Navegar

Colección

Datos Estadísticas

Artículo

Moratorio, G.; Martínez, M.; Gutiérrez, M.F.; González, K.; Colina, R.; López-Tort, F.; López, L.; Recarey, R.; Schijman, A.G.; Moreno, M.P.; García-Aguirre, L.; Manascero, A.R.; Cristina, J. "Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region" (2007) Virology Journal. 4
Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

Background. Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America. Methods. Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program. Results. Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region. Conclusion. Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations. © 2007 Moratorio et al; licensee BioMed Central Ltd.

Registro:

Documento: Artículo
Título:Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
Autor:Moratorio, G.; Martínez, M.; Gutiérrez, M.F.; González, K.; Colina, R.; López-Tort, F.; López, L.; Recarey, R.; Schijman, A.G.; Moreno, M.P.; García-Aguirre, L.; Manascero, A.R.; Cristina, J.
Filiación:Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Cra 7 # 43-82 Ed 50 of 313, Bogotá, Colombia
Facultad de Ciencias Médicas Y Bioquímicas, Universidad Mayor de San Andrés, Av. Villazón No. 1995 Monoblock Central, La Paz, Bolivia
Laboratorio de Biología Molecular, Grupo CentraLab, Buenos Aires, Argentina
Instituto de Investigaciones en Ingeniería Genética Y Biología Molecular, Vuelta de Obligado 2490, 1428 Buenos Aires, Argentina
Department of Biochemistry, McGill Cancer Center, McGill University, Montreal, Que. H3G 1Y6, Canada
Palabras clave:untranslated RNA; article; Bolivia; Colombia; controlled study; genetic analysis; genetic distance; genetic line; genotype; Hepatitis C virus; molecular evolution; neighbor joining method; nonhuman; nucleotide sequence; phylogeny; RNA structure; South America; unindexed sequence; Uruguay; virus isolation; virus strain; 5' untranslated region; adult; aged; chemistry; child; female; gene frequency; genetic variability; genetics; hepatitis C; human; male; middle aged; molecular evolution; virology; Hepatitis C virus; 5' Untranslated Regions; Adult; Aged; Child; Colombia; Evolution, Molecular; Female; Gene Frequency; Hepacivirus; Hepatitis C, Chronic; Humans; Male; Middle Aged; Phylogeny; Uruguay; Variation (Genetics)
Año:2007
Volumen:4
DOI: http://dx.doi.org/10.1186/1743-422X-4-79
Título revista:Virology Journal
Título revista abreviado:Virol. J.
ISSN:1743422X
CAS:5' Untranslated Regions
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_1743422X_v4_n_p_Moratorio

Referencias:

