Archives of Virology

, Volume 156, Issue 9, pp 1591–1601 | Cite as

Identification and characterization of a natural inter-genotypic (2b/1b) recombinant hepatitis C virus in Japan

  • Koji Yokoyama
  • Masaharu Takahashi
  • Tsutomu Nishizawa
  • Shigeo Nagashima
  • Suljid Jirintai
  • Shigeru Yotsumoto
  • Hiroaki Okamoto
  • Mariko Y. Momoi
Original Article


A hepatitis C virus (HCV) strain (HC10-0804) recovered from a 12-year-old Japanese female with chronic hepatitis C segregated into discordant genotypes, 2b and 1b, in the 5’UTR/core and NS5B regions, respectively, thus suggesting an inter-genotypic recombination. The HC10-0804 isolate had a genomic length of 9,423 nucleotides (nt), excluding the poly(U) tract at the 3’ terminus, and encoded a single open reading frame (ORF) for a polyprotein of 3,014 amino acids (aa). Based on Simplot and Bootscan analyses, the crossover point from 2b to 1b was estimated at nt 3443/3444 (aa 1034/1035), just after the beginning of the NS3 region. Comparison of the entire genomic sequence showed that the HC10-0804 strain was only 90.2% identical to the previously reported 2b/1b recombinant strain (SE-03-07-1689) from the Philippines, whose putative crossover point was 24 nt downstream of that of HC10-0804. These results indicate the circulation of a novel inter-genotypic (2b/1b) recombinant HCV in Japan.


Sustained Virological Response Recombinant Strain NS5B Region Bootscan Analysis Recombination Crossover Point 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported in part by a grant from the Ministry of Education, Culture Sports, Sciences and Technology of Japan.


