Bayesian Coalescent Analysis of the Intra-Host Evolution of Hepatitis C Virus: Memory Genomes and Clinical Implications

DOI: 10.4236/ns.2014.69061   PDF   HTML   XML   6,063 Downloads   7,242 Views  


Genetic variability plays a key role in the biology and medical treatment of RNA viruses. As an RNA virus, Hepatitis C virus (HCV) replicate as complex distributions of closely related genomes termed viral quasispecies. The behavior of the evolving HCV quasispecies population is influenced by the ensemble of mutants that compose the viral population. One such influence is the presence of minority subpopulations, termed memory genomes, in the mutant spectra. Biologically relevant mutants have been previously observed to be present as memory genomes in RNA viral populations. For that reason, an in-depth analysis of HCV quasispecies populations is crucial for our understanding viral evolution, drug resistance and therapy outcome. Recently developed next-generation sequencing (NGS) platforms make it possible to investigate viral quasispecies at much greater detail. In order to gain insight into these matters, we have performed a Bayesian coalescent analysis of hypervariable region 1 (HVR1) sequences of a HCV quasispecies population circulating in a chronic patient, recently obtained by ultra-deep sequencing. The results of these studies revealed a mean rate of evolution of HCV HVR1 of the intra-host quasispecies population of 4.80 × 10-2 amino acid substitutions/site/year. A sharp and rapid diversification of the HCV quasispecies isolated from the patient in three different sub-populations was observed. The most abundant sequence in the quasispecies population was not found to be the center of a tight and complex network around this sequence, suggesting that the quasispecies population as a whole efficiently explore a wide sequence space. Co-evolution of relevant amino acid sites had been identified in the HVR1. This speaks of the possible roll of these residues in HVR1 to allow the virus to shift between combinations of residues to escape the immune system while retaining its structure and functions. The results of these studies highlight the importance of minority genomes in HCV population history and evolution, the mutant clouds as reservoirs of phenotypic and genetic variants for virus adaptability, as well as the roll of the mutant spectra to overcome selective constraints.

