GENOME ORGANIZATION AND GEOGRAPHICAL DISTRIBUTION OF THE NATURAL INTERGENOTYPIC RECOMBINANT OF HEPATITIS C VIRUS RF1_2k/1b

Cover Page

Cite item

Abstract

Abstract. For many years, the viral hepatitis C is considered as one of the most actual infectious pathologies of human. During the last decade the number of registered cases of chronic viral hepatitis C in Russia increased two times and reached 40.9‰. According to the current virological classification, hepatitis C virus (HCV) is differentiated into 6 genotypes and more than 200 subtypes. At the same time, increasing number of publications report about novel genetic variants of HCV. A high mutation rate is considered to be a major factor behind HCV genetic diversity. Recombination as another mechanism for creating genetic variation was not recognized as important factor for generating the HCV diversity. For a long time it was believed that the natural recombinants of hepatitis C virus were not viable. The first inter-genotype HCV recombinant RF1_2k/1b was identified in 2002 in Saint-Petersburg. The structural genes of the recombinant strain were similar to those of the HCV subtype 2k, while its nonstructural genes (except for the part of the NS2 gene) belonged to the HCV subtype 1b. Since that time, many studies were initiated to indentify natural HCV recombinants. This review presents current data regarding the genomic organization of HCV and its natural inter-genotype recombinant RF1_2k/1b as well as information about circulation of this recombinant in the world.

