Supplementary tables
Table S1. Details of 15 JEV isolates presently or previously reported from Henan province, central China.
No. / Isolate / Year & Month / Geographical location / Source / Genotype / Acc. No. of E gene(1) / HN10-BSF.ZZ-3 / 2010, Jul. / Henan, Zhengzhou / Swine, boar seminal fluid / 3 / HE565484
(2) / HN10-BSF.ZZ-1 / 2010, Jul. / Henan, Zhengzhou / Swine, boar seminal fluid / 3 / HE565483
(3) / HN09-CSF.XZ-2D / 2009, Jul. / Henan, Xinzheng / Swine, cerebrospinal fluid / 3 / HE565482
(4) / HN08-Mos.BF-2 / 2008, Aug. / Henan, Baofeng / Culex, unclassified / 3 / HE565478
(5) / HN08-Mos.WG-1 / 2008, Aug. / Henan, Wugang / Culex, unclassified / 3 / HE565479
(6) / HN08-Mos.XZ-4 / 2008, Aug. / Henan, Xinzheng / Culex, unclassified / 3 / HE565480
(7) / HN08-Mos.YY-1 / 2008, Aug. / Henan, Yuanyang / Culex, unclassified / 3 / HE565481
(8) / HN08-CSF.BY-1 / 2008, Jul. / Henan, Biyang / Swine, cerebrospinal fluid / 3 / GQ845081
(9) / HN08-CSF.ZY-2 / 2008, Jul. / Henan, Zhengyang / Swine, cerebrospinal fluid / 3 / GQ845082
(10) / HN08-CSF.ZMD-3 / 2008, Jul. / Henan, Zhumadian / Swine, cerebrospinal fluid / 3 / GQ336809
(11) / HN08-CSF.ZMD-4 / 2008, Jul. / Henan, Zhumadian / Swine, cerebrospinal fluid / 3 / GQ845083
(12) / HEN0701* / 2007, IU / Henan, Nanyang / Swine, aborted fetus / 1 / FJ495189
(13) / HN04-11* / 2004, IU / Henan, Nanyang / Culex, unclassified / 1 / DQ404087
(14) / HN04-21* / 2004, IU / Henan, Nanyang / Culex, unclassified / 1 / DQ404088
(15) / HN04-40* / 2004, IU / Henan, Nanyang / Culex, unclassified / 1 / DQ404089
Mosquitoes, cerebrospinal fluid (CSF), and boar seminal fluid (BSF) samples were collected from the piggeries, aborted fetuses or stillborn piglets, or diseased boars in large scale pig farms for virus isolation in present study, respectively.
* JEV isolates reported before this study.
IU, information unavailable.
Table S2. Details of 47 JEV isolates obtained from China before 2000.
No. / Strain / Year / Geographical location / Source / Genotype / GenBank Acc. No.prM gene / E gene
1 / A2 / 1949 / China, Beijing / Human brain / 3 / AY243809 / AY243843
2 / P3 / 1949 / China, Beijing / Human brain / 3 / AY243805 / AY243844
3 / 47 / 1950s / China, Heilongjiang / Human brain / 3 / AY243810 / AY243827
4 / YN / 1954 / China, Yunnan / Human brain / 3 / AY243820 / AY243838
5 / G35 / 1954 / China, Fujian / Mosquito pool / 3 / AY243815 / AY243831
6 / CBH / 1954 / China, Fujian / Human brain / 3 / AY243812 / DQ404116
7 / CZX / 1954 / China, Fujian / Human brain / 3 / AY243811 / AY243828
8 / YLG / 1955 / China, Fujian / Human brain / 3 / AY243824 / AY243837
9 / ZSZ / 1955 / China, Fujian / Human brain / 3 / AY243825 / AY243839
10 / CTS / 1955 / China, Fujian / Human brain / 3 / AY243814 / AY243830
11 / ZMT / 1955 / China, Fujian / Human brain / 3 / AY243821 / AY243840
