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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.

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