SG Information

Table 2 - Unassigned complete coding region sequences (May 2019)

UNASSIGNED COMPLETE CODING REGION SEQUENCES (May 2019)

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)

 

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_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)

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

 

 

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, 21-25. [PMID 25043585]

 

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. [PMID 16690936]

 

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. [PMID 22012719]

 

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. [PMID 23861126]

 

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. [PMID 19050819]

 

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. [PMID 22357752]

 

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. [PMID 23677792]

 

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. [PMID 25173194]

 

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. [PMID 24718832]

 

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. [PMID 23152370]

 

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. [PMID 16476984]

 

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. [PMID 25854865]

 

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. [PMID 23136221]

 

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. [PMID 23015745]

 

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. [PMID 30396187]

 

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. [PMID 24012950]

 

 

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