12 / LFM / 1955 / China, Fujian / Human blood / 3 / AY243817 / AY243833
13 / LYZ / 1957 / China, Fujian / Human brain / 3 / AY243818 / AY243834
14 / CH-13 / 1957 / China, Sichuan / Human brain / 3 / AY243813 / AY243829
15 / HA-3 / 1960s / China, Heilongjiang / Human brain / 3 / AY243806 / AY243842
16 / GSS / 1960s / China, Beijing / Human brain / 3 / AY243816 / AY243845
17 / SA14 / 1960 / China, Shanxi / Mosquito pool / 3 / AY243807 / AY243842
18 / SA14-14-2 / China, Vaccine / Vaccine / 3 / AF315119 / AF315119
19 / TLA / 1971 / China, Liaoning / Human brain / 3 / AY243808 / AY243832
20 / M28 / 1977 / China, Yunnan / Culex pesudovishui / 1 / UA / UA
21 / M10 / 1977 / China, Yunnan / Culex pesudovishui / 3 / UA / UA
22 / Yguoying / 1979 / China, Yunnan / Human serum / 3 / UA / UA
23 / Ecun / 1979 / China, Yunnan / Human serum / 3 / UA / UA
24 / Lyujie / 1979 / China, Yunnan / Human serum / 3 / FJ185041 / FJ185039
25 / Hyuzheng / 1979 / China, Yunnan / Human serum / 3 / UA / UA
26 / YN79-Bao83 / 1979 / China, Yunnan / Culex tritaeniorhynchus / 1 / DQ404060 / DQ404128
27 / BN19 / 1981 / China, Yunnan / Culex tritaeniorhynchus / 3 / FJ185040 / FJ185038
28 / DN82215 / 1982 / China, Yunnan / Culex annulus / 1 / UA / UA
29 / YN82-BN8219 / 1982 / China, Yunnan / Culex / 1 / DQ404061 / DQ404129
30 / YN83-Meng83-54 / 1983 / China, Yunnan / Forcipomyia taiwana Shiraki / 1 / DQ404062 / DQ404130
31 / YN83-83199 / 1983 / China, Yunnan / Culex / 1 / DQ404063 / DQ404131
32 / YN85-L86-99 / 1985 / China, Yunnan / Culex / 1 / DQ404064 / DQ404132
33 / YN86-B8639 / 1986 / China, Yunnan / Culex tritaeniorhynchus / 1 / DQ404065 / DQ404133
34 / YN86-86266 / 1986 / China, Yunnan / IU / 1 / DQ404066 / DQ404134
35 / SH-3 / 1987 / China, Shanghai / Human brain / 3 / AY243819 / AY243836
36 / HW (HW1) / 1988 / China, Hubei / Swine / 3 / AY849939† / AY849939†
37 / WHe (HW2) / 1988 / China, Hubei / Swine / 3 / EF107523† / EF107523†
38 / B58 / 1989 / China, Yunnan / Rousettus leschenaultia / 3 / FJ185036† / FJ185036†
39 / M89-48 / 1989 / China, Yunnan / Culex pesudovishui / 3 / UA / UA
40 / M89-48 / 1989 / China, Yunnan / Culex tritaeniorhynchus / 3 / UA / UA
41 / M89-55 / 1989 / China, Yunnan / Anopheles vagus / 3 / UA / UA
42 / DHl07 / 1989 / China, Yunnan / Aedes lineatopennis / 3 / UA / UA
43 / HB49 / 1990 / China, Yunnan / Rousettus leschenaultia blood / 3 / UA / UA
44 / HB97 / 1990 / China, Yunnan / Rousettus leschenaultia blood / 3 / UA / UA
45 / E21 / 1991 / China, Yunnan / Human blood / 3 / UA / UA
46 / E18 / 1991 / China, Yunnan / Human blood / 3 / UA / UA
47 / GB30 / 1997 / China, Yunnan / Murina aurata brain / 3 / FJ185037† / FJ185037†
48 / YN98-151 / 1998 / China, Yunnan / Mosquitoes / 3 / DQ404068 / DQ404136
IU, information unavailable; UA, unavailable in GenBank. †GenBank accession numbers of JEV complete genomes.