  1. 1.
    Chayama K, Tsubota A, Kobayashi M, Okamoto K, Hashimoto M, Miyano Y, Koike H, Koida I, Arase Y, Saitoh S, Suzuki Y, Murashima N, Ikeda K, Kumada H (1997) Pretreatment virus load and multiple amino acid substitutions in the interferon sensitivity-determining region predict the outcome of interferon treatment in patients with chronic genotype 1b hepatitis C virus infection. Hepatology 25:745–749PubMedCrossRefGoogle Scholar
  2. 2.
    Chung H, Ueda T, Kudo M (2010) Changing trends in hepatitis C infection over the past 50 years in Japan. Intervirology 53:39–43PubMedCrossRefGoogle Scholar
  3. 3.
    El-Shamy A, Nagano-Fujii M, Sasase N, Imoto S, Kim SR, Hotta H (2008) Sequence variation in hepatitis C virus nonstructural protein 5A predicts clinical outcome of pegylated interferon/ribavirin combination therapy. Hepatology 48:38–47PubMedCrossRefGoogle Scholar
  4. 4.
    Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, Yamamoto C, Ogura Y, Izumi N, Marumo F, Sato C (1996) Mutations in the nonstructural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection. N Engl J Med 334:77–81PubMedCrossRefGoogle Scholar
  5. 5.
    Farci P, Shimoda A, Coiana A, Diaz G, Peddis G, Melpolder JC, Strazzera A, Chien DY, Munoz SJ, Balestrieri A, Purcell RH, Alter HJ (2000) The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science 288:339–344PubMedCrossRefGoogle Scholar
  6. 6.
    Gao F, Nainan OV, Khudyakov Y, Li J, Hong Y, Gonzales AC, Spelbring J, Margolis HS (2007) Recombinant hepatitis C virus in experimentally infected chimpanzees. J Gen Virol 88:143–147PubMedCrossRefGoogle Scholar
  7. 7.
    Guillot S, Caro V, Cuervo N, Korotkova E, Combiescu M, Persu A, Aubert-Combiescu A, Delpeyroux F, Crainic R (2000) Natural genetic exchanges between vaccine and wild poliovirus strains in humans. J Virol 74:8434–8443PubMedCrossRefGoogle Scholar
  8. 8.
    Holland PV, Barrera JM, Ercilla MG, Yoshida CF, Wang Y, de Olim GA, Betlach B, Kuramoto K, Okamoto H (1996) Genotyping hepatitis C virus isolates from Spain, Brazil, China, and Macau by a simplified PCR method. J Clin Microbiol 34:2372–2378PubMedGoogle Scholar
  9. 9.
    Kageyama S, Agdamag DM, Alesna ET, Leaño PS, Heredia AM, Abellanosa-Tac-An IP, Jereza LD, Tanimoto T, Yamamura J, Ichimura H (2006) A natural inter-genotypic (2b/1b) recombinant of hepatitis C virus in the Philippines. J Med Virol 78:1423–1428PubMedCrossRefGoogle Scholar
  10. 10.
    Kalinina O, Norder H, Mukomolov S, Magnius LO (2002) A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg. J Virol 76:4034–4043PubMedCrossRefGoogle Scholar
  11. 11.
    Kalinina O, Norder H, Magnius LO (2004) Full-length open reading frame of a recombinant hepatitis C virus strain from St Petersburg: proposed mechanism for its formation. J Gen Virol 85:1853–1857PubMedCrossRefGoogle Scholar
  12. 12.
    Kanai K, Kako M, Okamoto H (1992) HCV genotypes in chronic hepatitis C and response to interferon. Lancet 339:1543PubMedCrossRefGoogle Scholar
  13. 13.
    Korenaga M, Hino K, Katoh Y, Yamaguchi Y, Okuda M, Yoshioka K, Okita K (2001) A possible role of hypervariable region 1 quasispecies in escape of hepatitis C virus particles from neutralization. J Viral Hepat 8:331–340PubMedCrossRefGoogle Scholar
  14. 14.
    Kurbanov F, Tanaka Y, Chub E, Maruyama I, Azlarova A, Kamitsukasa H, Ohno T, Bonetto S, Moreau I, Fanning LJ, Legrand-Abravanel F, Izopet J, Naoumov N, Shimada T, Netesov S, Mizokami M (2008) Molecular epidemiology and interferon susceptibility of the natural recombinant hepatitis C virus strain RF1_2k/1b. J Infect Dis 198:1448–1456PubMedCrossRefGoogle Scholar
  15. 15.
    Lai MM (1992) Genetic recombination in RNA viruses. Curr Top Microbiol Immunol 176:21–32PubMedGoogle Scholar
  16. 16.
    Lauer GM, Walker BD (2001) Hepatitis C virus infection. N Engl J Med 345:41–52PubMedCrossRefGoogle Scholar
  17. 17.
    Lee YM, Lin HJ, Chen YJ, Lee CM, Wang SF, Chang KY, Chen TL, Liu HF, Chen YM (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 82:57–68PubMedCrossRefGoogle Scholar
  18. 18.
    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 81:4357–4362PubMedCrossRefGoogle Scholar
  19. 19.
    Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160PubMedGoogle Scholar
  20. 20.
    Mohamed MK, Magder LS, Abdel-Hamid M, El-Daly M, Mikhail NN, Abdel-Aziz F, Medhat A, Thiers V, Strickland GT (2006) Transmission of hepatitis C virus between parents and children. Am J Trop Med Hyg 75:16–20PubMedGoogle Scholar
  21. 21.
    Moradpour D, Penin F, Rice CM (2007) Replication of hepatitis C virus. Nat Rev Microbiol 5:453–463PubMedCrossRefGoogle Scholar
  22. 22.
    Moreau I, Hegarty S, Levis J, Sheehy P, Crosbie O, Kenny-Walsh E, Fanning LJ (2006) Serendipitous identification of natural intergenotypic recombinants of hepatitis C in Ireland. Virol J 3:95PubMedCrossRefGoogle Scholar
  23. 23.
    Morel V, Fournier C, Francois C, Brochot E, Helle F, Duverlie G, Castelain S (2011) Genetic recombination of the hepatitis C virus: clinical implications. J Viral Hepat 18:77–83PubMedCrossRefGoogle Scholar
  24. 24.
    Nakatani SM, Santos CA, Riediger IN, Krieger MA, Duarte CA, Lacerda MA, Biondo AW, Carrilho FJ, Ono-Nita SK (2010) Development of hepatitis C virus genotyping by real-time PCR based on the NS5B region. PLoS ONE 5:e10150PubMedCrossRefGoogle Scholar
