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REFERENCES
Data from the following 68 publications have been used to compile the database.
Sequence and structural analysis of the 5' noncoding region of hepatitis C virus in patients with chronic infection.
Araujo FM, Machado-Lima A, Durham AM, Teixeira R, Oliveira G
J Med Virol. 2009 Jul;81(7):1212-9. doi: 10.1002/jmv.21507.
Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation.
Barria MI, Gonzalez A, Vera-Otarola J, Leon U, Vollrath V, Marsac D, Monasterio O, Perez-Acle T, Soza A, Lopez-Lastra M
Nucleic Acids Res. 2009 Feb;37(3):957-71. doi: 10.1093/nar/gkn1022. Epub 2008 Dec 23.
The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit.
Berry KE, Waghray S, Doudna JA
RNA. 2010 Aug;16(8):1559-69. doi: 10.1261/rna.2197210. Epub 2010 Jun 28.
Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning.
Berry KE, Waghray S, Mortimer SA, Bai Y, Doudna JA
Structure. 2011 Oct 12;19(10):1456-66. doi: 10.1016/j.str.2011.08.002.
Phylogenetic conservation of the stem-loop III structure of the 5' untranslated region of Hepatitis C virus RNA among natural variants in samples collected from Southern India.
Bhattacharyya S, Mapa K, Prabhavathi S, Sudhamani SR, Menon PK, John KP, Shivaram C, Amarnath S, Das S
Arch Virol. 2004 May;149(5):1015-26. Epub 2004 Jan 29.
Sequence analysis of the 5' noncoding region of hepatitis C virus.
Bukh J, Purcell RH, Miller RH
Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):4942-6.
In vivo translational efficiency of different hepatitis C virus 5'-UTRs.
Buratti E, Gerotto M, Pontisso P, Alberti A, Tisminetzky SG, Baralle FE
FEBS Lett. 1997 Jul 14;411(2-3):275-80.
Structure of replicating hepatitis C virus (HCV) quasispecies in the liver may not be reflected by analysis of circulating HCV virions.
Cabot B, Esteban JI, Martell M, Genesca J, Vargas V, Esteban R, Guardia J, Gomez J
J Virol. 1997 Feb;71(2):1732-4.
A conserved RNA structure within the HCV IRES eIF3-binding site.
Collier AJ, Gallego J, Klinck R, Cole PT, Harris SJ, Harrison GP, Aboul-Ela F, Varani G, Walker S
Nat Struct Biol. 2002 May;9(5):375-80.
Conserved functional domains and a novel tertiary interaction near the pseudoknot drive translational activity of hepatitis C virus and hepatitis C virus-like internal ribosome entry sites.
Easton LE, Locker N, Lukavsky PJ
Nucleic Acids Res. 2009 Sep;37(16):5537-49. doi: 10.1093/nar/gkp588. Epub 2009 Jul 13.
Positional effect of mutations in 5'UTR of hepatitis C virus 4a on patients' response to therapy.
El Awady MK, Azzazy HM, Fahmy AM, Shawky SM, Badreldin NG, Yossef SS, Omran MH, Zekri AR, Goueli SA
World J Gastroenterol. 2009 Mar 28;15(12):1480-6.
HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove.
Filbin ME, Kieft JS
RNA. 2011 Jul;17(7):1258-73. doi: 10.1261/rna.2594011. Epub 2011 May 23.
Molecular and bioinformatic evidence of hepatitis C virus evolution in brain.
Fishman SL, Murray JM, Eng FJ, Walewski JL, Morgello S, Branch AD
J Infect Dis. 2008 Feb 15;197(4):597-607. doi: 10.1086/526519.
Identification of unique hepatitis C virus quasispecies in the central nervous system and comparative analysis of internal translational efficiency of brain, liver, and serum variants.
Forton DM, Karayiannis P, Mahmud N, Taylor-Robinson SD, Thomas HC
J Virol. 2004 May;78(10):5170-83.
Complete 5' noncoding region is necessary for the efficient internal initiation of hepatitis C virus RNA.
Fukushi S, Katayama K, Kurihara C, Ishiyama N, Hoshino FB, Ando T, Oya A
Biochem Biophys Res Commun. 1994 Mar 15;199(2):425-32.
Selection of different 5' untranslated region hepatitis C virus variants during post-transfusion and post-transplantation infection.
Gallegos-Orozco JF, Arenas JI, Vargas HE, Kibler KV, Wilkinson JK, Nowicki M, Radkowski M, Nasseri J, Rakela J, Laskus T
J Viral Hepat. 2006 Jul;13(7):489-98.
Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA.
Honda M, Brown EA, Lemon SM
RNA. 1996 Oct;2(10):955-68.
