SG Information

Table 1 - Confirmed HCV genotypes/subtypes (May 2019)

CONFIRMED HCV GENOTYPES/SUBTYPES

 

Genotype1       Locus/Isolate(s)2                      Accession number(s)               Reference(s)

Genotype 1

1a                    HPCPLYPRE, HPCCGAA       M62321, M67463                     (Choo et al., 1991; Inchauspe et al., 1991)

1b                    HPCJCG, HPCHUMR              D90208, M58335                     (Kato et al., 1990; Takamizawa et al., 1991)

1c                    HPCCGS, AY051292               D14853, AY051292                 (Okamoto et al., 1994)(Guntaka et al.  unpublished 2001)

1d                    QC103                                     KJ439768                                (Lu et al., 2014)

1e                    148636, QC172                        KC248194, KJ439769               (Li et al., 2013), (Lu et al., 2014)

1g                    1804, QC78                             AM910652, KJ439770              (Bracho et al., 2008) (Lu et al., 2014)

1h                    EBW443, EBW9                      KC248198, KC248199             (Li et al., 2013)

1i                     QC181                                     KJ439772                                (Lu et al., 2014)

1j                     QC329                                     KJ439773                                 (Lu et al., 2014)

1k                    QC82                                       KJ439774                                 (Lu et al., 2014)

1l                     136142, EBW424                     KC248193, KC248197             (Li et al., 2013)

1m                   QC196, QC87                          KJ439778, KJ439782               (Lu et al., 2014)

1n                    QC113, QC74                          KJ439775, KJ439781               (Lu et al., 2014)

1o                    QC316, DE/17-0414                 KJ439779, MH885469              (Lu et al., 2014; Wang et al., 2019)

Genotype 2                                                     

2a                    HPCPOLP, JFH-1                     D00944, AB047639                  (Kato et al., 2001; Okamoto et al., 1991)

2b                    HPCJ8G, JPUT971017             D10988, AB030907                  (Murakami et al., 2001; Okamoto et al., 1992)

2c                    BEBE1                                     D50409                                    (Nakao et al., 1996)

2d                    QC259                                     JF735114                                 (Li et al., 2012)

2e                     QC64                                       JF735120                                 (Li et al., 2012)

2f                     ZS542, GZ98799                      KC844042, KC844050             (Xu et al., 2013)          

2i                     D54                                         DQ155561                               (Noppornpanth et al., 2006)

2j                     C1799, QC232                         HM777358 JF735113               (Sulbarán et al., 2010) (Li et al., 2012)

2k                    VAT96                                    AB031663                               (Samokhvalov et al., 2000)

2l                     MRS89, PTR7904                    KC197235, KC197240             (Jordier et al., 2013)    

2m                   QC178, BID-G1314                 JF735111, JX227967                (Li et al., 2012; Newman et al., 2013)

2q                    963, 852                                   FN666428, FN666429              (Martró et al., 2011)

2r                     QC283                                     JF735115                                 (Li et al., 2012)

2t                     MRS40                                   KC197238                               (Jordier et al., 2013)

2u                    QC182                                     JF735112                                 (Li et al., 2012)

Genotype 3

3a                    HPCEGS, HPCK3A                 D17763, D28917                      (Sakamoto et al., 1994; Yamada et al., 1994)

3b                    HPCFG                                    D49374                                    (Chayama et al., 1994)

3d                    NE274                                     KJ470619                                (Li et al., 2014a)  

3e                    NE145                                     KJ470618                                (Li et al., 2014a)

3g                    BID-G1243, QC260                 JX227954, JF735123                (Lu et al., 2013; Newman et al., 2013)

3h                    QC29                                       JF735121                                 (Lu et al., 2013)

3i                     IND-HCV, BID-G1244             FJ407092, JX227955                (Arankalle & Gupte 2008 unpublished)(Newman et al., 2013)

3k                    HPCJK049E1, QC105              D63821, JF735122                   (Lu et al., 2013; Tokita et al., 1996)

Genotype 4

4a                    ED43                                       Y11604                                    (Chamberlain et al., 1997a)

4b                    QC264                                     FJ462435                                 (Li et al., 2009a)          

4c                    QC381                                     FJ462436                                 (Li et al., 2009a)          

4d                    03-18, QC382                          DQ418786, FJ462437               (Timm et al., 2007) (Li et al., 2009a)           

4f                     IFBT88, PS6                            EF589161, EU392175              (Hmaied et al., 2007) (Kuntzen et al., 2008) 

4g                     QC193                                     FJ462432                                 (Li et al., 2009a)          

4k                    PS3, QC383                             EU392173, FJ462438               (Kuntzen et al., 2008) (Li et al., 2009a)

4l                     QC274                                     FJ839870                                 (Li et al., 2009a)          

4m                   QC249                                     FJ462433                                 (Li et al., 2009a)          

4n                    QC97                                       FJ462441                                 (Li et al., 2009a)          

4o                    QC93                                       FJ462440                                 (Li et al., 2009a)          

4p                    QC139                                     FJ462431                                 (Li et al., 2009a)          

4q                    QC262                                     FJ462434                                 (Li et al., 2009a)          

4r                     QC384                                     FJ462439                                 (Li et al., 2009a)          

4s                     QC361                                     JF735136                                 (Lu et al., 2015)

4t                     QC155                                     FJ839869                                 (Li et al., 2009a)          

4v                    CYHCV073, BID-G1248          HQ537009, JX227959              (Demetriou & Kostrikis, 2011)  (Newman et al., 2013)

4w3                  P212, P245                              FJ025855, FJ025856                 (Koletzki et al., 2009)

Genotype 5                                                     

5a                    EUH1480, SA134                     Y13184 ,AF064490                   (Bukh et al., 1998; Chamberlain et al., 1997b)

Genotype 6  

6a                    EUHK2, 6a33                          Y12083, AY859526                 (Tokita et al., 1998)

6c                    Th846                                      EF424629                                 (Lu et al., 2007a)

6d                    VN235                                     D84263                                    (Tokita et al., 1998)

6e                    GX004                                     DQ314805                               (Li et al., 2006)

6f                     C-0044                                    DQ835760                               (Lu et al., 2007b)

6g                    HPCJK046E2                           D63822                                    (Tokita et al., 1996)

6h                    VN004                                     D84265                                    (Tokita et al., 1998)

6i                     Th602                                      DQ835770                               (Lu et al., 2007b)

6j                     Th553                                      DQ835769                               (Lu et al., 2007b)

6k                     VN405                                     D84264                                    (Tokita et al., 1998)

6l                     537796                                    EF424628                                (Lu et al., 2007a)

6m                   B4/92                                       DQ835767                               (Lu et al., 2007b)

6n                    KM42, D86/93                         DQ278894, DQ835768             (Lu et al., 2007b; Lu et al., 2006)

6o                    QC227                                     EF424627                                (Lu et al., 2007a)

6p                     QC216                                     EF424626                                (Lu et al., 2007a)

6q                    QC99                                       EF424625                                (Lu et al., 2007a)

6r                     QC245                                     EU408328                               (Li et al., 2009b)

6s                     QC66                                       EU408329                               (Li et al., 2009b)

6t                     VT21, D49                               EF632071, EU246939              (Lu et al., 2008; Noppornpanth et al., 2008)

6u                    D83                                         EU246940                               (Noppornpanth et al., 2008)

6v                    NK46, KMN-02                       EU158186, EU798760              (Lu et al., 2008) (Wang et al., 2009)

6w                   GZ52557, D140                       DQ278892, EU643834             (Lee et al., 2010; Lu et al., 2006)

6xa5                 DH012, DH028                        EU408330, EU408332              (Xia et al., 2008)

6xb                  TV476, VN110                        JX183552, KJ567645               (Li et al., 2014b; Wang et al., 2013)

6xc                  TV520                                     KJ567651                                 (Li et al., 2014b)

6xd                  L23, L347                                KM252789, KM252790 (Li et al., 2015)

6xe                  DH027, KM98                         JX183557, KM252792              (Li et al., 2015; Wang et al., 2013)

6xf                   VN214, TV469                        KJ567647, KJ567646               (Li et al., 2014b)

6xg                  KS27, KS81                             MH492360, MH492361            (Ye et al., 2019)

6xh                  1350-1                                     MG879000                              (Wu et al., 2018)

Genotype 7

7a                    QC69                                       EF108306                                 (Murphy et al., 2015)

7b                    BAK1                                      KX092342                                (Salmona et al., 2016)

Genotype 8

8a                    GT8-1                                      MH590698                              (Borgia et al., 2018)

 

An alignment of representatives of these genotypes / subtypes is available at http://hcv.lanl.gov/content/sequence/NEWALIGN/align.html

1 Consensus proposed genotype/subtype names. Where multiple sequences of a HCV genotype are available, two sequences have been listed, prioritised by (a) publication date or (b) submission date when unpublished.

2 Locus (or isolate name if locus is the same as the accession number).

3 Previously described as 4b, (Koletzki et al., 2009; Nakano et al., 2012)

4 Sequence obtained from acute phase plasma of a chimpanzee experimentally infected with (human-derived) isolate SA13.

5 Previously described as 6u (Xia et al., 2008).

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