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]