Natural variation in translational activities of the 5' nontranslated RNAs of hepatitis C virus genotypes 1a and 1b: evidence for a long-range RNA-RNA interaction outside of the internal ribosomal entry site.
Honda M, Rijnbrand R, Abell G, Kim D, Lemon SM
J Virol. 1999 Jun;73(6):4941-51.
Involvement of the 5' proximal coding sequences of hepatitis C virus with internal initiation of viral translation.
Hwang LH, Hsieh CL, Yen A, Chung YL, Chen DS
Biochem Biophys Res Commun. 1998 Nov 18;252(2):455-60.
Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA.
Ji H, Fraser CS, Yu Y, Leary J, Doudna JA
Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):16990-5. Epub 2004 Nov 24.
Characterization of mimotopes mimicking an immunodominant conformational epitope on the hepatitis C virus NS3 helicase.
Jolivet-Reynaud C, Adida A, Michel S, Deleage G, Paranhos-Baccala G, Gonin V, Battail-Poirot N, Lacoux X, Rolland D
J Med Virol. 2004 Mar;72(3):385-95.
Hepatitis C virus internal ribosome entry site (IRES) stem loop IIId contains a phylogenetically conserved GGG triplet essential for translation and IRES folding.
Jubin R, Vantuno NE, Kieft JS, Murray MG, Doudna JA, Lau JY, Baroudy BM
J Virol. 2000 Nov;74(22):10430-7.
Mutational analysis of the apical region of domain II of the HCV IRES.
Kalliampakou KI, Psaridi-Linardaki L, Mavromara P
FEBS Lett. 2002 Jan 30;511(1-3):79-84.
Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation.
Kieft JS, Zhou K, Grech A, Jubin R, Doudna JA
Nat Struct Biol. 2002 May;9(5):370-4.
Mechanism of ribosome recruitment by hepatitis C IRES RNA.
Kieft JS, Zhou K, Jubin R, Doudna JA
RNA. 2001 Feb;7(2):194-206.
The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold.
Kieft JS, Zhou K, Jubin R, Murray MG, Lau JY, Doudna JA
J Mol Biol. 1999 Sep 24;292(3):513-29.
eIF2A mediates translation of hepatitis C viral mRNA under stress conditions.
Kim JH, Park SM, Park JH, Keum SJ, Jang SK
EMBO J. 2011 May 10;30(12):2454-64. doi: 10.1038/emboj.2011.146.
A potential RNA drug target in the hepatitis C virus internal ribosomal entry site.
Klinck R, Westhof E, Walker S, Afshar M, Collier A, Aboul-Ela F
RNA. 2000 Oct;6(10):1423-31.
[Distribution of HBV genotypes in the Czech population--pilot study].
Krekulova L, Rehak V, Killoran P, Zavoral M, Riley LW
Vnitr Lek. 2004 Feb;50(2):106-11.
Genotypic and epidemiologic characteristics of hepatitis C virus infections among recent injection drug user and nonuser populations.
Krekulova L, Rehak V, Madrigal N, Johnson M, Killoran P, Riley LW
Clin Infect Dis. 2001 Oct 15;33(8):1435-8. Epub 2001 Sep 17.
Human La protein interaction with GCAC near the initiator AUG enhances hepatitis C Virus RNA replication by promoting linkage between 5' and 3' untranslated regions.
Kumar A, Ray U, Das S
J Virol. 2013 Jun;87(12):6713-26. doi: 10.1128/JVI.00525-13. Epub 2013 Apr 3.
Differential distribution and internal translation efficiency of hepatitis C virus quasispecies present in dendritic and liver cells.
Laporte J, Bain C, Maurel P, Inchauspe G, Agut H, Cahour A
Blood. 2003 Jan 1;101(1):52-7. Epub 2002 Jun 28.
Detection and sequence analysis of hepatitis B virus integration in peripheral blood mononuclear cells.
Laskus T, Radkowski M, Wang LF, Nowicki M, Rakela J
J Virol. 1999 Feb;73(2):1235-8.
Cell type-specific enhancement of hepatitis C virus internal ribosome entry site-directed translation due to 5' nontranslated region substitutions selected during passage of virus in lymphoblastoid cells.
Lerat H, Shimizu YK, Lemon SM
J Virol. 2000 Aug;74(15):7024-31.
HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly.
Locker N, Easton LE, Lukavsky PJ
EMBO J. 2007 Feb 7;26(3):795-805. Epub 2007 Jan 25.
Selection of genetic variants of the 5' noncoding region of hepatitis C virus occurs only in patients responding to interferon alpha therapy.
Lu M, Wiese M, Roggendorf M
J Med Virol. 1999 Oct;59(2):146-53.
Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function.
