Recombinant (RF) HCV genomes

RF1 Breakpoint2 Accession Isolates3 Reference
RF2k/1b 3186 AY587845 33 (Kalinina et al., 2002, 2004; Kurbanov et al., 2010)
RF2i/6p 3405-3464 DQ155560 1 (Noppornpanth et al., 2006)
RF2b/1b_1 3456 DQ364460 1 (Kageyama et al., 2006)
RF2/5 3366-3389 AM408911 1 (Legrand-Abravanel et al., 2007)
RF2b/6w 3429 EU643835 1 (Lee et al., 2010)
RF2b/1b_2 3432 AB622121 1 (Yokoyama et al., 2011)
RF2b/1a 3429-3440 JF779679 1 (Bhattacharya et al., 2011)
RF2b/1b_3 3286-3293 AB677530 1 (Hoshino et al., 2012)
RF2b/1b_4 3286-3293 AB677527 1 (Hoshino et al., 2012)

 An alignment of  these RF will be made available for download from this site.

Recombinant forms(RF) for which complete genome sequences are available are named according to the subtypes from which they are derived and in the order in which these appear in the genome.

Breakpoints are numbered with reference to H77 (AF009606).

3 Number of individuals from whom the RF has been isolated.


Bhattacharya, D., Accola, M. A., Ansari, I. H., Striker, R. & Rehrauer, W. M. (2011). Naturally occurring genotype 2b/1a hepatitis C virus in the United States. Virol J 8, 458.

Hoshino, H., Hino, K., Miyakawa, H. & Takahashi, K. (2012). Inter-Genotypic Recombinant Hepatitis C Virus Strains in Japan Noted by Discrepancies Between Immunoassay and Sequencing 1024, 1018–1024.

Kageyama, S., Agdamag, D. M., Alesna, E. T., Leano, P. S., Heredia, A. M. L., Abellanosa-Tac-An, I. P., Jereza, L. D., Tanimoto, T., Yamamura, J. & Ichimura, H. (2006). A natural inter-genotypic (2b/1b) recombinant of hepatitis C virus in the Philippines. J Med Virol 78, 1423–1428. WILEY-LISS.

Kalinina, O., Norder, H., Mukomolov, S. & Magnius, L. O. (2002). A Natural Intergenotypic Recombinant of Hepatitis C Virus Identified in St. Petersburg. J Virol 76, 4034–4043. American Society for Microbiology.

Kalinina, O., Norder, H. & Magnius, L. O. (2004). Full-length open reading frame of a recombinant hepatitis C virus strain from St Petersburg: proposed mechanism for its formation. J Gen Virol 85, 1853–1857.

Kurbanov, F., Tanaka, Y., Chub, E., Maruyama, I., Azlarova, A., Kamitsukasa, H., Ohno, T., Bonetto, S., Moreau, I. & other authors(2010). Molecular epidemiology and Interferon-sensitivity of the natural recombinant hepatitis C virus strain RF1 _ 2k / 1b. J Infect Dis 151, 19–25.

Lee, Y. M., Lin, H. J., Chen, Y. J., Lee, C. M., Wang, S. F., Chang, K. Y., Chen, T. L., Liu, H. F. & Chen, Y. M. A. (2010). Molecular Epidemiology of HCV Genotypes Among Injection Drug Users in Taiwan: Full-Length Sequences of Two New Subtype 6w Strains and a Recombinant form_2b6w. J Med Virol 82, 57–68.

Legrand-Abravanel, F., Claudinon, J., Nicot, F., Dubois, M., Chapuy-Regaud, S., Sandres-Saune, K., Pasquier, C. & Izopet, J. (2007). New Natural Intergenotypic (2/5) Recombinant of Hepatitis C Virus. J Virol 81, 4357–4362. American Society for Microbiology.

Noppornpanth, S., Lien, T. X., Poovorawan, Y., Smits, S. L., Osterhaus, A. D. M. E. & Haagmans, B. L. (2006). Identification of a Naturally Occurring Recombinant Genotype 2/6 Hepatitis C Virus. J Virol 80, 7569–7577. American Society for Microbiology.

Yokoyama, K., Takahashi, M., Nishizawa, T., Nagashima, S., Jirintai, S., Yotsumoto, S., Okamoto, H. & Momoi, M. Y. (2011). Identification and characterization of a natural inter-genotypic (2b/1b) recombinant hepatitis C virus in Japan. Arch Virol 156, 1591–601.