|
|
Molecular Epidemiology of
Human Enterovirus 71 Strains and Recent Outbreaks in the Asia-Pacific
Region: Comparative Analysis of the VP1 and VP4 Genes
Mary Jane Cardosa,* David Perera,* Betty A. Brown,† Doosung Cheon,‡
Hung Ming Chan,* Kwai Peng Chan,§ Haewol Cho,‡ and Peter McMinn¶
*Universiti Malaysia Sarawak, Sarawak, Malaysia; †Centers for Disease
Control and Prevention, Atlanta, Georgia, USA; ‡National Institute of
Health, Seoul, Korea; §Singapore General Hospital, Singapore; and ¶Telethon
Institute for Child Health Research, Perth, Western Australia, Australia
Appendix
| Appendix Table
1. Human enterovirus 71 (HEV71) strains sequenced for this study |
|
|
|
|
Genogroup based on
|
|
| Identity (strain/origina/yr) |
Accession no.b
|
VP1
|
VP4
|
Clinical syndromec
|
|
|
2228-NY72/USA/72
|
AY123949
|
B1
|
B outlier
|
NA
|
|
2229-NY76/USA/76
|
AY123950
|
B1
|
B1
|
NA
|
|
2230-NY76/USA/76
|
AY123951
|
B1
|
B1
|
NA
|
|
2231-NY77/USA/77
|
AY123952
|
B1
|
B1
|
NA
|
|
2235-NY77/USA/77
|
AY123953
|
B1
|
B1
|
NA
|
|
10181-NM78/USA/78
|
AY123944
|
B1
|
B1
|
NA
|
|
1011-ND79/USA/79
|
AY123943
|
B1
|
B1
|
NA
|
|
6910-OK87/USA/87
|
AY123954
|
B1
|
B outlier
|
Rash
|
|
1413-CA87/USA/87
|
AY123945
|
B2
|
B2
|
Paralysis
|
|
7633-PA87/USA/87
|
AY123955
|
B2
|
B2
|
Gastroenteritis
|
|
7673-CT87/USA/87
|
AY123956
|
B2
|
B2
|
NA
|
|
8102-WA87/USA/87
|
AY123957
|
B2
|
B2
|
Meningitis
|
|
MY104-9/SAR/97
|
AY125997
|
B3
|
B3
|
Acute cardiogenic shock, fatal
|
|
MY821-3/SAR/97
|
AY125995
|
B3
|
B3
|
Meningitis
|
|
MY860-3/SAR/97
|
AY125996
|
B3
|
B3
|
HFMD
|
|
3526/SIN/98
|
AY125984
|
B3
|
B3
|
Encephalitis
|
|
3799/SIN/98
|
AY125985
|
B3
|
B3
|
HFMD
|
|
4915/SIN/99
|
AY125987
|
B3
|
B3
|
Meningitis
|
|
4F/AUS/4/99
|
AY126008
|
B3
|
B3
|
Guillain-Barré syndrome
|
|
10M/AUS/6/99
|
AY126007
|
B3
|
B3
|
HFMD
|
|
SB1647/SAR/00
|
AY126004
|
B4
|
B4
|
Meningitis
|
|
SB2864/SAR/00
|
AY126006
|
B4
|
B4
|
Poliomyelitis-like paralysis
|
|
CN0942/SAR/00
|
AY126001
|
B4
|
B4
|
HFMD
|
|
CN9502/SAR/00
|
AY126002
|
B4
|
B4
|
HFMD
|
|
S21082/SAR/00
|
AY126005
|
B4
|
B4
|
HFMD
|
|
5511/SIN/00
|
AY125988
|
B4
|
B4
|
HFMD
|
|
5536/SIN/00
|
AY125991
|