Lukavsky PJ, Otto GA, Lancaster AM, Sarnow P, Puglisi JD
Nat Struct Biol. 2000 Dec;7(12):1105-10.
Role of the 5'-proximal stem-loop structure of the 5' untranslated region in replication and translation of hepatitis C virus RNA.
Luo G, Xin S, Cai Z
J Virol. 2003 Mar;77(5):3312-8.
Seven nucleotide changes characteristic of the hepatitis C virus genotype 3 5' untranslated region: correlation with reduced in vitro replication.
Masante C, Mahias K, Lourenco S, Dumas E, Cahour A, Trimoulet P, Fleury H, Astier-Gin T, Ventura M
J Gen Virol. 2008 Jan;89(Pt 1):212-21.
Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region.
Moratorio G, Martinez M, Gutierrez MF, Gonzalez K, Colina R, Lopez-Tort F, Lopez L, Recarey R, Schijman AG, Moreno MP, Garcia-Aguirre L, Manascero AR, Cristina J
Virol J. 2007 Aug 2;4:79.
Translation efficiencies of the 5'-untranslated region of genotypes 1a and 3a in hepatitis C infected patients.
Motazakker M, Preikschat P, Elliott J, Smith CA, Mills PR, Oien K, Spence E, Elliott RM, McCruden EA
J Med Virol. 2007 Mar;79(3):259-69.
Odreman-Macchioli et al., 2001
Mutational analysis of the different bulge regions of hepatitis C virus domain II and their influence on internal ribosome entry site translational ability.
Odreman-Macchioli F, Baralle FE, Buratti E
J Biol Chem. 2001 Nov 9;276(45):41648-55. Epub 2001 Aug 9.
A mutational shift from domain III to II in the internal ribosome entry site of hepatitis C virus after interferon-ribavirin therapy.
Ogata K, Kashiwagi T, Iwahashi J, Hara K, Honda H, Ide T, Kumashiro R, Kohara M, Sata M, Watanabe H, Hamada N
Arch Virol. 2008;153(8):1575-9. doi: 10.1007/s00705-008-0143-5. Epub 2008 Jul 1.
The pathway of HCV IRES-mediated translation initiation.
Otto GA, Puglisi JD
Cell. 2004 Oct 29;119(3):369-80.
Characterizing the function and structural organization of the 5' tRNA-like motif within the hepatitis C virus quasispecies.
Piron M, Beguiristain N, Nadal A, Martinez-Salas E, Gomez J
Nucleic Acids Res. 2005 Mar 8;33(5):1487-502. Print 2005.
Nucleotide polymorphisms in the 5'-UTR region of HCV can affect the ability of two widely used assays to assign an HCV genotype.
Pollicita M, Cento V, Paba P, Perno CF, Ciotti M
J Virol Methods. 2013 Oct;193(1):205-8. doi: 10.1016/j.jviromet.2013.06.002. Epub 2013 Jun 19.
Mutational analysis of a conserved tetraloop in the 5' untranslated region of hepatitis C virus identifies a novel RNA element essential for the internal ribosome entry site function.
Psaridi L, Georgopoulou U, Varaklioti A, Mavromara P
FEBS Lett. 1999 Jun 18;453(1-2):49-53.
La protein binding at the GCAC site near the initiator AUG facilitates the ribosomal assembly on the hepatitis C virus RNA to influence internal ribosome entry site-mediated translation.
Pudi R, Srinivasan P, Das S
J Biol Chem. 2004 Jul 16;279(29):29879-88. Epub 2004 May 10.
Stem-loop structures II-IV of the 5' untranslated sequences are required for the expression of the full-length hepatitis C virus genome.
Qi ZT, Kalkeri G, Hanible J, Prabhu R, Bastian F, Garry RF, Dash S
Arch Virol. 2003 Mar;148(3):449-67.
Analysis of the 5'UTR of HCV genotype 3 grown in vitro in human B cells, T cells, and macrophages.
Revie D, Alberti MO, Prichard JG, Kelley AS, Salahuddin SZ
Virol J. 2010 Jul 13;7:155. doi: 10.1186/1743-422X-7-155.
Almost the entire 5' non-translated region of hepatitis C virus is required for cap-independent translation.
Rijnbrand R, Bredenbeek P, van der Straaten T, Whetter L, Inchauspe G, Lemon S, Spaan W
FEBS Lett. 1995 May 29;365(2-3):115-9.
Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites.
Rijnbrand R, Thiviyanathan V, Kaluarachchi K, Lemon SM, Gorenstein DG
J Mol Biol. 2004 Oct 29;343(4):805-17.
Internal initiation of translation efficiency in different hepatitis C genotypes isolated from interferon treated patients.
