV71C1_2251_NY_USA93
3.9
11.9
AF009555_EV71C1_2007_CT_USA94
13.63
16.92
4.86 AB433871_EV71C4_2147_Yama_JPN06 AF135950_EV71C2_2814_MO_USA98
AY940110_EV71C1_1095_AUS95
16.75
AF135942_EV71C2_2355_OK_USA97
AF135946_EV71C1_2640_AUS95
FJ556875_EV71C4_33951_THA08
AY940111_EV71C1_1232_AUS96 20.7
AB433875_EV71C4_2404_Yama_JPN06
12.33
AY722909_EV71C1_1065_AUS94 15.7
19.66
AB433883_EV71C4_1667_Yama_JPN07
7.21
AY940113_EV71C2_0964_AUS98
AF135936_EV71C1_1997_NC_USA94
5.58
14.44
AF009554_EV71C1_2006_CT_USA94 18.88 AF135933_EV71C1_0443_TX_USA91
AB213618_EV71C2_983_Yama_JPN99
FJ194964_EV71C4_GDFS_3_CHN08
12.76
7.82 AY905616_EV71C4_ZJ_3_CHN03
AF135943_EV71C2_2381_MA_USA97
AF135944_EV71C1_2583_CAN91
6.5
AF135956_EV71C1_9323_TX_USA89 21.31
AY905618_EV71C4_ZJ_5_CHN03
AY207611_EV71C2_03907_MYS97
AF135959_EV71C1_9873_NM_USA89 20.48 AF135938_EV71C1_2261_CA_USA91
12.78 DQ841965_EV71C4_E2004912_TWN04
AY207615_EV71C2_03750_MYS97
20.81
AF009551_EV71C1_1411_CA_USA90
DQ841969_EV71C4_E20051509_TWN05 5.49
AF176044_EV71C2_1245a_TWN98
AY722908_EV71C1_2978_AUS92 17.86 AY722907_EV71C1_5247_AUS92 18.37
22.37
11.46
5.82 AM490159_EV71C4_900S_VNM05
AF286497_EV71C2_2848_TWN98 11.68
AY722905_EV71C1_0681_AUS91 19.35
DQ841964_EV71C4_E2004104_TWN04 20.49AY722902_EV71C1_7784_AUS90 DQ841959_EV71C2_E98551_TW98
23.44
23.71
AF135958_EV71C1_9837_WA_USA89
EV71C4_CF192013_FRA04
AF009547_EV71C1_0925_OR_USA91 21.72 AF135953_EV71C1_8495_VA_USA88
AF286492_EV71C2_2732_TWN98 EV71C4_STU535542_GER04
AY722886_EV71C1_7610_AUS86
10.01
AF286505_EV71C2_2865_TWN98
AY722884_EV71C1_1058_AUS86 9.38
Subgroup C5
EV71C4_ULM275_GER04 5.71
15.03 AF304457_EV71C2_5746_CHN98 12.27
AF009549_EV71C1_0915_MA_USA87 22.8 AF009550_EV71C1_0916_MA_USA87
6.15 EV71C4_STU408070_GER04
EV71C4_VIE148_AUT04
AF119796_EV71C2_2086_TWN98 11.58
AF009542_EV71C1_2246_NY_USA87 23.54 AF135952_EV71C1_7238_AK_USA87 22.63 AF135951_EV71C1_7237_AK_USA87
AB177814_EV71C4_100_Yama_JPN03
AF286522_EV71C2_2912_TWN98
AB213629_EV71C4_2779_Yama_JPN02 7.31
15.5 AF135949_EV71C2_2644_AUS95
AF009546_EV71C1_2264_CA_USA94 13.33
14.62
17.17
AB213644_EV71C4_2316_Yama_JPN03
AF009553_EV71C1_1924_AZ_USA94 AF135947_EV71C2_2641_AUS95
19.48
6.54 7.65 AB213633_EV71C4_944_Yama_JPN03
AF009552_EV71C1_1919_NM_USA94 18.7 AF135932_EV71C1_0390_TX_USA91