B4
|
B4
|
HFMD
|
|
5769/SIN/00
|
AY125992
|
B4
|
B4
|
Encephalitis
|
|
2027/SIN/01
|
AY125993
|
B4
|
B4
|
Encephalitis, fatal
|
|
2267/SIN/01
|
AY125994
|
B4
|
B4
|
Febrile illness
|
|
0915-MA87/USA/87
|
AY123942
|
C1
|
C1
|
Meningitis
|
|
1873-CT94/USA/94
|
AY123946
|
C1
|
C1
|
Fatality
|
|
1919-NM94/USA/94
|
AY123947
|
C1
|
C1
|
Rash
|
|
2037-MD95/USA/95
|
AY123948
|
C1
|
C1
|
NA
|
|
4575/SIN/98
|
AY125986
|
C1
|
C1
|
HFMD
|
|
S10822/SAR/98
|
AY125998
|
C1
|
C1
|
HFMD
|
|
S10862/SAR/98
|
AY125999
|
C1
|
C1
|
HFMD
|
|
S11051/SAR/98
|
AY126000
|
C1
|
C1
|
HFMD
|
|
S40221/SAR/00
|
AY126003
|
C1
|
C1
|
HFMD
|
|
S18191/SAR/02
|
AY189153, AY189154 (VP1)
|
C1
|
C1
|
HFMD
|
|
1M/AUS/12/00
|
AY126014
|
C1
|
C1
|
HFMD
|
|
5M/AUS/5/99
|
AY126009
|
C2
|
C2
|
Meningitis
|
|
8M/AUS/6/99
|
AY126012
|
C2
|
C2
|
Myelitis
|
|
9F/AUS/6/99
|
AY126013
|
C2
|
C2
|
Cerebellar ataxia
|
|
7F/AUS/6/99
|
AY126010
|
C2
|
C2
|
Meningitis
|
|
14F/AUS/9/99
|
AY126011
|
C2
|
C2
|
Benign intracranial hypertension
|
|
KOR-EV71-01/KOR/00
|
|
C3
|
C3
|
HFMD
|
|
KOR-EV71-03/KOR/00
|
AY125968 (VP1), AF525221
|
C3
|
C3
|
HFMD
|
|
KOR-EV71-06/KOR/00
|
AY125970 (VP1), AF525222
|
C3
|
C3
|
Aseptic meningitis
|
|
KOR-EV71-10/KOR/00
|
AY125974 (VP1), AF525223
|
C3
|
C3
|
HFMD/Herpangina
|
|
KOR-EV71-13/KOR/00
|
AY125976 (VP1), AF525224
|
C3
|
C3
|
Paralysis
|
|
KOR-EV71-02/KOR/00
|
AY125967 (VP1)
|
C3
|
-
|
HFMD
|
|
KOR-EV71-05/KOR/00
|
AY125969 (VP1)
|
C3
|
-
|
Aseptic meningitis
|
|
KOR-EV71-07/KOR/00
|
AY125971 (VP1)
|
C3
|
-
|
Aseptic meningitis
|
|
KOR-EV71-08/KOR/00
|
AY125972 (VP1)
|
C3
|
-
|
Aseptic meningitis
|
|
KOR-EV71-09/KOR/00
|
AY125973 (VP1)
|
C3
|
-
|
HFMD/Herpangina
|
|
KOR-EV71-11/KOR/00
|
AY125975 (VP1)
|
C3
|
-
|
HFMD/Herpangina
|
|
aPlace of origin
is abbreviated as follows: AUS, Australia; KOR, Korea; SAR, Sarawak,
Malaysian Borneo; SIN, Singapore; USA, United States of America.
bUnless otherwise indicated, accession number refers to
a VP4 sequence.
cNA, not available; HFMD, hand, foot and mouth disease. |
| Appendix Table
2. Human enterovirus 71 (HEV71) sequences obtained from GenBank |
|
|
Identity strain(origina/yr)b
|
Accession no.