Saiz JC, Lopez de Quinto S, Ibarrola N, Lopez-Labrador FX, Sanchez-Tapias JM, Rodes J, Martinez-Salas E
Arch Virol. 1999;144(2):215-29.
Flow cytometric assay using two fluorescent proteins for the function of the internal ribosome entry site of hepatitis C virus.
Shi G, Yagyu F, Shimizu Y, Shimizu K, Oshima M, Iwamoto A, Gao B, Liu W, Gao GF, Kitamura Y
Cytometry A. 2011 Aug;79(8):653-60. doi: 10.1002/cyto.a.21094. Epub 2011 Jun 27.
Quasispecies heterogeneity and constraints on the evolution of the 5' noncoding region of hepatitis C virus (HCV): relationship with HCV resistance to interferon-alpha therapy.
Soler M, Pellerin M, Malnou CE, Dhumeaux D, Kean KM, Pawlotsky JM
Virology. 2002 Jun 20;298(1):160-73.
Alterations to both the primary and predicted secondary structure of stem-loop IIIc of the hepatitis C virus 1b 5' untranslated region (5'UTR) lead to mutants severely defective in translation which cannot be complemented in trans by the wild-type 5'UTR sequence.
Tang S, Collier AJ, Elliott RM
J Virol. 1999 Mar;73(3):2359-64.
Lack of clinical significance of variability in the internal ribosome entry site of hepatitis C virus.
Thelu MA, Drouet E, Hilleret MN, Zarski JP
J Med Virol. 2004 Mar;72(3):396-405.
IRES complexity before IFN-alpha treatment and evolution of the viral load at the early stage of treatment in peripheral blood mononuclear cells from chronic hepatitis C patients.
Thelu MA, Leroy V, Ramzan M, Dufeu-Duchesne T, Marche P, Zarski JP
J Med Virol. 2007 Mar;79(3):242-53.
Mutational analysis of two unstructured domains of the 5' untranslated region of HCV RNA.
Varaklioti A, Georgopoulou U, Kakkanas A, Psaridi L, Serwe M, Caselmann WH, Mavromara P
Biochem Biophys Res Commun. 1998 Dec 30;253(3):678-85.
Hepatitis C virus quasispecies in plasma and peripheral blood mononuclear cells of treatment naive chronically infected patients.
Vera-Otarola J, Barria MI, Leon U, Marsac D, Carvallo P, Soza A, Lopez-Lastra M
J Viral Hepat. 2009 Sep;16(9):633-43. doi: 10.1111/j.1365-2893.2009.01112.x. Epub 2009 Feb 25.
An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region.
Wang C, Le SY, Ali N, Siddiqui A
RNA. 1995 Jul;1(5):526-37.
A conserved helical element is essential for internal initiation of translation of hepatitis C virus RNA.
Wang C, Sarnow P, Siddiqui A
J Virol. 1994 Nov;68(11):7301-7.
Nucleotide sequence variations in the internal ribosome entry site of hepatitis C virus-1b: no association with efficacy of interferon therapy or serum HCV-RNA levels.
Yamamoto C, Enomoto N, Kurosaki M, Yu SH, Tazawa J, Izumi N, Marumo F, Sato C
Hepatology. 1997 Dec;26(6):1616-20.
Correlation between translation efficiency and outcome of combination therapy in chronic hepatitis C genotype 3.
Yasmeen A, Hamid S, Granath FN, Lindstrom H, Elliott RM, Siddiqui AA, Persson MA
J Viral Hepat. 2006 Feb;13(2):87-95.
Genetic variations in a well conserved 5'-untranslated region of hepatitis C virus genome isolated in Pakistan.
Yasmeen A, Siddiqui AA, Hamid S, Sultana T, Jafri W, Persson MA
J Virol Methods. 2009 Sep;160(1-2):38-47. doi: 10.1016/j.jviromet.2009.04.007. Epub 2009 May 3.
A single nucleotide insertion in the 5'-untranslated region of hepatitis C virus leads to enhanced cap-independent translation.
Zhang J, Yamada O, Ito T, Akiyama M, Hashimoto Y, Yoshida H, Makino R, Masago A, Uemura H, Araki H
Virology. 1999 Sep 1;261(2):263-70.
Genetic analysis of a poliovirus/hepatitis C virus chimera: new structure for domain II of the internal ribosomal entry site of hepatitis C virus.
Zhao WD, Wimmer E
J Virol. 2001 Apr;75(8):3719-30.
Evolution of naturally occurring 5' non-translated region variants of hepatitis C virus genotype 1b in selectable replicons.
van Leeuwen HC, Reusken CB, Roeten M, Dalebout TJ, Riezu-Boj JI, Ruiz J, Spaan WJ
J Gen Virol. 2004 Jul;85(Pt 7):1859-66.