AB213616_EV71C2_932_Yama_JPN99
AF135939_EV71C1_2262_CA_USA92
7.93 AY547499_EV71C4_SHH02_6_CHN02
11.48
AF135931_EV71C1_0359_TX_USA90
16.13
24.36
AB213614_EV71C2_671_Yama_JPN98 13.56
AY547501_EV71C4_CQ03_1_CHN03
21.31AF135957_EV71C1_9718_TX_USA89 AB059817_EV71C2_1095_JPN97
AY722904_EV71C1_1182_AUS91
AY465356_EV71C4_SHZH_CHN03
21.85 20.32 AB491216_EV71C1_1134_NLD91 AB213630_EV71C2_452_Yama_JPN03
AF135955_EV71C1_9243_OK_USA89 9.32
AY722895_EV71C1_3032_AUS86
AB115490_EV71C4_F1_CHN00 14.45 FJ556874_EV71C4_29961_THA08
AB177810_EV71C2_1116_Yama_JPN00
AY722894_EV71C1_7870_AUS86
14.76
2.13
AF135945_EV71C1_2623_AUS86
FJ556873_EV71C4_29778_THA08
AF135941_EV71C2_2286_TX_USA97 3.48
AY722888_EV71C1_6955_AUS86
FJ151494_EV71C4_12242_THA08
AY722897_EV71C1_0863_AUS87 23.98 AY722890_EV71C1_6560_AUS86
2.92 FJ151496_EV71C4_17462_THA08 11.53
AY722893_EV71C1_5408_AUS86 23.67
15.93
AY722891_EV71C1_5409_AUS86
AB115492_EV71C4_H25_CHN00
25.32
10.47
AY722889_EV71C1_2197_AUS86 23.8 AY722887_EV71C1_6887_AUS86
13.11
AY722898_EV71C1_4812_AUS89 20.33 AY722900_EV71C1_5088_AUS90
AY547500_EV71C4_SHH02_17_CHN02
AF302996_EV71C4_SHZH_CHN98
20.74AY722903_EV71C1_4615_AUS90 26.86 21.05
AY722906_EV71C1_9855_AUS91 AF286531_EV71C4_3254_TWN98
AY722899_EV71C1_5596_AUS89 20.44 AY722901_EV71C1_0649_AUS90
Subgroup C2
16.13
28.83
EU131776_EV71C4_N3340_TWN02
AY125966_EV71C3_01_KOR00 9.59 AY125971_EV71C3_07_KOR00 10.03 DQ341356_EV71C3_03_KOR00
21.58
19.06
DQ341355_EV71C3_06_KOR00
38.66
AB115494_EV71C3_97_56_CHN97
Subgroup C4
15.93 AF135934_EV71C_0667_CHN87 AB059816_EV71C_Yamanashi_JPN80 68.97
DQ841973_EV71B4_E99194_TWN99 14.3 17.56
AF135888_EV71B2_2952_SD_USA81 AF135868_EV71B1_2229_NY_USA76
AB491212_EV71B0_5603_NLD65
AF376121_EV71B5_5511_SGP00 AY207636_EV71B3_04716_MYS97
30.82 35.09 49.07
Outgroup (genogroup B sequences)
6.0
Supplementary Fig. S4. Bayesian tree topology inferred with the 1D gene sequences of genogroup C showing tip labels and node age. Mirand, A., Schuffenecker, I., Henquell, C., Billaud, G., Jugie, G., Falcon, D., Mahul, A., Archimbaud, C., Terletskaia-Ladwig, E., Diedrich, S., Huemer, H. P., Enders, M., Lina, B., Peigue-Lafeuille, H. & Bailly, J.-L. (2010). Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries. J Gen Virol 91, 2263–2277.