|
Gene(s) used in analysis
|
|
|
CA16-G10(SAF/51)
|
NC001612
|
VP4
|
|
BrCr-CA-70(USA/70)
|
U22521
|
VP1 and VP4
|
|
MS/7423/87(USA/87)
|
U22522
|
VP4
|
|
SHZH98(CHN/98)
|
AF302996
|
VP4
|
|
Nagoya(JPN/73)
|
AB051301
|
VP4
|
|
258(BGR/75)
|
AB051302
|
VP1 and VP4
|
|
Hungary(HGR/78)
|
AB051303
|
VP1 and VP4
|
|
Yamanashi(JPN/78)
|
AB051305
|
VP4
|
|
Taiwan 80(TWN/80)
|
AB051304
|
VP4
|
|
V-14375(JPN/97)
|
AB051319
|
VP4
|
|
V-14389(JPN/97)
|
AB051320
|
VP4
|
|
V-14405(JPN/97)
|
AB051321
|
VP4
|
|
V-14433(JPN/97)
|
AB051322
|
VP4
|
|
V-14429(JPN/97)
|
AB051323
|
VP4
|
|
V-14570(JPN/97)
|
AB051324
|
VP4
|
|
V-14600(JPN/97)
|
AB051325
|
VP4
|
|
V-14653(JPN/97)
|
AB051326
|
VP4
|
|
V-14707(JPN/97)
|
AB051327
|
VP4
|
|
C7/Osaka(JPN/97)
|
AB051328
|
VP4
|
|
V-14457(JPN/97)
|
AB051329
|
VP4
|
|
SK-EV006(SAR/97)
|
AB051331
|
VP4
|
|
SK026(MAL/97)
|
AB051332
|
VP4
|
|
SK036(MAL/97)
|
AB051333
|
VP4
|
|
KED005(MAL/97)
|
AB051334
|
VP4
|
|
KED60(MAL/97)
|
AB051335
|
VP4
|
|
1334(TWN/98)
|
AB051306
|
VP4
|
|
1457(TWN/98)
|
AB051307
|
VP4
|
|
1524(TWN/98)
|
AB051308
|
VP4
|
|
981394(TWN/98)
|
AB051309
|
VP4
|
|
981186(TWN/98)
|
AB051310
|
VP4
|
|
981334(TWN/98)
|
AB051311
|
VP4
|
|
981435(TWN/98)
|
AB051312
|
VP4
|
|
E1387(TWN/98)
|
AB051313
|
VP4
|
|
E1558(TWN/98)
|
AB051314
|
VP4
|
|
J1263P4(TWN/98)
|
AB051315
|
VP4
|
|
J1166P4(TWN/98)
|
AB051316
|
VP4
|
|
E1354(TWN/98)
|
AB051317
|
VP4
|
|
E1360(TWN/98)
|
AB051318
|
VP4
|
|
TW/2272/98(TWN/98)
|
AF119795
|
VP4
|
|
TW/2086/98(TWN/98)
|
AF119796
|
VP4
|
|
240/86(TWN/86)
|
AB037267
|
VP4
|
|
244/86(TWN/86)
|
AB037268
|
VP4
|
|
5033/98(TWN/98)
|
AB037250
|
VP4
|
|
5142/98(TWN/98)
|
AB037251
|
VP4
|
|
H0106/98(TWN/98)
|
AB037252
|
VP4
|
|
1657/98(TWN/98)
|
AB037253
|
VP4
|
|
1658/98(TWN/98)
|
AB037254
|
VP4
|
|
1569/98(TWN/98)
|
AB037255
|
VP4
|
|
1499/98(TWN/98)
|
AB037256
|
VP4
|
|
480/98(TWN/98)
|
AB037257
|
VP4
|
|
874/98(TWN/98)
|
AB037258
|
VP4
|
|
737/98(TWN/98)
|
AB037259
|
VP4
|
|
607/98(TWN/98)
|
AB037260
|
VP4
|
|
602/98(TWN/98)
|
AB037261
|
VP4
|
|
588/98(TWN/98)
|
AB037262
|
VP4
|
|
1226/98(TWN/98)
|
AB037263
|
VP4
|
|
1288/98(TWN/98)
|
AB037264
|
VP4
|
|
693/98(TWN/98)
|
AB037266
|
VP4
|
|
5929/98(TWN/98)
|
AB046739
|
VP4
|
|
7008/98(TWN/98)
|
AB046740
|
VP4
|
|
1245a/98/tw(TWN/98)
|
AF176044
|
VP4
|
|
Tainan/5746/98(TWN/98)
|
AF304457
|
VP4
|
|
Tainan/4643/98(TWN/98)
|
AF304458
|
VP4
|
|
Tainan/6092/98(TWN/98)
|
AF304459
|
VP4
|
|
NCKU9822(TWN/98)
|
AF136379
|
VP4
|
|
ZS6844/96(UK/96)
|
AJ300756
|
VP4
|
|
JM8336/97(UK/97)
|
AJ300761
|
VP4
|
|
JH17760/98(UK/98)
|
AJ300760
|
VP4
|
|
MT17728/98(UK/98)
