Table 2 - Unassigned complete coding region sequences (March 2022)


Genotype1         Locus/Isolate(s)2             Accession no(s)               Reference

Genotype 1

1_AJ851228                 AJ851228                     AJ851228                     (Bracho et al., 2006)

1_KC248195                160526                         KC248195                    (Li et al., 2013)

1_HQ537007                CYHCV025                  HQ537007                    (Demetriou & Kostrikis, 2011)

1_KJ439780                 QC60                           KJ439780                     (Lu et al., 2014)

1_KJ439776                 QC152                         KJ439776                     (Lu et al., 2014)

1_KJ439777                 QC180                         KJ439777                     (Lu et al., 2014)

1_KY348757                G1_bcn_new                KY348757                    (Ordeig et al., 2018)     

1_MH921830               G1                                MH921830                   (von Massow et al., 2019)


Genotype 2

2_JF735119                  QC331                         JF735119                      (Li et al., 2012)

2_JF735110                  QC114                         JF735110                      (Li et al., 2012)

2_JF735117                  QC297                         JF735117                      (Li et al., 2012)

2_JF735116                  QC289                         JF735116                      (Li et al., 2012)

2_JF735118                  QC302                         JF735118                      (Li et al., 2012)

2_KC197236                MRS41                         KC197236                    (Jordier et al., 2013)

2_KC197237                MRS117                       KC197237                    (Jordier et al., 2013)

2_KC197239                PTR9203                      KC197239                    (Jordier et al., 2013)

2_MW041294               116-04                          MW041294, MW041296            (Rajhi et al., 2021)


Genotype 3

3_JF735124                  QC115                         JF735124                      (Lu et al., 2013)


Genotype 4

4_JX227964                 BID-G1253                   JX227964                     (Newman et al., 2013)

4_FJ0258543                 P026                             FJ025854                      (Koletzki et al., 2009)

4_JF735127                  QC108                         JF735127                      (Lu et al., 2015)

4_JF735132                  QC215                         JF735132                      (Lu et al., 2015)

4_JF735131                  QC147                         JF735131                      (Lu et al., 2015)

4_JF735130                  QC132                         JF735130                      (Lu et al., 2015)

4_JF735129                  QC127                         JF735129                      (Lu et al., 2015)

4_JF735138                  QC58                           JF735138                      (Lu et al., 2015)

4_JF735135                  QC352                         JF735135                      (Lu et al., 2015)

4_JF735134                  QC253                         JF735134                      (Lu et al., 2015)


Genotype 5

5_KT595242                 BF16                            KT595242                    (Henquell et al., 2016)


Genotype 6

6_JX183550                 QC273                         JX183550                     (Wang et al., 2013)

6_JX183551                 TV257, VN139             JX183551, KJ567644    (Li et al., 2014; Wang et al., 2013)

6_JX183553                 TV533                          JX183553                     (Wang et al., 2013)

6_JX183554                 L349                            JX183554                     (Wang et al., 2013)

6_JX183558                 QC271                         JX183558                     (Wang et al., 2013)

6_KJ470620                 HKP7                           KJ470620                     (An et al., 2014)

6_KJ470621                 HKP16                         KJ470621                     (An et al., 2014)

6_KJ470622                 HK25                           KJ470622                     (An et al., 2014)

6_KJ470623                 HK26                           KJ470623                     (An et al., 2014)

6_KJ470624                 HK38                           KJ470624                     (An et al., 2014)

6_KJ470625                 HK43                           KJ470625                     (An et al., 2014)

6_KC844039                ZS96                            KC844039                    (Xu et al., 2013)

6_KC844040                ZS202                          KC844040                    (Xu et al., 2013)

6_KJ567652                 TV566                          KJ567652                     (Li et al., 2014)

6_KJ567648                 TV453                          KJ567648                     (Li et al., 2014)

6_KJ567650                 TV548, TV443              KJ567650, KJ567649    (Li et al., 2014)

6_MG878999               1316-1                          MG878999                   (Wu et al., 2018)

6_MN240359               HVH-HCV334              MN240359                   (Pedersen et al., 2019)




1 Classification of sequences into genotypes but without subtype assignments using the format “genotype_Accession number”

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

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

4 Previously described as 6k (Lu et al., 2006)


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Bracho, M. A., Carrillo-Cruz, F. Y., Ortega, E., Moya, A. & González-Candelas, F. (2006). A new subtype of hepatitis C virus genotype 1: complete genome and phylogenetic relationships of an Equatorial Guinea isolate. J Gen Virol 87, 1697-1702.

Demetriou, V. L. & Kostrikis, L. G. (2011). Near-full genome characterization of unclassified hepatitis C virus strains relating to genotypes 1 and 4. J Med Virol 83, 2119-2127.

Henquell, C., Yameogo, S. & Sangaré, L. (2016). First genome characterization of a novel hepatitis C virus genotype 5 variant. Infect Genet Evol 39, 173-175.