EV71C1_LYO02346_FRA06
0.23
EV71C1_NAN387_FRA06
0.16
EV71C1_LYO25400_FRA06 0.97 EV71C1_CF210042_FRA06 0.89 EV71C1_GRE29_FRA07 0.83 EV71C1_GRE594_FRA06
1
EV71C1_GRE580_FRA06
1
1
EV71C1_LYO10531_FRA06 EV71C1_CAE571_FRA03
0.99 0.36
EV71C1_POI777_FRA05 0.76 EV71C1_LYO6972_FRA04
EV71C1_LYO16282_FRA03
0.5
EV71C1_ANG100_FRA06
0.23
EV71C1_STU565802_GER03
0.87 1
EV71C1_STU554409_GER03 EV71C1_VIE21_AUT03
0.99 0.2
EV71C1_NAN696_FRA04
EV71C1_STU565890_GER03
0.19
1 EV71C1_CAE869_FRA04
EV71C1_ANG737_FRA03
1
0.87 EV71C1_LYO11868_FRA03 0.82 0.72
EV71C1_CAE201_FRA04
EV71C1_STU563449_GER03
0.98
DQ341361_EV71C1_1M_12_AUS00
0.82
DQ452074_EV71C1_804_NOR03 EV71C1_CAE1053_FRA00
0.97
EV71C1_ULM705_GER00
0.2
EV71C1_BER409_GER00
0.16 0.93 1 EV71C1_HAN540_GER00
EV71C1_GRE454_FRA03 EV71C1_VIE94_AUT01 0.67
EV71C1_LYO26277_FRA06
0.97
EV71C1_LYO05158_FRA05
1
EV71C1_STU246711_GER08
1 0.34 0.17
EV71C1_STU562356_GER03
EV71C1_NAN23154_FRA00 EV71C1_CF605_FRA00
0.71
EV71C1_ANN1254_FRA00
0.91 0.7
1 EV71C1_LYO28978_FRA99
EV71C1_CF1744_FRA00 0.86
EV71C1_CF097017_FRA03
1
EV71C1_LYO23597_FRA03
1
DQ341358_EV71C1_S40221_MYS00 1
DQ341360_EV71C1_J115_MAL_MYS01 DQ341359_EV71C1_S10862_MYS98
0.99
EV71C1_NAN10838_FRA94 EV71C2_ANG261_FRA09
0.7
EV71C2_ULM63_GER07
0.07
EV71C2_STU563062_GER07 0.04
EV71C2_BRE537_FRA08
0.13
EV71C2_NAN74_FRA07
0.03
EV71C2_BRE324_FRA07 0.06 EV71C2_STU543078_GER08
0.27 FJ172159_EV71C2_NUH0075_SGP08 0.08 0.64
EV71C2_LYO23284_FRA07 EV71C2_CAE739_FRA06 EV71C2_NAN198_FRA07
1
EV71C2_NAN215_FRA07
0.99 1 EV71C2_NAN197_FRA07 0.5 0.83
EV71C2_LMA55_FRA07
EV71C2_DIJ494_FRA07 0.12 EV71C2_NAN256_FRA08
1 0.12
EV71C2_NAN257_FRA08
0.56 0.81
EV71C2_CF139030_FRA07
EV71C2_CF078034_FRA07 EV71C2_STU572078_GER08
1
1 1 EV71C2_STU583939_GER08 0.4
EV71C2_STU545774_GER07 0.78 0.28EV71C2_CF341034_FRA06
EV71C2_STU537622_GER07 EV71C2_STU553555_GER07 0.44 EV71C2_LYO24365_FRA06 0.72 1
EV71C2_NAN293_FRA07
EV71C2_NAN488_FRA06 0.49 1 0.21 EV71C2_NAN405_FRA06
