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Table 3. Provisionally Assigned HCV Subtypes (Simmonds P, et al., 2005)


List of
and list of used for subtyping

Isolate** Accession Number(s)*
Reference(s)
Core/E1 NS5B

Genotype 1
   1d HC1-N15,
HC1-N16
L39299,
L39302
L38377,
L38378 ++
Van Doorn LJ, et al.(1995) + ,
Stuyver L, et al.(1995)
   1e CAM1078,
QC248
L38349(C),
AY894555
L38361,
AY894553
Stuyver L, et al.(1995) ,
Murphy D, et al.(2003)
   1f FR2 L38350 L38371 Stuyver L, et al.(1995)
   1g 2152,
1382
AF271822,
AF271820
AF271798,
AF271797
Ray SC, et al.(2000)
   1h 98CM1521,
QC94
AY256790(C),
AY434131
AY257087,
AY434132
Ndjomou J, et al.(2003) ,
Murphy D, et al.(2003)
   1i FR16,
QC77
n.a.,
AY434119
L48495,
AY434120
Murphy D, et al.(2003) ,
Stuyver L, et al.(1996)
   1j QC2,
QC89
AY434158,
AY434128
AY434106,
AY434129
Murphy D, et al.(2003)
   1k QC68,
QC82
AY434112,
AY434122
AY434113,
AY434123
Murphy D, et al.(2003)
   1l 98CM1383,
98CM1427
AY256789(C),
AY256792(C)
AY257083,
AY257091
Ndjomou J, et al.(2003)
Genotype 2
   2d NE92,
BN177
L39294,
n.a.
L29634,
AF037244
Van Doorn LJ, et al.(1995) ,
Stuyver L, et al.(1994) ,
Jeannel D, et al.(1998) +
   2e JK020,
JK025
D49745,
D49746
D49760,
D49761
Tokita H, et al.(1996)
   2f JK081,
JK139
D49754,
D49757
D49769,
D49777
Tokita H, et al.(1996)
   2g MED017 n.a. X93323 Ruggieri A, et al.(1996)
   2h MED007 n.a. X93327 Ruggieri A, et al.(1996)
   2i FR13,
HN4
n.a.,
X76411/ X76415
L48492,
L48499
Qu D, et al.(1994) ,
Stuyver L, et al.(1996)
   2j BA047,
QC106
n.a.,
AY894528
D86530,
AY894526
Murphy D, et al.(2003) ,
Tokita H, et al.(1998)
   2l FR15 n.a. L48494 Stuyver L, et al.(1996) ,
Giannini C, et al.(1995)
   2m QC76,
QC104
AY434116
AY434143
AY434117,
AY434144
Murphy D, et al.(2003)
   2n NL50 L39309 L44602 Van Doorn LJ, et al.(1995) + ,
Stuyver L, et al.(1995)
   2o FR4 L38333 L38373 Stuyver L, et al.(1995)
   2p NL33 L39300 L44601 Van Doorn LJ, et al.(1995) + ,
Stuyver L, et al.(1995)
   2q BA045 n.a. D86529 Tokita H, et al.(1998)
   2r QC101,
QC171,
QC241,
QC283
EF115810,
EF115818,
EF115829,
EF115836
EF116032,
EF116040,
EF116051,
EF116059
Murphy D, et al.(2007)
Genotype 3
   3c NE048 D16612 D14198/ D16613 Tokita H, et al.(1994)
   3d NE274 D16620 D14200/ D16621 Tokita H, et al.(1994)
   3e NE145 D16618 D16619 Tokita H, et al.(1994)
   3f NE125,
PK64
D16614,
n.a.
D14203/ D16615,
L78842
Tokita H, et al.(1994) ,
Stuyver L, et al.(1996)
   3g IND1751,
IND1452
X91423/ X91307,
X91306(C)
X91417,
X91418
Panigrahi AK, et al.(1996)
   3h QC29,
SOM1
U33437(C),
AF216792/ AF216786
AF279120,
AF216789
Bernier L, et al.(1996) ,
Abid K, et al.(2000)
   3i IND674,
QC100
X91300(C),
AY434137
X91422,
AY434138
Murphy D, et al.(2003) ,
Panigrahi AK, et al.(1996)
Genotype 4
   4b Z1 U10235/ L16677 n.a. Bukh J, et al.(1993) ,
Bukh J, et al.(1994)
   4c Z6,
GB358
U10238/ L16678,
L29606
n.a.,
L29607
Bukh J, et al.(1993) ,
Bukh J, et al.(1994) ,
Stuyver L, et al.(1994)
   4d DK13,
SD006
U10192/ L16656,
n.a.
n.a.,
D86537
Bukh J, et al.(1993) ,
Bukh J, et al.(1994) ,
Tokita H, et al.(1998)
   4e CAM600,
GB809
L29589,
L29629
L29590,
L29626
Stuyver L, et al.(1994)
   4f G22,
FR12
L29595,
L38332
L29593,
L38370
Stuyver L, et al.(1994) ,
Stuyver L, et al.(1995)
   4g GB549 L29620 L29621 Stuyver L, et al.(1994)
   4h GB438,
FrSSD35
L29610,
n.a.
L29611,
AJ291249
Stuyver L, et al.(1994) ,
Morice Y, et al.(2001)
   4i CAR4/1205 L36439 L36437 Fretz C, et al.(1995)