About the authors

O. V. Kalinina

ФБУН НИИ эпидемиологии и микробиологии имени Пастера, Санкт-Петербург

Author for correspondence.
Email: olgakalinina@mail.ru

к.б.н., ведущий научный сотрудник лаборатории молекулярной микробиологии

197101, Санкт-Петербург, ул. Мира, 14

Russian Federation

References

  1. Вирусные гепатиты в Российской Федерации: Справочник / Под ред. Онищенко Г.Г., Жебруна А.Б. — СПб: НИИЭМ им. Пастера, 2010. — 204 с.
  2. Budkowska A., Kakkanas A., Nerrienet E., Kalinina O., Maillard P., Horm S.V., Dalagiorgou G., Vassilaki N., Georgopoulou U., Martinot M., Sall A.A., Mavromara P. Synonymous mutations in the core gene are linked to unusual serological profile in hepatitis C virus infection // PLoS One. — 2011. — Vol. 6, N 1. — P. 1–12.
  3. Choo Q.L., Richman K.H., Han J.H., Berger K., Lee C., Dong C., Gallegos C., Coit D., Medina-Selby R., Barr P.J. Genetic organization and diversity of the hepatitis C virus // Proc. Natl. Acad. Sci. USA. — 1991. — Vol. 88, N 6. — P. 2451–2455.
  4. De Francesco R. Molecular virology of the hepatitis C virus // J. Hepatolol. — 1999. — Vol. 31, Suppl. 1. — P. 47–53.
  5. Demetriou V.L., Kyriakou E., Kostrikis L.G. Nearfull genome characterization of two natural intergenotypic 2k/1b recombinant hepatitis C virus isolates // Advances in Virology. — 2011. — Vol. 2011. — P. 1–7.
  6. Enomoto N., Sakuma I., Asahina Y., Kurosaki M., Murakami T., Yamamoto C., Ogura Y., Izumi N., Marumo F., Sato C. Mutations in the nonstructural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection // New Eng. J. Med. — 1996. — Vol. 334. — P. 77–81.
  7. Gale M.Jr, Foy E.M. Evasion of intracellular host defence by hepatitis C virus // Nature. — 2005. — Vol. 436. — P. 939–945.
  8. Grakoui A., Wychowski C., Lin C., Feinstone S.M., Rice C.M. Expression and identification of hepatitis C virus polyprotein cleavage products // J. Virol. — 1993. — Vol. 67, N 3. — P. 1385–1395.
  9. Hijikata M., Kato N., Ootsuyama Y., Nakagawa M., Shimotohno K. Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis // Proc. Natl. Acad. Sci. USA. — 1991. — Vol. 88, N 13. — P. 5547–5551.
  10. Kalinina O., Norder H., Vetrov T., Zhdanov K., Barzunova M., Plotnikova V., Mukomolov S., Magnius L. Shift in predominating subtype of HCV from 1b to 3a in St. Petersburg mediated by increase in injecting drug use // J. Med. Virol. — 2001. — Vol. 65. — P. 517–524.
  11. Kalinina O., Norder H., Mukomolov S., Magnius L. A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg // J. Virol. — 2002. — Vol. 76. — P. 4034–4043.
  12. Kalinina O., Norder H., Thcakharian V., Zhdanov K., Kislii P., Vetrov T., Mukomolov S., Magnius L. More recombinant HCV strains recovered in St. Petersburg // 9th International Meeting on HCV and Related Viruses. — San-Diego, USA, 2002. — P. 225.
  13. Kalinina O., Norder H., Magnius L. Full-length open reading frame of a recombinant hepatitis C virus strain from St. Petersburg: proposed mechanism for its formation // J. Gen. Virol. — 2004. — Vol. 85. — P. 1853–1857.
  14. Kalinina O., Jern C., Tallo T., Thcakharian V., Gusev D., Znoiko O., Isaguliants M., Mukomolov S., Norder H., Magnius L. Spread of the natural hepatitis C virus recombinant outside Russia // 12th International symposium on viral hepatitis and liver disease. — Paris, 2006. — P. 189.
  15. Kato N., Ootsuyama Y., Ohkoshi S., Nakazawa T., Sekiya H., Hijikata M., Shimotohno K. Characterization of hypervariable regions in the putative envelope protein of hepatitis C virus // Biochem. Biophys. Res. Commun. — 1992. — Vol. 189, N 1. — P. 119–127.
  16. Kolykhalov A.A., Feinstone S.M., Rice C.M. Identification of a highly conserved sequence element at the 3’ terminus of hepatitis C virus genome RNA // J. Virol. — 1996. — Vol. 70, N 6. — P. 3363–3371.
  17. Kuiken C., Simmonds P. Nomenclature and numbering of the hepatitis C virus // Methods Mol. Biol. — 2009. — Vol. 510, Hepatitis C, part II. — P. 33–53.
  18. Kurbanov F., Tanaka Y., Chub E., Maruyama I., Azlarova A., Kamitsukasa H., Ohno T., Bonetto S., Moreau I., Fanning L.J., Legrand-Abravanel F., Izopet J., Naoumov N., Shimada T., Netesov S., Mizokami M. Molecular epidemiology and interferon susceptibility of the natural recombinant hepatitis C virus strain RF1_2k/1b // J. Infect. Dis. — 2008. — Vol. 198, N 10. — P. 1448–1456.
  19. 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. Molecular epidemiology of HCV genotypes among injection drug users in Taiwan: Full-length sequences of two new subtype 6w strains and a recombinant form_2b/6w // J. Med. Virol. — 2009. — Vol. 82. — P. 57–68.
  20. Legrand-Abravanel F., Claudinon J., Nicot F., Dubois M., Chapuy-Regaud S., Sandres-Saune K., Pasquier C., Izopet J. New natural intergenotypic (2/5) recombinant of hepatitis C virus // J. Virol. — 2007. — Vol. 81, N 8. — P. 4357–4362.
  21. Lindenbach B.D., Rice C.M. Unravelling hepatitis C virus replication from genome to function // Nature. — 2005. — Vol. 436. — P. 933–938.
  22. Lu W., Lo S.Y., Chen M., Wu K., Fung Y.K., Ou J.H. Activation of p53 tumor suppressor by hepatitis C virus core protein // Virology. — 1999. — Vol. 264. — P. 134 –141.
  23. Macdonald A., Crowder K., Street A., McCormick C., Saksela K., Harris M. The hepatitis C virus nonstructural NS5A protein inhibits activating protein-1 function by perturbing ras-ERK pathway signaling // J. Biol. Chem. — 2003. — Vol. 278, N 20. — P. 17775–17784.