Table S3. Details of 158 JEV isolates from China in last decade, 2001-2010.
No. / Geographical location and strain / Year / Source / Genotype / GenBank accession no.prM gene / E gene
(a) / Yunnan province, China / 28 strains
(1) / YNDL04-1 / 2004 / Culex tritaeniorhynchus / 3 / DQ404069 / DQ404137
(2) / YNDL04-6 / 2004 / Culex pipiens quinquef ascitatus / 3 / DQ404070 / DQ404138
(3) / YNDL04-29 / 2004 / Culex theileri / 3 / DQ404071 / DQ404139
(4) / YNDL04-31 / 2004 / Culex theileri / 3 / DQ404072 / DQ404140
(5) / YNDL04-37 / 2004 / Anopheles sinensis / 3 / DQ404073 / DQ404141
(6) / YNDL04-39 / 2004 / Culex tritaeniorhynchus / 3 / DQ404074 / DQ404142
(7) / YNDL04-42 / 2004 / Armigeres subalbatus / 3 / DQ404075 / DQ404143
(8) / YNDL04-44 / 2004 / Culex theileri / 3 / DQ404076 / DQ404144
(9) / YNDL04-45 / 2004 / Mosquito pool / 3 / DQ404077 / DQ404145
(10) / YNJH04-18 / 2004 / Mosquito pool / 3 / DQ404078 / DQ404146
(11) / YNJH04-19 / 2004 / Unclassified Culex / 3 / DQ404079 / DQ404147
(12) / YNJH04-25-3 / 2004 / Culex / 3 / DQ404080 / DQ404148
(13) / YN-Xiang JE / IU / Human blood / 1 / DQ404067 / DQ404135
(14) / YN0528 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(15) / YN0553 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(16) / YN0555 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(17) / YN0572 / 2005 / Culex tritaeniorhynchus / 3 / UA / UA
(18) / YN0581 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(19) / YN0591 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(20) / YN05124 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(21) / YN05128 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(22) / YN05133 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(23) / YN05155 / 2005 / Culex tritaeniorhynchus / 1 / UA / UA
(24) / YN05194 / 2005 / Mosquito pool / 1 / UA / UA
(25) / YN0623 / 2006 / Culex tritaeniorhynchus / 1 / UA / UA
(26) / YN0686 / 2006 / Culex tritaeniorhynchus / 1 / UA / UA
(27) / M0633 / 2006 / Culex / 3 / UA / UA
(28) / M0672 / 2006 / Culex / 3 / UA / UA
(29) / YN114 / 2008 / Human cerebrospinal fluid, CSF / 1 / HM366550 / UA
(30) / YN135 / 2008 / Human cerebrospinal fluid, CSF / 1 / HM366549 / UA
(31) / LX10P-09 / 2009 / Human cerebrospinal fluid, CSF / 1 / GU371870 / HM204528
(32) / LX29P-09 / 2009 / Human cerebrospinal fluid, CSF / 1 / GU371871, / HM204529
(b) / Guangxi province, China / six strains
(1) / GX0519 / 2005 / Culex tritaeniorhynchus* / 1 / UA / FJ161967
(2) / GX0523 / 2005 / Culex tritaeniorhynchus* / 1 / UA / FJ161968
(3) / GX0558 / 2005 / Culex tritaeniorhynchus* / 1 / UA / FJ161969