EV71C2_MUE66_GER07 0.36 0.46
EV71C2_BER180_GER06
EV71C2_ANG544_FRA06 EV71C2_ANN1256_FRA00
1
0.51
EV71C2_POI515_FRA00
0.91
DQ341357_EV71C2_7F_6_AUS99
0.97 0.98
EV71C2_CF1113_FRA00
1
EV71C2_GRE1244_FRA00 DQ381846_EV71C2_6F_6_AUS99 1
AF304459_EV71C2_Tainan_6092_CHN98
0.3
AF304458_EV71C2_Tainan_4643_CHN98
0.34
1
AF176044_EV71C2_1245a_TWNN98 0.99 0.85
AF304457_EV71C2_Tainan_5746_CHN98
1
AF119795_EV71B_2272_TWNN98
1
AF119796_EV71C2_2086_TWNN98 1
DQ341355_EV71C3_06_KOR00 DQ341356_EV71C3_03_KOR00
AY421766_CA8_Donovan_USA50 EU527983_EV71C5_07364_TWN07 FJ357385_EV71B5_M0380_TWNN08
1
EU527985_EV71B5_08747_TWN07
0.18
FJ461781_EV71B5_NUH0083_SGP08
0.48
DQ341363_EV71B5_S19841_MYS03
1 0.99
DQ341362_EV71B5_SB12736_MYS03
1
FJ357378_EV71B5_N2838_TWN03
0.52 DQ341364_EV71B5_5511_SGP00
FJ357375_EV71B4_N7008_TWN99 1
FJ357377_EV71B4_S0296_TWN00
1 0.65
FJ357376_EV71B4_S0318_TWN01
1
DQ341366_EV71B4_SB2864_MYS00
1
DQ341365_EV71B4_PP37_MYS01 FJ357380_EV71B1_237_TWN86
0.97
1
FJ357379_EV71B1_236_TWN86
0.34
FJ357381_EV71B1_244_TWN86 0.99 FJ357382_EV71B1_238_TWN86 0.78 1 1
FJ357383_EV71B1_252_TWNN86 FJ357384_EV71B1_266_TWNN86
AB482183_EV71B1_Nagoya_JPN73
0.98
U22522_EV71B2_MS_7423_87
1
EV71B_CHE516_GER87 1
EU262658_CA16_SHZ_CHN05
0.99
FJ198212_CA16_GZ08_CHN08
1
AY790926_CA16_shzh_1_CHN00
0.96
0.9
AF177911_CA16_Tainan_CHN98
0.97
U22521_EV71_BrCr_USA69 AY421761_CA3_Olson
0.97
1
0.99
AY421764_CA6_Gdula_USA50
0.83
1
AY421768_CA12_Texas_12_USA51 AY421767_CA10_Kowalik_USA50
0.94
AY421760_CA2_Fleetwood_USA47 AY421765_CA7_Parker_USA50 AY421763_CA5_Swartz_USA50 FJ158601_EV71C4_DTID_ZJU_74_CHN08
0.97
FJ158600_EV71C4_DTID_ZJU_62_CHN08
0.18
EU812515_EV71C4_FY23_CHN08 0.06
EU703814_EV71C4_Fuyang_CHN08
1
EU703812_EV71C4_Fuyang_CHN08
0.08 0.11
FJ360546_EV71C4_GZ_08_03_CHN08 FJ606449_EV71C4_BJ08_Z020_1_CHN08
0.9
EU703813_EV71C4_Fuyang_CHN08
0.33
FJ439769_EV71C4_Fuyang_0805_CHN08
0.92 1
FJ606448_EV71C4_BJ08_Z011_4_CHN08 GQ892830_EV71C4_GX_LZ_CHN08