   4j CAR1/501 n.a. L36438 Fretz C, et al.(1995)
   4k B14,
FrSSD174
L39282,
n.a.
L44597,
AJ291294
Van Doorn LJ, et al.(1995) + ,
Stuyver L, et al.(1995) ,
Morice Y, et al.(2001)
   4l SD002,
2116
n.a.,
AF271881
D86534,
AF271816
Ray SC, et al.(2000) ,
Tokita H, et al.(1998)
   4m SD035,
1797
n.a.,
AF271876
D86543,
AF271813
Ray SC, et al.(2000) ,
Tokita H, et al.(1998)
   4n 1359,
QC97
AF271874,
AY434134
n.a.,
AY434135
Ray SC, et al.(2000) ,
Murphy D, et al.(2003)
   4o 2153,
QC59
AF271882,
AY434107
AF271815,
AY434108
Ray SC, et al.(2000) ,
Murphy D, et al.(2003)
   4p FrSSD158,
QC139
AJ401099(E),
AY434149
AJ291285,
AY434150
Morice Y, et al.(2001) ,
Murphy D, et al.(2003)
   4q QC86,
QC107
AY434125,
AY434146
AY434126,
AY434147
Murphy D, et al.(2003)
   4r Z4,
FrSSD120
U10236/ L16652,
AJ401097(E)
n.a.,
AJ291282
Bukh J, et al.(1993) ,
Bukh J, et al.(1994) ,
Morice Y, et al.(2001)
   4t 98CM1458,
QC85
AY256808(C),
AY706996
AY257072,
AY706997
Ndjomou J, et al.(2003) ,
Murphy D, et al.(2003)
   4u N.A. N.A. N.A. Valérie Thiers (France)
Genotype 6
   6c Th846 D37843 D37857 Tokita H, et al.(1995)
   6e VN540,
VN998
D88474,
D31971
D87361,
D30797
Tokita H, et al.(1994)
   6f Th271,
EUTH36
D37844,
U31261(C)
D37858,
U31276
Tokita H, et al.(1995) ,
Mellor J,, et al.(1995)
   6i Th555,
EUTH100
D37849,
L50554(C)
D37863,
L50535
Tokita H, et al.(1995) ,
Simmonds P, et al.(1996)
   6j Th553,
EUTH1
D37848,
L49473(C)
D37862,
L49481
Tokita H, et al.(1995),
Mellor J, et al.(1996)
   6l VN507,
VN531
D88470,
D88472
D87357,
D87359
Tokita H, et al.(1994)
   6m EUBUR1,
B4/92
L49480(C),
D63943/ D63944
L49484,
D28543
Mellor J, et al.(1996) ,
Doi H, et al.(1996) ,
Apichartpiyakul C, et al.(1994) +
   6n D86/93,
EUTH86
D63945,
U31259(C)
D28545,
U31275
Doi H, et al.(1996) + ,
Mellor J, et al.(1995) ,
Apichartpiyakul C, et al.(1994)
   6o VN4,
QC33
L38341,
AY894537
L38382,
AY894535
Stuyver L, et al.(1995) ,
Murphy D, et al.(2003)
   6p VN12,
QC123
L38340,
AY894534
L38380,
AY894532
Stuyver L, et al.(1995) ,
Murphy D, et al.(2003)
   6q QC57,
QC176
AY754632,
AY754617
AY754633,
AY754618
Murphy D, et al.(2003)
   6r QC117,
QC120,
QC174,
QC245,
QC247,
QC291,
QC295,
QC330
EF115710,
EF115711,
EF115720,
EF115730,
EF115731,
EF115741,
EF115743,
EF115756
EF116153,
EF116154,
EF116163,
EF116173,
EF116174,
EF116184,
EF116186,
EF116199
Murphy D, et al.(2007)
   6s QC66,
QC225,
QC292
AY434111,
EF115946,
EF115962
AY434110,
EF116169,
EF116185
Murphy D, et al.(2007)
   6t QC131,
QC145,
QC351
EF115932,
EF115934,
EF127993
EF116155,
EF116157,
EF127994
Murphy D, et al.(2007)
Lu L, et al.(2007)

  *  Accession numbers of sequences from the core/E1 and NS5B regions. Where two examples are listed,a comma divides the accession numbers from the two entries; "n.a.": not available; "/": denotes that the core/E1 or NS5B sequences are available from two different accession numbers; (C): only core sequence available; (E): only E1 sequence available.
  **  Listing of up to two examples of each provisionally assigned HCV subtype prioritized according to (1) availability of complete or near complete core/E1 and NS5B sequences, (2) publication date, (3) GenBank/EMBL/DDBJ submission date. Where possible, the isolate names referred to in associated publications (last column) are listed for ease of reference.
  + Added references.
  ++ Corrected accession number.
Subtypes in blue are new since publication of Simmmonds et al., Hepatology, 2005.