(4) / BL50 / 2006 / Armigeres obturbans* / 1 / UA / UA
(5) / BL53 / 2006 / Armigeres obturbans* / 1 / UA / UA
(6) / BL54 / 2006 / Armigeres obturbans* / 1 / UA / UA
(c) / Guizhou province, China / nine strains
(1) / GZ04-2 / 2004 / Armigeres / 3 / DQ404042 / DQ404109
(2) / GZ04-4 / 2004 / Armigeres / 3 / DQ404043 / DQ404110
(3) / GZ04-29 / 2004 / Culex / 3 / DQ404044 / DQ404111
(4) / GZ04-36 / 2004 / Culex / 3 / DQ404045 / DQ404112
(5) / GZ04-43 / 2004 / Culex / 3 / DQ404046 / DQ404113
(6) / GZ04-71 / 2004 / Armigeres / 3 / DQ404047 / DQ404114
(7) / GZ04-89 / 2004 / Armigeres / 3 / DQ404048 / DQ404115
(8) / GZ56 / 2006 / Human cerebrospinal fluid, CSF / 1 / HM366552† / HM366552†
(9) / GZ1 / 2006 / Human cerebrospinal fluid, CSF / 1 / HM366551 / UA
(d) / Jiangxi province, China / one strain
(1) / JX0939 / 2009 / Culex tritaeniorhynchus / 1 / UA / UA
(e) / Fujian province, China / 22 strains
(1) / 02-41 / 2002 / Human blood / 3 / AY555752 / AY555763
(2) / 02-43 / 2002 / Human blood / 3 / AY555753 / AY555764
(3) / 02-102 / 2002 / Human blood / 3 / AY555756 / AY555767
(4) / 02-76 / 2002 / Human blood / 3 / AY555754 / AY555765
(5) / 02-84 / 2002 / Human blood / 3 / AY555755 / AY555766
(6) / FJ03-31 / 2003 / Human blood / 3 / DQ404049 / DQ404117
(7) / FJ03-35 / 2003 / Human blood / 3 / DQ404050 / DQ404118
(8) / 02-29 / 2002 / Human cerebrospinal fluid / 3 / AY555751 / AY555762
(9) / FJ03-39 / 2003 / Human blood / 3 / DQ404051 / DQ404119
(10) / FJ03-46 / 2003 / Human blood / 3 / DQ404052 / DQ404120
(11) / FJ03-56 / 2003 / Human blood / 3 / DQ404053 / DQ404121
(12) / FJ03-66 / 2003 / Human blood / 3 / DQ404054 / DQ404122
(13) / FJ03-67 / 2003 / Human blood / 3 / DQ404055 / DQ404123
(14) / FJ03-68 / 2003 / Human blood / 3 / DQ404056 / DQ404124
(15) / FJ03-69 / 2003 / Human blood / 3 / DQ404057 / DQ404125
(16) / FJ03-94 / 2003 / Human blood / 3 / DQ404058 / DQ404126
(17) / FJ03-97 / 2003 / Human blood / 3 / DQ404059 / DQ404127
(18) / FJ05-62 / 2005 / Human serum / 3 / UA / GQ856660
(19) / FJ05-139 / 2005 / Human cerebrospinal fluid / 3 / UA / GQ856661
(20) / FJ07-51 / 2007 / Human serum / 3 / UA / GQ856662
(21) / FJ08-48 / 2008 / Human serum / 3 / UA / GQ856663
(22) / FJ08-65 / 2008 / Human cerebrospinal fluid / 3 / UA / GQ856664
(f) / Zhejiang province, China / five strains
(1) / XJ69 / 2007 / Culex pipiens pallens* / 1 / EU258742‡ / EU258742‡
(2) / XJP613 / 2007 / Culex tritaeniorhynchus* / 1 / EU258741‡ / EU258741‡
(3) / L5 / 2007 / Culex tritaeniorhynchus* / 1 / UA / UA
(4) / Ningbo27 / 2007 / Culex tritaeniorhynchus / 1 / UA / UA
(5) / Ningbo30 / 2007 / Culex tritaeniorhynchus / 1 / UA / UA