Jordier, F., Deligny, M. L., Barré, R., De Micco, P. & Cantaloube, J. F. (2013). Evidence for two phylogenetic clusters within hepatitis C virus (HCV) genotype 2 inferred from analysis of complete coding sequences of 15 HCV strains. J Med Virol 85, 1754-1764.

Koletzki, D., Dumont, S., Vermeiren, H., Peixe, P., Nina, J., Camacho, R. J. & Stuyver, L. J. (2009). Full genome sequence of three isolates of hepatitis C virus subtype 4b from Portugal. Arch Virol 154, 127-132.

Li, C., Cao, H., Lu, L. & Murphy, D. (2012). Full-length sequences of 11 hepatitis C virus genotype 2 isolates representing five subtypes and six unclassified lineages with unique geographical distributions and genetic variation patterns. J Gen Virol 93, 1173-1184.

Li, C., Njouom, R., Pepin, J., Nakano, T., Bennett, P., Pybus, O. G. & Lu, L. (2013). Characterization of full-length hepatitis C virus sequences for subtypes 1e, 1h and 1l, and a novel variant revealed Cameroon as an area in origin for genotype 1. J Gen Virol 94, 1780-1790.

Li, C., Pham, V. H., Abe, K. & Lu, L. (2014). Nine additional complete genome sequences of HCV genotype 6 from Vietnam including new subtypes 6xb and 6xc. Virology 468-470, 172-177.

Lu, L., Li, C., Xu, Y. & Murphy, D. G. (2014). Full-length genomes of 16 hepatitis C virus genotype 1 isolates representing subtypes 1c, 1d, 1e, 1g, 1h, 1i, 1j and 1k, and two new subtypes 1m and 1n, and four unclassified variants reveal ancestral relationships among subtypes. J Gen Virol 95, 1479-1487.

Lu, L., Li, C., Yuan, J., Lu, T., Okamoto, H. & Murphy, D. G. (2013). Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant. J Gen Virol 94, 543-548.

Lu, L., Nakano, T., Li, C., Fu, Y., Miller, S., Kuiken, C., Robertson, B. H. & Hagedorn, C. H. (2006). Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6. J Gen Virol 87, 629-634.

Lu, L., Xu, Y., Yuan, J., Li, C. & Murphy, D. G. (2015). The full-length genome sequences of nine HCV genotype 4 variants representing a new subtype 4s and eight unclassified lineages. Virology 482, 111-116.

Newman, R. M., Kuntzen, T., Weiner, B., Berical, A., Charlebois, P., Kuiken, C., Murphy, D. G., Simmonds, P., Bennett, P., Lennon, N. J., Birren, B. W., Zody, M. C., Allen, T. M. & Henn, M. R. (2013). Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants. J Infect Dis 208, 17-31.

Ordeig, L., Garcia-Cehic, D., Gregori, J., Soria, M. E., Nieto-Aponte, L., Perales, C., Llorens, M., Chen, Q., Riveiro-Barciela, M., Buti, M., Esteban, R., Esteban, J. I., Rodriguez-Frias, F. & Quer, J. (2018). New hepatitis C virus genotype 1 subtype naturally harbouring resistance-associated mutations to NS5A inhibitors. J Gen Virol 99, 97-102.

Pedersen, M. S., Mollerup, S., Nielsen, L. G., Jenssen, H., Bukh, J. & Schønning, K. (2019). Genome sequence of an unknown subtype of hepatitis C virus genotype 6: another piece for the taxonomic puzzle. Microbiol Resour Announc 8.

Rajhi, M., Haddad-Boubaker, S., Chouikha, A., Bourquain, D., Michel, J., Hammami, W., Sadraoui, A., Touzi, H., Ghedira, K. & Triki, H. (2021). Identification of two novel hepatitis C virus subtype 2 from Tunisia (2v and 2w). PLoS One 16, e0248249.

von Massow, G., Garcia-Cehic, D., Gregori, J., Rodriguez-Frias, F., Macià, M. D., Escarda, A., Esteban, J. I. & Quer, J. (2019). Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype. Infect Drug Resist 12, 947-955.

Wang, H., Yuan, Z., Barnes, E., Yuan, M., Li, C., Fu, Y., Xia, X., Li, G., Newton, P. N., Vongsouvath, M., Klenerman, P., Pybus, O. G., Murphy, D., Abe, K. & Lu, L. (2013). Eight novel hepatitis C virus genomes reveal the changing taxonomic structure of genotype 6. J Gen Virol 94, 76-80.

Wu, T., Xing, Z., Yuan, M., Ge, J., Yuan, G., Liang, K., Wu, B., Xiao, F., Li, C., Zhou, Y., Lin, F. & Lu, L. (2018). Analysis of HCV isolates among the Li ethnic in Hainan Island of South China reveals their HCV-6 unique evolution and a new subtype. Cell Physiol Biochem 50, 1832-1839.

Xu, R., Tong, W., Gu, L., Li, C., Fu, Y. & Lu, L. (2013). A panel of 16 full-length HCV genomes was characterized in China belonging to genotypes 1-6 including subtype 2f and two novel genotype 6 variants. Infect Genet Evol 20, 225-229.