|
AJ300764
|
VP4
|
|
LH7415/99(UK/99)
|
AJ300753
|
VP4
|
|
JK815/99(UK/99)
|
AJ300754
|
VP4
|
|
WM10620/99(UK/99)
|
AJ300755
|
VP4
|
|
CS9410/99(UK/99)
|
AJ300758
|
VP4
|
|
FW10756/99(UK/99)
|
AJ300759
|
VP4
|
|
MC11418/99(UK/99)
|
AJ300762
|
VP4
|
|
MC9178/99(UK/99)
|
AJ300763
|
VP4
|
|
LT449/00(UK/00)
|
AJ300757
|
VP4
|
|
5865/sin/000009(SIN/00)
|
AF316321
|
VP4
|
|
5666/sin/002209(SIN/00)
|
AF352027
|
VP4
|
|
S0309-TW-00(TWN/00)
|
AY055176
|
VP1
|
|
M0267-TW-00(TWN/00)
|
AY055184
|
VP1
|
|
M0225-TW-00(TWN/00)
|
AY055190
|
VP1
|
|
N1034-TW-00(TWN/00)
|
AY044181
|
VP1
|
|
N7008-TW-99(TWN/99)
|
AY055201
|
VP1
|
|
N5101-TW-98(TWN/98)
|
AY055174
|
VP1
|
|
N5202-TW-98(TWN/98)
|
AY055200
|
VP1
|
|
N4643-TW-98(TWN/98)
|
AY055194
|
VP1
|
|
H0139-TWN-98(TWN/98)
|
AY055193
|
VP1
|
|
7673-CT-87(USA/87)
|
AF009535
|
VP1
|
|
MY104-9/SAR/97
|
AF376072
|
VP1
|
|
MY821-3/SAR/97
|
AF376077
|
VP1
|
|
3799/SIN/98
|
AF376117
|
VP1
|
|
4F/AUS/4/99
|
AF376105
|
VP1
|
|
SB2864/SAR/00
|
AF376066
|
VP1
|
|
5511/SIN/00
|
AF376121
|
VP1
|
|
2027/SIN/01
|
AF376111
|
VP1
|
|
4575/SIN/98
|
AF376120
|
VP1
|
|
S10822/SAR/98
|
AF376079
|
VP1
|
|
S11051/SAR/98
|
AF376081
|
VP1
|
|
1M/AUS/12/00
|
AF376098
|
VP1
|
|
14F/AUS/9/99
|
AF376091
|
VP1
|
|
TW/2086/98(TWN/98)
|
AF119796
|
VP1
|
|
CN04104/SAR/00
|
AF376067
|
VP1
|
|
26M/AUS/2/99
|
AF376101
|
VP1
|
|
18/Sin/97(SIN/97)
|
AF251359
|
VP1
|
|
4350/SIN/98
|
AF376119
|
VP1
|
|
2289-MAA-97(SAR/97)
|
AF135914
|
VP1
|
|
2222-IA-88(USA/88)
|
AF009540
|
VP1
|
|
2258-CA-79(USA/79)
|
AF135880
|
VP1
|
|
2609-AUS-74(AUS/74)
|
AF135886
|
VP1
|
|
TW/1465/98(TWN/98)
|
AF116814
|
VP1
|
|
2641-AUS-95(AUS/95)
|
AF135947
|
VP1
|
|
2286-TX-97(USA/97)
|
AF135941
|
VP1
|
|
27M/AUS/2/99
|
AF376102
|
VP1
|
|
6F/AUS/6/99
|
AF376107
|
VP1
|
|
2M/AUS/3/99
|
AF376103
|
VP1
|
|
7238-AK-87(USA/87)
|
AF135952
|
VP1
|
|
2623-AUS-86(AUS/86)
|
AF135945
|
VP1
|
|
0756-MAA-97(MAL/97)
|
AF135935
|
VP1
|
|
aPlace of origin
is abbreviated as follows: AUS, Australia; BGR, Bulgaria; CHN, China;
HGR, Hungary; JPN, Japan; KOR, Korea; MAL, Peninsular Malaysia; SAF,
South Africa; SAR, Sarawak, Malaysian Borneo; SIN, Singapore; TWN,
Taiwan; U.K., United Kingdom; USA, United States of America.
bAll sequences retrieved from GenBank are referred to by
the strain name recorded in the GenBank record followed by place of
origin and year of isolation in brackets. Strains sequenced during
this collaborative project have been deposited with the information
on origin and year already included in the strain name following the
same nomenclature as in Appendix Table 1. |
|