(g) / Shanghai, China / 22 strains
(1) / SH-53 / 2001 / Culex tritaeniorhynchus* / 1 / AY555746 / AY555757
(2) / SH-80 / 2001 / Culex tritaeniorhynchus* / 1 / AY243823 / AY243841
(3) / SH-81 / 2001 / Culex tritaeniorhynchus* / 1 / AY555747 / AY555758
(4) / SH-83 / 2001 / Culex tritaeniorhynchus* / 1 / AY555748 / AY555759
(5) / SH-90 / 2001 / Culex tritaeniorhynchus* / 1 / AY243822 / AY243835
(6) / SH-96 / 2001 / Culex tritaeniorhynchus* / 1 / AY555749 / AY555760
(7) / SH-101 / 2001 / Culex tritaeniorhynchus* / 1 / AY555750 / AY555761
(8) / SH03-115 / 2003 / Culex tritaeniorhynchus / 1 / DQ404032 / DQ404099
(9) / SH03-124 / 2003 / Culex tritaeniorhynchus / 1 / DQ404033 / DQ404100
(10) / SH03-127 / 2003 / Culex tritaeniorhynchus / 1 / DQ404034 / DQ404101
(11) / SH03-128 / 2003 / Culex tritaeniorhynchus / 1 / DQ404035 / DQ404102
(12) / SH03-129 / 2003 / Culex tritaeniorhynchus / 1 / DQ404036 / DQ404103
(13) / SH03-130 / 2003 / Culex tritaeniorhynchus / 1 / DQ404037 / DQ404104
(14) / SH03-103 / 2003 / Culex tritaeniorhynchus / 1 / DQ404029 / DQ404096
(15) / SH03-105 / 2003 / Culex tritaeniorhynchus / 1 / DQ404030 / DQ404097
(16) / SH03-109 / 2003 / Culex tritaeniorhynchus / 1 / DQ404031 / DQ404098
(17) / SH04-3 / 2004 / Culex tritaeniorhynchus / 3 / DQ404038 / DQ404105
(18) / SH04-5 / 2004 / Culex tritaeniorhynchus / 3 / DQ404039 / DQ404106
(19) / SH04-10 / 2004 / Culex tritaeniorhynchus / 3 / DQ404040 / DQ404107
(20) / SH05-24 / 2005 / Culex tritaeniorhynchus / 1 / DQ404041 / DQ404108
(21) / SH0601 / 2006 / Swine / 3 / EF543861† / EF543861†
(22) / SH17M-07 / 2007 / Culex tritaeniorhynchus / 1 / EU429297† / EU429297†
(h) / Hubei province, China / two strains
(1) / HBZG08-09 / 2008 / Mosquito pool / 1 / UA / UA
(2) / HBZG08-55 / 2008 / Mosquito pool / 1 / UA / UA
(i) / Sichuan province, China / six strains
(1) / SC04-12 / 2004 / Culex / 1 / DQ404023 / DQ404090
(2) / SC04-15 / 2004 / Culex tritaeniorhynchus / 1 / DQ404024 / DQ404091
(3) / SC04-16 / 2004 / Armigeres / 1 / DQ404025 / DQ404092
(4) / SC04-17 / 2004 / Culex tritaeniorhynchus / 1 / DQ404026 / DQ404093
(5) / SC04-25 / 2004 / Culex / 1 / DQ404027 / DQ404094
(6) / SC04-27 / 2004 / Culex / 1 / DQ404028 / DQ404095
(j) / Gansu province, China / six strains
(1) / GS105 / 2006 / Human cerebrospinal fluid, CSF / 1 / HM366548 / UA
(2) / GSBY0801 / 2008 / Mosquito pool / 1 / UA / UA
(3) / GSBY0810 / 2008 / Mosquito pool / 1 / UA / UA
(4) / GSBY0804 / 2008 / Mosquito pool / 1 / UA / UA
(5) / GSBY0816 / 2008 / Mosquito pool / 1 / UA / UA
(6) / GSBY0827 / 2008 / Mosquito pool / 1 / UA / UA
(7) / GSBY0861 / 2008 / Mosquito pool / 1 / UA / UA