  • Simmonds, P., Bukh, J., Combet, C., Deleage, G., Enomoto, N., Feinstone, S., Halfon, P., Widell, A., Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes (2005) Hematology, 42, pp. 962-973
  • Simmonds, P., Genetic diversity and evolution of hepatitis C virus 15 years on (2004) J Gen Virol, 85, pp. 3173-3188. , 10.1099/vir.0.80401-0. 15483230
  • Hoofnagle, J.H., Course and outcome of hepatitis C (2002) Hepatology, 36, pp. 21-S29. , 10.1002/hep.1840360704. 12407573
  • Pawlotski, J.M., The nature of interferon-alfa resistance in hepatitis C virus infection (2003) Curr Opin Infect Dis, 16, pp. 587-592. , 10.1097/00001432-200312000-00012. 14624110
  • You, S., Stump, D.D., Branch, A.D., Rice, C.M., A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication (2004) J Virol, 78, pp. 1352-1366. , 14722290. 10.1128/JVI.78.3.1352-1366.2004
  • Pestova, T.V., Shatsky, I.N., Fletcher, S.P., Jackson, R.J., Hellen, C.U.T., A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binging to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs (1998) Genes Dev, 12, p. 6783
  • Cristina, J., Genetic diversity and evolution of hepatitis C virus in the Latin American region (2005) J Clin Virol, 34, pp. 1-S7. , 10.1016/S1386-6532(05)00393-8. 16461234
  • Gismondi, M.I., Becker, P.D., Valva, P., Guzman, C.A., Preciado, M.V., Phylogenetic analysis of previously nontypeable Hepatitis C virus isolates from Argentina (2006) J Cin Microbiol, 44, pp. 2229-2232. , 10.1128/JCM.02569-05
  • Gismondi, M.I., Staendner, L.H., Grinstein, S., Guzman, C.A., Preciado, M.V., Hepatitis C virus isolates from Argentina disclose a novel genotype 1-associated restriction pattern (2004) J Clin Microbiol, 42, pp. 1298-12301. , 15004102. 10.1128/JCM.42.3.1298-1301.2004
  • San Roman, M., Lezama, L., Rojas, E., Colina, R., Garcia, L., Carlos, A., Khan, B., Cristina, J., Analysis of genetic heterogeneity of hepatitis C viruses in Central America reveals a novel genetic lineage (2002) Arch Virol, 147, pp. 2239-2246. , 10.1007/s00705-002-0869-4. 12417958
  • Vega, I., Colina, R., García, L., Uriarte, R., Mogdasy, C., Cristina, J., Diversification of hepatitis C viruses in South America reveals a novel genetic lineage (2001) Arch Virol, 146, pp. 1623-1629. , 10.1007/s007050170084. 11676423
  • Colina, R., Azambuja, C., Uriarte, R., Mogdasy, C., Cristina, J., Evidence of increasing diversification of hepatitis C viruses (1999) J Gen Virol, 80, pp. 1377-1382. , 10374954
  • Felsenstein, J., (1993) Phylogeny Interference Package, Version 3.5, , Department of Genetics, University of Washington, Seattle, U.S.A
  • Kuiken, C., Yusim, K., Boykin, L., Richardon, R., The HCV Sequence Database (2005) Bioinformatics, 21, pp. 379-384. , 10.1093/bioinformatics/bth485. 15377502
  • Rijnbrand, R.C., Lemon, S.M., Internal ribosome entry site-mediated translation in hepatitis C replication (2000) Curr Top Microbiol Immunol, 242, pp. 85-116. , 10592657
  • Van Leeuwen, H.C., Reusken, C.B., Roeten, M., Dalebout, T.J., Riezu-Boj, J.I., Ruiz, J., Spaan, W.J., Evolution of naturally occurring 5'non-translated region variants of hepatitis C virus genotype 1b in selectable replicons (2004) J Gen Virol, 85, pp. 1859-1866. , 10.1099/vir.0.79924-0. 15218170
  • Yepes, A., Alvarez, C., Restrepo, J.C., Correa, G., Zapata, J.C., [Viral genotypes in patients with hepatitis C virus infection in Medellin] [Article in Spanish] (2002) Gastroenterol Hepatol, 25, pp. 334-335. , 11985808
  • Biswas, S., Sanyal, A., Hemadri, D., Tosh, C., Mohapatra, J.K., Manoj, R., Bandyopadhvav, S.K., Sequence analysis of non-structural 3A and 3C protein-coding regions of foot-and-mouth disease virus serotype Asia 1 field isolates from an endemic country (2006) Vet Microbiol, 116, pp. 187-193. , 10.1016/j.vetmic.2006.03.001. 16621341
  • Pistello, M., Del Santo, B., Butto, S., Bargagna, M., Domenici, R., Bendinelli, M., Genetic and phylogenetic analyses of HIV-1 corroborate the transmission link hypothesis (2004) J Clin Virol, 30, pp. 11-18. , 10.1016/j.jcv.2003.08.008. 15072748
  • Burke, B., Derby, N.R., Kraft, Z., Sauders, C.J., Dai, C., Llewellyn, N., Zharkikh, I., Stamatatos, L., Viral evolution in macaques coinfected with CCR5-and CXCR4-tropic SHIVs in the presence or absence of vaccine-elicited anti-CCR5 SHIV neutralizing antibodies (2006) Virology, 355, pp. 138-151. , 10.1016/j.virol.2006.07.026. 16920175
  • Soares, M.A., De Oliveira, T., Brindeiro, R.M., Diaz, R.S., Sabino, E.C., Brigido, L., Pires, I.L., Tanuri, A., A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil (2003) AIDS, 17, pp. 11-21. , 10.1097/00002030-200301030-00004. 12478065