0.27 0.14GQ994990_EV71C4_Chongqing_CHN09 0.99
0.38
FJ607338_EV71C4_605_SHENZHEN_CHN08 FJ194965_EV71C4_GDSG_17_CHN08 1
FJ607335_EV71C4_4_SHENZHEN_CHN08
1
FJ607334_EV71C4_1_SHENZHEN_CHN08
0.99
EU864507_EV71C4_Zhejiang_CHN08
0.44 0.99 1
FJ360544_EV71C4_GZ_08_01_CHN08 GQ994991_EV71C4_Chongqing_3_CHN09
10.73
FJ713137_EV71C4_Shanghai_036_CHN09 GQ994988_EV71C4_Anhui_1_CHN09 FJ360545_EV71C4_GZ_08_02_CHN08
1 1 FJ828519_EV71C4_BJ08_CHN08 0.93
FJ607336_EV71C4_28_SHENZHEN_CHN08 FJ606447_EV71C4_BJ08_Z004_3_CHN08
0.79 1
GQ994992_EV71C4_Henan_CHN09 1
FJ194964_EV71C4_GDFS_3_CHN08
1
GQ994989_EV71C4_Chongqing_1_CHN09 1
FJ357374_EV71C4_N2121_TWN05
FJ357373_EV71C4_S0584_TWN04 EV71C4_ULM275_GER04
0.27
1
1
EV71C4_CF192013_FRA04
0.21
EV71C4_STU535542_GER04
0.94
EV71C4_STU408070_GER04
1
1 0.89
EV71C4_STU499202_GER04
0.54 EV71C4_VIE148_AUT04
AY465356_EV71C4_SHZH03_CHN03 1
EU131776_EV71C4_N3340_TWNN02
0.99
AF302996_EV71C4_SHZH_CHN98 FJ607337_EV71C4_121_SHENZHEN_CHN08
1
FJ606450_EV71C4_BJ08_Z025_5_CHN08
1
AB469182_EV71B3_SK_EV006_MYS97
0.21
DQ341367_EV71B3_MY821_3_MYS97
0.25
EU364841_EV71B3_26M_4_AUS99
0.81
0.07 1
DQ341368_EV71B3_MY104_9_MYS97 DQ341354_EV71B3_3799_SGP98
1
U05876__CA16_G10_RSA51 0.59
AY421769_CA14_G14_RSA51 AY421762_CA4_HighPoint_USA48 AY697458_EV76_10369_FRA91
1
AY697459_EV89_10359_BAN00
1 1
AY697461_EV91_10406_BAN00
Supplementary Fig. S5. Bayesian tree topology inferred with the 3CD gene sequences of EV-71 and related HEV-A serotypes showing genetic distances (nucleotide substitution per site), tip labels and posterior probability values at nodes.
AY697460_EV90_10399_BAN99 0.07
Mirand, A., Schuffenecker, I., Henquell, C., Billaud, G., Jugie, G., Falcon, D., Mahul, A., Archimbaud, C., Terletskaia-Ladwig, E., Diedrich, S., Huemer, H. P., Enders, M., Lina, B., Peigue-Lafeuille, H. & Bailly, J.-L. (2010). Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries. J Gen Virol 91, 2263–2277.
