Table 1. EV71 reference strains used in this study.
| Strain | GenBank no. | Strain | GenBank no. |
| SHZH98|1998 | AF302996 | Fuyang5|2008 | HQ694984 |
| F1CHN00|2000 | AB115490 | Fuyang22|2008 | EU913466 |
| H26CHN00|2000 | AB115493 | BJ08Z0255|2008 | FJ606450 |
| H25CHN00|2000 | AB115492 | BJ08Z0201|2008 | FJ606449 |
| F2CHN00|2000 | AB115491 | BJ08Z0114|2008 | FJ606448 |
| shzh018|2001 | AY895091 | BJ08Z0043|2008 | FJ606447 |
| EV71SHH026|2002 | AY547499 | Chen1/GZ/CHN/2008 | GU190181 |
| EV71SHH0217|2002 | AY547500 | 168/GZ/CHN/2008 | GU190178 |
| SHZH03|2003 | AY465356 | 152/GZ/CHN/2008 | GU190177 |
| ZJCHN603|2003 | AY905619 | 145/GZ/CHN/2008 | GU190176 |
| ZJCHN503|2003 | AY905618 | 142/GZ/CHN/2008 | GU190175 |
| ZJCHN403|2003 | AY905617 | 136/GZ/CHN/2008 | GU190174 |
| ZJCHN303|2003 | AY905616 | 133/GZ/CHN/2008 | GU190173 |
| ZJCHN203|2003 | AY905615 | 130/GZ/CHN/2008 | GU190172 |
| ZJCHN103|2003 | AY905614 | 129/GZ/CHN/2008 | GU190171 |
| EV71CQ031|2003 | AY547501 | 122/GZ/CHN/2008 | GU190170 |
| AnHuiHeFei1|2006 | EU697903 | 1/GZ/CHN/2008 | GU190169 |
| BJ4211|2007 | EU024958 | DTID/ZJU74|2008 | FJ158601 |
| BJ4243|2007 | EU019910 | DTID/ZJU62|2008 | FJ158600 |
| 0723F/NM/CHN/07|2007 | EU910869 | EV71/Zhejiang08|2008 | EU864507 |
| 0718F/NM/CHN/07|2007 | EU910868 | AnHuiFuYang17|2008 | EU697902 |
| 0717F/NM/CHN/07|2007 | EU910867 | AnHuiFuYang12|2008 | EU697901 |
| 0716F/NM/CHN/07|2007 | EU910866 | EV71/Lanzhou10|2008 | GQ855294 |
| 0715F/NM/CHN/07|2007 | EU910865 | EV71/Lanzhou09|2008 | GQ855293 |
| 0712F/NM/CHN/07|2007 | EU910864 | EV71/Lanzhou08|2008 | GQ855292 |
| 0711F/NM/CHN/07|2007 | EU910863 | EV71/Lanzhou07|2008 | GQ855291 |
| 0709F/NM/CHN/07|2007 | EU910862 | EV71/Lanzhou06|2008 | GQ855290 |
| 0708T/NM/CHN/07|2007 | EU910861 | EV71/Lanzhou05|2008 | GQ855289 |
| EV71/FuyangAnhuiPRC/1708/3|2008 | EU703814 | EV71/Lanzhou04|2008 | GQ855288 |
| EV71/FuyangAnhuiPRC/1708/2|2008 | EU703813 | EV71/Lanzhou03|2008 | GQ855287 |
| EV71/FuyangAnhuiPRC/1708/1|2008 | EU703812 | EV71/Lanzhou02|2008 | GQ855286 |
| CY44/BJ/CHN/2008 | FJ469161 | EV71/Lanzhou01|2008 | GQ855285 |
| CY43/BJ/CHN/2008 | FJ469160 | Henan109China|2009 | GU196833 |
| Cy29/BJ/CHN/2008 | FJ469159 | Henan209China|2009 | GQ994992 |
| CY28/BJ/CHN/2008 | FJ469158 | Chongqing309China|2009 | GQ994991 |
| CY21/BJ/CHN/2008 | FJ469157 | Chongqing209China|2009 | GQ994990 |
| CY20/BJ/CHN/2008 | FJ469156 | Chongqing109China|2009 | GQ994989 |
| CY17/BJ/CHN/2008 | FJ469155 | Anhui109China|2009 | GQ994988 |
| CY15/BJ/CHN/2008 | FJ469154 | 373/GZ/CHN/2009 | GU190179 |
| CY11/BJ/CHN/2008 | FJ469153 | 06/ZJ/CHN/Z|2010 | HM855955 |
| CY6/BJ/CHN/2008 | FJ469152 | 05/ZJ/CHN/Z|2010 | HM855954 |
| HN08HLF3|2008 | GQ121134 | 04/ZJ/CHN/Z|2010 | HM855953 |
| HN08HLF2|2008 | GQ121133 | 03/ZJ/CHN/Z|2010 | HM855952 |
| Xinhui9|2008 | EU999179 | 02/ZJ/CHN/Z|2010 | HM855951 |
| Xinhui8|2008 | EU999178 | 01/ZJ/CHN/Z|2010 | HM855950 |
| Xinhui7|2008 | EU999177 | 265-NL-2008 | AB491220 |
| Zhuhai152|2008 | EU999176 | 1245a-TW-98 | AF176044 |
| Zhuhai164|2008 | EU999175 | 01-KOR-00 | AY125966 |
| Zhuhai171|2008 | EU999174 | BrCr-CA-USA-70 | U22521 |
| Zhuhai213|2008 | EU999173 | 9923-SYD-01 | AY940107 |
| ZhuhaiJC498|2008 | EU999172 | 2027-SIN-01 | AF376111 |
| ZhuhaiJC455|2008 | EU999171 | 06-KOR-00 | AY125970 |
| ZhuhaiJC467|2008 | EU999170 | 730T-VNM-05 | AM490156 |
| Fuyang49|2008 | EU913471 | 1134-NL-91 | AB491216 |
| Fuyang31|2008 | EU913470 | 1091S-VNM-05 | AM490143 |
| Fuyang44|2008 | EU913469 | 1277S-VNM-05 | AM490148 |
| Fuyang26|2008 | EU913468 | 203 reference strains* |
*
The GenBank numbers of the 203 reference strains are AY895129-AY895145, EU753363 - EU753418, FJ765416 - FJ765435, GQ121417 - GQ121441, GQ253391 - GQ253423, GQ487666 - GQ487689 and GU353079 - GU353106. All of these strains are part of the 305 GenBank EV71 C4 reference strains collected in Mainland China from 1998 to 2010.