  • Chambers, T.J., Fan, X., Droll, D.A., Hembrador, E., Slater, T., Nickells, M.W., Dustin, L.B., Dibisceglie, A.M., Quasispecies heterogeneity within the E1/E2 region as a pretreatment variable during pegylated interferon therapy of chronic hepatitis C virus infection (2005) J Virol, 79, pp. 3071-3083. , 15709027. 10.1128/JVI.79.5.3071-3083.2005
  • Domingo, E., Antiviral strategy on the horizon (2005) Virus Res, 107, pp. 115-116. , 10.1016/j.virusres.2004.11.001
  • Feliu, A., Gay, E., Garcia-Retortillo, M., Saiz, J.C., Foms, X., Evolution of hepatitis C virus quasispecies immediately following liver transplantation (2004) Liver Transpl, 10, pp. 1131-1139. , 10.1002/lt.20206. 15350003
  • Laskus, T., Wilkinson, J., Gallegos-Orozco, J.F., Radkowski, M., Adair, D.M., Nowicki, M., Operskalski, E., Rakela, J., Analysis of hepatitis C virus quasispecies transmission and evolution in patients infected through blood transfusion (2004) Gastroenterology, 127, pp. 764-776. , 10.1053/j.gastro.2004.06.005. 15362033
  • Lu, M., Kruppenbacher, J., Roggendorf, M., The importance of the quasispecies nature of hepatitis C virus (HCV) for the evolution of HCV populations in patients: Study on a single source outbreak of HCV infection Arch Virol, 145, pp. 2201-2210. , 10.1007/s007050070050. 11087102
  • Laporte, J., Bain, C., Maurel, P., Inchauspe, G., Agut, H., Cahour, A., Differential distribution and internal translation efficiency of hepatitis C virus quasispecies present in dendritic and livel cells (2003) Blood, 101, pp. 52-57. , 10.1182/blood-2002-03-0818. 12393733
  • Laporte, J., Malet, I., Andrieu, T., Comparative analysis of translation efficiencies of hepatitis C virus 5' untranslated regions among intraindividual quasispecies present in chronic infection: Opposite behaviours depending on cell type (2000) J Virol, 74, pp. 10827-10833. , 11044132. 10.1128/JVI.74.22.10827-10833.2000
  • Lerat, H., Shimizu, Y.K., Lemon, S.M., 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 (2000) J Virol, 74, pp. 7024-7031. , 10888641. 10.1128/JVI.74.15.7024-7031.2000
  • Kurreck, J., Antisense technologies. Improvement through novel chemical modifications (2003) Eur J Biochem, 270, pp. 1628-1644. , 10.1046/j.1432-1033.2003.03555.x. 12694176
  • Chan, S.W., McOmish, F., Holmes, E.C., Dow, B., Peutherer, J.F., Follett, E., Yap, P.L., Simmonds, P., Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants (1991) J Gen Virol, 73, pp. 1131-1141
  • Davidson, F., Simmonds, P., Ferguson, J.C., Jarvis, L.M., Dow, B.C., Follett, E.A., Seed, C.R., Madyuesi, G.A., Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5' non-coding regions (1995) J Gen Virol, 76, pp. 1197-1204. , 7730804
  • Kwok, S., Higuchi, R., Avoiding false positives with PCR (1989) Nature, 339, pp. 237-238. , 10.1038/339237a0. 2716852
  • Thompson, J.D., Higgins, D.G., Gibson, T.J., CLUSTAL W: Improvingthe sensitivity of progressive multiple sequence alignment throughsequence weighting, position-specific gap penalties and weight matrix choice (1994) Nucleic Acid Res, 22, pp. 4673-4680. , 7984417. 10.1093/nar/22.22.4673
  • Kumar, S., Tamura, K., Nei, M., MEGA 3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment (2004) Brief Bioinformatics, 5, pp. 150-163. , 10.1093/bib/5.2.150. 15260895
  • Korber, B., Myers, G., Signature pattern analysis: A method for assessing viral sequence relatedness (1992) AIDS Res Hum Retroviruses, 8, pp. 1549-1560. , 1457200
  • http://hcv.lanl.gov/content/hcv-db/P-vespa/vespa.html; http://hcv.lanl.gov/content/hcv-db/BASIC_BLAST/basic_blast.html; Mathews, D.H., Sabina, J., Zuker, M., Turner, D.H., Expanded sequence dependence of thermodynamic parameters improve prediction of RNA secondary structure (1999) J Mol Biol, 288, pp. 911-940. , 10.1006/jmbi.1999.2700. 10329189
  • http://www.bioinfo.rpi.edu/applications/mfold

Citas:

---------- APA ----------
Moratorio, G., Martínez, M., Gutiérrez, M.F., González, K., Colina, R., López-Tort, F., López, L.,..., Cristina, J. (2007) . Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region. Virology Journal, 4.
http://dx.doi.org/10.1186/1743-422X-4-79
---------- CHICAGO ----------
Moratorio, G., Martínez, M., Gutiérrez, M.F., González, K., Colina, R., López-Tort, F., et al. "Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region" . Virology Journal 4 (2007).
http://dx.doi.org/10.1186/1743-422X-4-79
---------- MLA ----------
Moratorio, G., Martínez, M., Gutiérrez, M.F., González, K., Colina, R., López-Tort, F., et al. "Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region" . Virology Journal, vol. 4, 2007.
http://dx.doi.org/10.1186/1743-422X-4-79
---------- VANCOUVER ----------
Moratorio, G., Martínez, M., Gutiérrez, M.F., González, K., Colina, R., López-Tort, F., et al. Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region. Virol. J. 2007;4.
http://dx.doi.org/10.1186/1743-422X-4-79