EV71C1_LYO02346_FRA06 EV71C1_NAN387_FRA06 EV71C1_LYO25400_FRA06 3.43 EV71C1_CF210042_FRA06 3.65 3.9 EV71C1_GRE29_FRA07
EV71C1_GRE594_FRA06
4.29
EV71C1_GRE580_FRA06 3.34
6.93
EV71C1_LYO10531_FRA06
EV71C1_CAE571_FRA03
7.67
EV71C1_POI777_FRA05 8.53
EV71C1_LYO6972_FRA04 EV71C1_LYO16282_FRA03 EV71C1_ANG100_FRA06 EV71C1_STU565802_GER03
6.93
EV71C1_STU554409_GER03
7.46
EV71C1_VIE21_AUT03 EV71C1_NAN696_FRA04
9.03
EV71C1_STU565890_GER03 6.74EV71C1_CAE869_FRA04
EV71C1_ANG737_FRA03
7.51 9.65
EV71C1_LYO11868_FRA03
8.4 7.07
EV71C1_CAE201_FRA04
EV71C1_STU563449_GER03
9.98
DQ341361_EV71C1_1M_12_AUS00 9.31
DQ452074_EV71C1_804_NOR03 EV71C1_CAE1053_FRA00
10.47
EV71C1_ULM705_GER00 EV71C1_BER409_GER00 10.95 EV71C1_HAN540_GER00 10.02
EV71C1_GRE454_FRA03 EV71C1_VIE94_AUT01 11.53
EV71C1_LYO26277_FRA06 4.49
EV71C1_LYO05158_FRA05
5.62
EV71C1_STU246711_GER08
9.02
EV71C1_STU562356_GER03 EV71C1_NAN23154_FRA00 EV71C1_CF605_FRA00 10.14
EV71C1_ANN1254_FRA00
10.67 12.05
EV71C1_LYO28978_FRA99 11.13 EV71C1_CF1744_FRA00 12.5
EV71C1_CF097017_FRA03 8.74
EV71C1_LYO23597_FRA03
13.56
DQ341358_EV71C1_S40221_MYS00 19.98
DQ341360_EV71C1_J115_MAL_MYS01 DQ341359_EV71C1_S10862_MYS98
17.53
EV71C1_NAN10838_FRA94 EV71C2_ANG261_FRA09 2.47
EV71C2_ULM63_GER07 EV71C2_STU563062_GER07 EV71C2_BRE537_FRA08 EV71C2_NAN74_FRA07 EV71C2_BRE324_FRA07 EV71C2_STU543078_GER08 FJ172159_EV71C2_NUH0075_SGP08
2.92
EV71C2_LYO23284_FRA07 EV71C2_CAE739_FRA06 EV71C2_NAN198_FRA07 2.33
EV71C2_NAN215_FRA07 2.67 3.66EV71C2_NAN197_FRA07 2.49 2.87
EV71C2_LMA55_FRA07 EV71C2_DIJ494_FRA07 EV71C2_NAN256_FRA08 1.32
EV71C2_NAN257_FRA08 4.21 3.16
EV71C2_CF139030_FRA07 EV71C2_CF078034_FRA07 EV71C2_STU572078_GER08
28.87
1.43
4.49
EV71C2_STU583939_GER08
3.74EV71C2_STU545774_GER07
EV71C2_CF341034_FRA06 EV71C2_STU537622_GER07 EV71C2_STU553555_GER07 EV71C2_LYO24365_FRA06 3.56
EV71C2_NAN293_FRA07
3.87
EV71C2_NAN488_FRA06 6.11
EV71C2_NAN405_FRA06 EV71C2_MUE66_GER07 EV71C2_BER180_GER06 EV71C2_ANG544_FRA06
EV71C2_ANN1256_FRA00
12.38
70.67
EV71C2_POI515_FRA00 10.97
DQ341357_EV71C2_7F_6_AUS99 11.44 13.43
EV71C2_CF1113_FRA00
9.55
EV71C2_GRE1244_FRA00 DQ381846_EV71C2_6F_6_AUS99 16.7
AF304459_EV71C2_Tainan_6092_CHN98 AF304458_EV71C2_Tainan_4643_CHN98
75.65
AF176044_EV71C2_1245a_TWNN98 11.81 24.17
14.52
AF304457_EV71C2_Tainan_5746_CHN98 AF119795_EV71B_2272_TWNN98
13.9
AF119796_EV71C2_2086_TWNN98 DQ341355_EV71C3_06_KOR00 10.53
DQ341356_EV71C3_03_KOR00 AY421766_CA8_Donovan_USA50 EU527983_EV71C5_07364_TWN07 FJ357385_EV71B5_M0380_TWNN08 3.98
EU527985_EV71B5_08747_TWN07 FJ461781_EV71B5_NUH0083_SGP08 DQ341363_EV71B5_S19841_MYS03 8.6
6.93
11.24 14.65
DQ341362_EV71B5_SB12736_MYS03 FJ357378_EV71B5_N2838_TWN03