  25. 25.
    National Institutes of Health (2002) NIH consensus statement on management of hepatitis C: 2002. NIH Consens State Sci Statements 19:1–46Google Scholar
  26. 26.
    Noppornpanth S, Lien TX, Poovorawan Y, Smits SL, Osterhaus AD, Haagmans BL (2006) Identification of a naturally occurring recombinant genotype 2/6 hepatitis C virus. J Virol 80:7569–7577PubMedCrossRefGoogle Scholar
  27. 27.
    Ohto H, Terazawa S, Sasaki N, Hino K, Ishiwata C, Kako M, Ujiie N, Endo C, Matsui A et al (1994) Transmission of hepatitis C virus from mothers to infants. The Vertical Transmission of Hepatitis C Virus Collaborative Study Group. N Engl J Med 330:744–750PubMedCrossRefGoogle Scholar
  28. 28.
    Okada S, Akahane Y, Suzuki H, Okamoto H, Mishiro S (1992) The degree of variability in the amino terminal region of the E2/NS1 protein of hepatitis C virus correlates with responsiveness to interferon therapy in viremic patients. Hepatology 16:619–624PubMedCrossRefGoogle Scholar
  29. 29.
    Okamoto H, Kojima M, Okada S, Yoshizawa H, Iizuka H, Tanaka T, Muchmore EE, Peterson DA, Ito Y, Mishiro S (1992) Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: variability and stability. Virology 190:894–899PubMedCrossRefGoogle Scholar
  30. 30.
    Okamoto H, Kurai K, Okada S, Yamamoto K, Lizuka H, Tanaka T, Fukuda S, Tsuda F, Mishiro S (1992) Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188:331–341PubMedCrossRefGoogle Scholar
  31. 31.
    Okamoto H, Tokita H, Sakamoto M, Horikita M, Kojima M, Iizuka H, Mishiro S (1993) Characterization of the genomic sequence of type V (or 3a) hepatitis C virus isolates and PCR primers for specific detection. J Gen Virol 74(Pt 11):2385–2390PubMedCrossRefGoogle Scholar
  32. 32.
    Reiter J, Perez-Vilaro G, Scheller N, Mina LB, Diez J, Meyerhans A (2011) Hepatitis C virus RNA recombination in cell culture. J Hepatol. doi: 10.1016/j.jhep.2010.12.038
  33. 33.
    Santti J, Hyypia T, Kinnunen L, Salminen M (1999) Evidence of recombination among enteroviruses. J Virol 73:8741–8749PubMedGoogle Scholar
  34. 34.
    Shepard CW, Finelli L, Alter MJ (2005) Global epidemiology of hepatitis C virus infection. Lancet Infect Dis 5:558–567PubMedCrossRefGoogle Scholar
  35. 35.
    Simmonds P, Bukh J, Combet C, Deléage G, Enomoto N, Feinstone S, Halfon P, Inchauspé G, Kuiken C, Maertens G, Mizokami M, Murphy DG, Okamoto H, Pawlotsky JM, Penin F, Sablon E, Shin-I T, Stuyver LJ, Thiel HJ, Viazov S, Weiner AJ, Widell A (2005) Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42:962–973PubMedCrossRefGoogle Scholar
  36. 36.
    Tallo T, Norder H, Tefanova V, Krispin T, Schmidt J, Ilmoja M, Orgulas K, Pruunsild K, Priimägi L, Magnius LO (2007) Genetic characterization of hepatitis C virus strains in Estonia: fluctuations in the predominating subtype with time. J Med Virol 79:374–382PubMedCrossRefGoogle Scholar
  37. 37.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (submitted) (Publication PDF at
  38. 38.
    Tanaka T, Tsukiyama-Kohara K, Yamaguchi K, Yagi S, Tanaka S, Hasegawa A, Ohta Y, Hattori N, Kohara M (1994) Significance of specific antibody assay for genotyping of hepatitis C virus. Hepatology 19:1347–1353PubMedCrossRefGoogle Scholar
  39. 39.
    Taniguchi S, Okamoto H, Sakamoto M, Kojima M, Tsuda F, Tanaka T, Munekata E, Muchmore EE, Peterson DA, Mishiro S (1993) A structurally flexible and antigenically variable N-terminal domain of the hepatitis C virus E2/NS1 protein: implication for an escape from antibody. Virology 195:297–301PubMedCrossRefGoogle Scholar
  40. 40.
    Trowbridge R, Gowans EJ (1998) Identification of novel sequences at the 5′ terminus of the hepatitis C virus genome. J Viral Hepat 5:95–98PubMedCrossRefGoogle Scholar
  41. 41.
    Wakita T, Pietschmann T, Kato T, Date T, Miyamoto M, Zhao Z, Murthy K, Habermann A, Krausslich HG, Mizokami M, Bartenschlager R, Liang TJ (2005) Production of infectious hepatitis C virus in tissue culture from a cloned viral genome. Nat Med 11:791–796PubMedCrossRefGoogle Scholar
  42. 42.
    Weiner AJ, Brauer MJ, Rosenblatt J, Richman KH, Tung J, Crawford K, Bonino F, Saracco G, Choo QL, Houghton M et al (1991) Variable and hypervariable domains are found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins. Virology 180:842–848PubMedCrossRefGoogle Scholar
  43. 43.
    Worobey M, Holmes EC (1999) Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80:2535–2543PubMedGoogle Scholar
  44. 44.
    Zein NN (2000) Clinical significance of hepatitis C virus genotypes. Clin Microbiol Rev 13:223–235PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Koji Yokoyama
    • 1
    • 2
  • Masaharu Takahashi
    • 2
  • Tsutomu Nishizawa
    • 2
  • Shigeo Nagashima
    • 2
  • Suljid Jirintai
    • 2
  • Shigeru Yotsumoto
    • 1
    • 2
    • 3
  • Hiroaki Okamoto
    • 2
  • Mariko Y. Momoi
    • 1
  1. 1.Department of PediatricsJichi Medical University School of MedicineShimotsukeJapan
  2. 2.Division of Virology, Department of Infection and ImmunityJichi Medical University School of MedicineShimotsukeJapan
  3. 3.Sato Pediatric ClinicMiyazakiJapan

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