SG Information

Table 2 - Unassigned complete coding region sequences (June 2017)

UNASSIGNED COMPLETE CODING REGION SEQUENCES

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_KJ439779                QC316                                     KJ439779                    (Lu et al., 2014)

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

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

 

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)

 

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 6

6_DQ2788914             KM45, KM41                          DQ278891, DQ278893           (Lu et al., 2006)

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

6_JX183552                TV476                                     JX183552                    (Wang et al., 2013)

6_JX183549                KM35                                      JX183549                    (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)

 

 

Footnotes                                                          

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)

References

An, Y., Wu, T., Wang, M., Lu, L., Li, C., Zhou, Y., Fu, Y. & Chen, G. (2014). Conservation in China of a novel group of HCV variants dating to six centuries ago. Virology 464-465, 21–5.

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, 2119–27.

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, 1754–64.

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, 127–32.

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, 1173–84.

Li, C., Njouom, R., Pépin, J., Nakano, T., Bennett, P., Pybus, O. G. & Lu, L. (2013). Characterization of full-length HCV 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, 172–177.

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., 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, 543–8.

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, 1479–87.

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. & other authors. (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.

Wang, H., Yuan, Z., Barnes, E., Yuan, M., Li, C., Fu, Y., Xia, X., Li, G., Newton, P. N. & other authors. (2013). Eight novel hepatitis C virus genomes reveal the changing taxonomic structure of genotype 6. J Gen Virol 94, 76–80.

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, 225–9.

 

 

 

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