DQ341364_EV71B5_5511_SGP00 FJ357375_EV71B4_N7008_TWN99
16.13
FJ357377_EV71B4_S0296_TWN00 9.53
FJ357376_EV71B4_S0318_TWN01
147.41
11.98
DQ341366_EV71B4_SB2864_MYS00 10.16
DQ341365_EV71B4_PP37_MYS01 FJ357380_EV71B1_237_TWN86 24.32
56.53
FJ357379_EV71B1_236_TWN86 FJ357381_EV71B1_244_TWN86 25.12 FJ357382_EV71B1_238_TWN86 26.25 27.65 FJ357383_EV71B1_252_TWNN86 40.18 49.26
FJ357384_EV71B1_266_TWNN86 AB482183_EV71B1_Nagoya_JPN73 U22522_EV71B2_MS_7423_87 30.69
EV71B_CHE516_GER87 EU262658_CA16_SHZ_CHN05
105.79
10.07
FJ198212_CA16_GZ08_CHN08 14.36
AY790926_CA16_shzh_1_CHN00 12.07
54.38 63.21
AF177911_CA16_Tainan_CHN98 U22521_EV71_BrCr_USA69 AY421761_CA3_Olson
72.68
122.45
AY421764_CA6_Gdula_USA50 77.36
69.68
AY421768_CA12_Texas_12_USA51 AY421767_CA10_Kowalik_USA50
95.84
72.67
AY421760_CA2_Fleetwood_USA47 AY421765_CA7_Parker_USA50 AY421763_CA5_Swartz_USA50 FJ158601_EV71C4_DTID_ZJU_74_CHN08 1.27
FJ158600_EV71C4_DTID_ZJU_62_CHN08 EU812515_EV71C4_FY23_CHN08 EU703814_EV71C4_Fuyang_CHN08 1.13
EU703812_EV71C4_Fuyang_CHN08 FJ360546_EV71C4_GZ_08_03_CHN08 FJ606449_EV71C4_BJ08_Z020_1_CHN08
2.14
EU703813_EV71C4_Fuyang_CHN08 FJ439769_EV71C4_Fuyang_0805_CHN08
1.58 2.46
FJ606448_EV71C4_BJ08_Z011_4_CHN08
GQ892830_EV71C4_GX_LZ_CHN08 GQ994990_EV71C4_Chongqing_CHN09
2.05
FJ607338_EV71C4_605_SHENZHEN_CHN08 FJ194965_EV71C4_GDSG_17_CHN08 3.16
FJ607335_EV71C4_4_SHENZHEN_CHN08
1.26
FJ607334_EV71C4_1_SHENZHEN_CHN08
1.92
EU864507_EV71C4_Zhejiang_CHN08 4.01
FJ360544_EV71C4_GZ_08_01_CHN08 1.78
GQ994991_EV71C4_Chongqing_3_CHN09 FJ713137_EV71C4_Shanghai_036_CHN09
4.56 3.29
GQ994988_EV71C4_Anhui_1_CHN09 FJ360545_EV71C4_GZ_08_02_CHN08 2.23 5.32 FJ828519_EV71C4_BJ08_CHN08 4.01
FJ607336_EV71C4_28_SHENZHEN_CHN08 6.56
FJ606447_EV71C4_BJ08_Z004_3_CHN08 3.63
GQ994992_EV71C4_Henan_CHN09 7.2
FJ194964_EV71C4_GDFS_3_CHN08 4.66
GQ994989_EV71C4_Chongqing_1_CHN09 FJ357374_EV71C4_N2121_TWN05 5.81
FJ357373_EV71C4_S0584_TWN04 EV71C4_ULM275_GER04 10.58
186
EV71C4_CF192013_FRA04 EV71C4_STU535542_GER04
5.84
EV71C4_STU408070_GER04 5.4 6.37
15.39
EV71C4_STU499202_GER04
9.61
EV71C4_VIE148_AUT04 AY465356_EV71C4_SHZH03_CHN03
28.77
EU131776_EV71C4_N3340_TWNN02 13.45
AF302996_EV71C4_SHZH_CHN98 FJ607337_EV71C4_121_SHENZHEN_CHN08 1.8
FJ606450_EV71C4_BJ08_Z025_5_CHN08
47.84
AB469182_EV71B3_SK_EV006_MYS97 DQ341367_EV71B3_MY821_3_MYS97 EU364841_EV71B3_26M_4_AUS99
72.36 12.99
DQ341368_EV71B3_MY104_9_MYS97 DQ341354_EV71B3_3799_SGP98
81.56
U05876__CA16_G10_RSA51 AY421769_CA14_G14_RSA51 76.31
AY421762_CA4_HighPoint_USA48 AY697458_EV76_10369_FRA91 30.21
AY697459_EV89_10359_BAN00 47.05
AY697461_EV91_10406_BAN00 15.68
AY697460_EV90_10399_BAN99 20.0
Supplementary Fig. S6. Bayesian tree topology inferred with the 3CD gene sequences of EV-71 and related HEV-A serotypes showing evolutionary distances (nucleotide substitution per site per year), tip labels and the estimated divergence (year) at nodes.
Mirand, A., Schuffenecker, I., Henquell, C., Billaud, G., Jugie, G., Falcon, D., Mahul, A., Archimbaud, C., Terletskaia-Ladwig, E., Diedrich, S., Huemer, H. P., Enders, M., Lina, B., Peigue-Lafeuille, H. & Bailly, J.-L. (2010). Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries. J Gen Virol 91, 2263–2277.
2005
S7A 2003
2001
1999
T 1997 M R 1995 C A 1993 1991
1989
1987
1985
C1
C1b
C2
C2b
C4
C4EU
2005
S7B 2003
2001
1999
T 1997 M R 1995 C A 1993 1991
1989
1987
1985
Supplementary Fig. S7. Divergence dates (TMRCA) estimated with a multilocus model for exemplary clades within the EV-71 genogroup C. The Bayesian relaxed clock analyses were performed with the beast program (Drummond & Rambaut, 2007) assuming either an unlinked multilocus model (Lemey et al., 2004) or a model in which loci 1D and 3CD were linked (concatenated sequences). The coalescent investigations of EV-71 history were carried with virus strains (n=134) for which sequences were available for both 1D and 3CD loci. Two analyses assuming that the 1D and 3CD loci were unlinked but shared a common demographic history were done separately; the TMRCA values estimated in the two analyses are indicated with squares and diamonds. The TMRCA values obtained with the linked analysis (concatenated sequence dataset, same coalescent pathway) are indicated with dots. The values indicated are the mean estimates (with the 95 % confidence interval) of the time to the MRCA for clades representative of the EV71 genogroup C (subgenogroups C1, lineage C1b, subgenogroup C2, lineage C2b, subgenogroup C4, lineage C4EU including the C4 virus strains detected in Europe). In the unlinked analyses, the TMRCA estimates are indicated separately for the single loci 1D (Supplementary Fig. S7a) and 3CD (Supplementary Fig. S7b). In the case of subgenogroup C4, two distant sequences FJ606450 and FJ607337 were taken into account for the TMRCA estimate. For the linked loci analysis, the TMRCA estimates are identical in Supplementary Fig. S7(a, b). The MCMC analyses were run for 60 million steps and sampled every 2000 states. The posterior densities were calculated with a 10 % burnin and checked for convergence (see Methods). Mirand, A., Schuffenecker, I., Henquell, C., Billaud, G., Jugie, G., Falcon, D., Mahul, A., Archimbaud, C., Terletskaia-Ladwig, E., Diedrich, S., Huemer, H. P., Enders, M., Lina, B., Peigue-Lafeuille, H. & Bailly, J.-L. (2010). Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries. J Gen Virol 91, 2263–2277.