  24. Matsuura Y., Harada T., Makimura M., Sato M., Aizaki H., Suzuki T., Miyamura T. Characterization of HCV structural proteins expressed in various animal cells // Intervirology. — 1994. — Vol. 37, N 2. — P. 114–118.
  25. Melyan E., Curran J., Hofmann K., Moradpour D., Binder M., Bartenschlager R., Tschopp J. Cardif is an adaptor protein in the RIG-I antiviral pathway and istargeted by hepatitis C virus // Nature. — 2005. — Vol. 437. — P. 1167–1172.
  26. Mizushima H., Hijikata M., Tanji Y., Kimura K., Shimotohno K. Analysis of N-terminal processing of hepatitis C virus nonstructural protein 2 // J. Virol. — 1994. — Vol. 68, N 4. — P. 2731–2734.
  27. Moreau I., Hegarty S., Levis J., Sheehy P., Crosbie O., Kenny-Walsh E., Fanning L.J. Serendipitous identification of natural intergenotypic recombinants of hepatitis C in Ireland // Virol J. — 2006. — Vol. 3. — P. 1–7.
  28. Morel V., Descamps V., Franois C., Fournier C., Brochot E., Capron D., Duverlie G., Castelain S. Emergence of a genomic variant of the recombinant 2k/1b strain during a mixed hepatitis C infection: a case report // J. Clin. Virol. — 2010. — Vol. 47. — P. 382–386.
  29. Noppornpanth S., Lien T.X., Poovorawan Y., Smits S.L., Osterhaus A.D., Haagmans B.L. Identification of a naturally occurring recombinant genotype 2/6 hepatitis C virus // J. Virol. — 2006. —Vol 80, N 15. — P. 7569–7577.
  30. Okamoto H., Mishiro S. Genetic heterogeneity of hepatitis C virus // Intervirology. — 1994. — Vol. 37, N 2. — P. 68–76.
  31. Okamoto H., Kobata S., Tokita H., Inoue T., Woodfield G.D., Holland P.V., Al-Knawy B.A., Uzunalimoglu O., Miyakawa Y.,Mayumi M. A second-generation method of genotyping hepatitis C virus by the polymerase chain reaction with sense and antisense primers deduced from the core gene // J. Virol. Methods. — 1996. — Vol. 57, N 1. — P. 31–45.
  32. Raghwani J., Thomas X.V., Koekkoek S.M., Schinkel J., Molenkamp R., Thijs J. van de Laar, Takebe Y., Tanaka Y., Mizokami M., Rambaut A., Pybus O.G. Origin and Evolution of the unique hepatitis C virus circulating recombinantform 2k/1b // J. Virol. — 2012. — Vol. 86, N 4. — P. 2211–2220.
  33. Roohvand F., Maillard P., Lavergne J.P., Boulant S., Walic M., Andréo U., Goueslain L., Helle F., Mallet A., McLauchlan J., Budkowska A. Initiation of hepatitis C virus infection requires the dynamic microtubule network: role of the viral nucleocapsid protein // J. Biol. Chem. — 2009. — Vol. 284, N 20. — P. 13778–13791.
  34. Santolini E., Migliaccio G., La M.N. Biosynthesis and biochemical properties of the hepatitis C virus core protein // J. Virol. — 1994. — Vol. 68, N 6. — P. 3631–3641.
  35. Schwer B., Ren S., Pietschmann T. Kartenbeck J., Kaehlcke K., Bartenschlager R., Yen T.S., Ott M. Targeting of hepatitis C virus core protein to mitochondria through a novel C-terminal localization motif // J. Virol. — 2004. — Vol. 78. — P. 7958–7568.
  36. Simmonds P., Holmes E.C., Cha T.A., Chan S.W., McOmish F., Irvine B., Beall E., Yap P.L., Kolberg J., Urdea M.S. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region // J.Gen.Virol. — 1993. — Vol. 74, N 11. — P. 2391–2399.
  37. Simmonds P. Viral heterogeneity of the hepatitis C virus // J. Hepatol. — 1999. — Vol. 31, Suppl. 1. — P. 54 – 60.
  38. Simmonds P., Bukh J., Combet Ch., Delґeage G., Enomoto N., Feinstone S., Halfon Ph., Inchauspґe G., Kuiken C., Maertens G., Mizokami M., Murphy D.G., Okamoto H., Pawlotsky J.-M., Penin F., Sablon E., Shin T., Stuyver L.J., Thiel H.J., Viazov S., Weiner A.J., Widell A. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes // Hepatology. — 2005. — Vol. 42, N 4. — P. 962–973.
  39. Spahn C.M., Kieft J.S., Grassucci R.A., Penczek P.A., Zhou K., Doudna J.A., Frank J. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit // Science. — 2001. — Vol. 291. — P. 1959 –1962.
  40. Tallo T., Norder H., Tefanova V., Krispin T., Schmidt J., Ilmoja M., Orgulas K., Pruunsild K., Priimagi L., Magnius L. Genetic characterization of hepatitis C virus strains in Estonia: fluctuations in the predominating subtype with time // J. Med. Virol. — 2007. — Vol. 79, N 4. — P. 374–382.
  41. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods // Mol. Biol. Evol. — 2011. — Vol. 28. — P. 2731–2739.
  42. Tanaka T., Kato N., Cho M.J., Sugiyama K., Shimotohno K. Structure of the 3’ terminus of the hepatitis C virus genome // J. Virol. — 1996. — Vol. 70, N 5. — P. 3307–3312.
  43. Taylor D.R., Shi S.T., Romano G.N., Lai M.M. Inhibition of the interferon-inducible protein kinase PKR by HCV E2 protein // Science. — 1999. — Vol. 285. — P. 107–110.
  44. Vassilaki N., Mavromara P. Two alternative translation mechanisms areresponsible for the expression of the HCV ARFP/F/core+1 coding openreading frame // J. Biol. Chem. — 2003. — Vol. 278. — P. 40503–40513.
  45. Viazov S., Widell A., Nordenfelt E. Mixed infection with two types of hepatitis C virus is probably a rare event // Infection. — 2000. — Vol.28, N 1. — P. 21–25.
  46. Walewski J.L., Keller T.R., Stump D.D., Branch A.D. Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame // RNA. — 2001. — Vol. 7. — P. 710–721.
  47. Yamamura J., Ichimura H. A natural intergenotypic (2b/1b) recombinant of hepatitis C virus in the Philippines // J. Med. Virol. — 2006. — Vol. 78. — P. 1423–1428.

Copyright (c) 2014 Kalinina O.V.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies