SG Information

Table 1 - Confirmed HCV genotypes/subtypes (June 2017)

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  unpublished 2001)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)

 

 

Genotype 2                                                    

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

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

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             (Newman et al., 2013)(Lu 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                 (Tokita et al., 1996) (Lu et al., 2013)

 

Genotype 4

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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      (Chamberlain et al., 1997b) (Bukh et al., 1998)

                                      

Genotype 6  

6a                    EUHK2, 6a33                          Y12083, AY859526                (Adams et al., 1997), (Zhou et al., 2010)

6b                    Th580                                      D84262                                   (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., 2006)(Lu et al., 2007b)

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., 2009a)

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

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           (Lu et al., 2006)(Lee et al., 2010)

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

6xb                  TV476, VN110                       JX183552, KJ567645             (Wang et al., 2013)

6xc                  TV520                                     KJ567651                               (Wang et al., 2013)

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

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

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

 

Genotype 7

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

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

 

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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