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Recarey, R. and Cristina, J. (2014) Bayesian Coalescent Analysis of the Intra-Host Evolution of Hepatitis C Virus: Memory Genomes and Clinical Implications. Natural Science, 6, 615-627. doi: 10.4236/ns.2014.69061.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Lemon, S.M., Walker, C.M., Alter, M.J. and Yi, M. (2007) Hepatitis C Virus. In: Knipe, D.M. and Howley, P.M., Eds., Fields Virology, Vol. 1, Lippincott Williams & Wilkings, Philadelphia, 1253-1304.
[2] Alter, M.J. (2007) Epidemiology of Hepatitis C Virus Infection. World Journal of Gastroenterology, 13, 2436-2441.
[3] Lavanchy, D. (2011) Evolving Epidemiology of Hepatitis C Virus. Clinical Microbiology and Infection, 17, 107-115.
[4] Farci, P., Alter, H.J., Wong, D., Miller, R.H., Shih, J.W., Jett, B. and Purcell, R.H. (1991) A Long-Term Study of Hepatitis C Virus Replication in Non-A, Non-B Hepatitis. New England Journal of Medicine, 325, 98-104.
[5] Moradpour, D., Penin, F. and Rice, C.M. (2007) Replication of Hepatitis C Virus. Nature Review Microbiolology, 5, 453-463.
[6] Martell, M., Esteban, J.I., Quer, J., Genescà, J., Weiner, A., Esteban, R., Guardia, J. and Gómez, J. (1992) Hepatitis C Virus (HCV) Circulates as a Population of Different But Closely Related Genomes: Quasispecies Nature of HCV Genome Distribution. Journal of Virology, 66, 3225-3229.
[7] Pawlotsky, J.M. (2006) Hepatitis C Virus Population Dynamics during Infection. Current Topical Microbiology Immunology, 299, 261-284.
[8] Forns, X., Purcell, R.H. and Bukh, J. (1999) Quasispecies in Viral Persistence and Pathogenesis of Hepatitis C Virus. Trends in Microbiology, 7, 402-410.
[9] Rong, L., Dahari, H., Ribeiro, R.M. and Perelson, A.S. (2010) Rapid Emergence of Protease Inhibitor Resistance in Hepatitis C Virus. Science Translational Medicine, 2, 30-32.
[10] Ray, S.C., Fanning, L., Wang, X.H., Netski, D.M., Kenny-Walsh, E. and Thomas, D.L. (2005) Divergent and Convergentevolution after a Common-Source Outbreak of Hepatitis C Virus. Journal of Experimental Medicine, 201, 17531759.
[11] Domingo, E., Martin, V., Perales, C., Grande-Pérez, A., García-Arriaza, J. and Arias, A. (2006) Viruses as Quasispecies: Biological Implications. Current Topics in Microbiology and Immunology, 299, 51-82.
[12] Briones, C. and Domingo, E. (2008) Minority Report: Hidden Memory Genomes in HIV-1 Quasispecies and Possible Clinical Implications. AIDS Review, 10, 93-109.
[13] Forns, X., Purcell, R.H. and Bukh, J. (1999) Quasispecies in Viral Persistence and Pathogenesis of Hepatitis C Virus. Trends in Microbiology, 7, 402-410.
[14] Hong, S.K., Cho, S.I., Ra, E.K., Kim, E.C., Park, J.S., Park, S.S. and Seong, M.W. (2012) Evaluation of Two Hepatitis C Virus Genotyping Assays Based on the 5’-Untranslated Region: The Limitations of 5’UTR Based Assays and the Need for a Supplementary Sequencing-Based Approach. Journal of Clinical Microbiology, 50, 3741-3743.
[15] Ramachandran, S., Campo, D.S., Dimitrova, Z.E., Xia, G.L., Purdy, M.A. and Khudyakov, Y.E. (2011) Temporal Variations in the Hepatitis C Virus Intrahostpopulation during Chronic Infection. Journal of Virology, 85, 6369-6380.
[16] Vizmanos, J.L., Gonzalez-Navarro, C.J., Novo, F.J., Civeira, M.P., Prieto, J., Gullon, A. and Garcia-Delgado, M. (1998) Degree and Distribution of Variability in the 5’Untranslated, E1, E2/NS1 and NS5 Regions of the Hepatitis C Virus (HCV). Journal of Viral Hepatitis, 5, 227-240.
[17] Guan, M., Wang, W., Liu, X., Tong, Y., Liu, Y. et al. (2012) Three Different Functional Microdomains in the Hepatitis C Virus Hypervariable Region 1 (HVR1) Mediate Entry and Immune Evasion. The Journal of Biological Chemistry, 287, 35631-35645.
[18] Saludes,V., Bascunana, E., Jordana-Lluch, E., Casanovas, S., Ardevol, M. et al.(2013) Relevance of Baseline Viral Genetic Heterogeneity and Host Factors for Treatment Outcome Prediction in Hepatitis C Virus 1b-Infected Patients. PLoS ONE, 8, e72600.
[19] Schijman, A., Colina, R., Mukomolov, S., Kalinina, O., García, L., Broor, S. et al. (2004) Comparison of Hepatitis C Viral Loads in Patients with or without Coinfection with Different Genotypes. Clinical and Diagnostic Laboratory Immunology, 11, 433-435.
[20] Cristina, J., Moreno, M.P. and Moratorio, G. (2007) Hepatitis C Virus Genetic Variability in Patients Undergoing Antiviral Therapy. Virus Research, 127, 185-194.
[21] Bittar, C., Gomes-Jardim, A.C., Tomonari, L.H., Carareto, C.M., Rebello, J.R. and Lemey, P. (2013) On Hepatitis C Virus Evolution: The Interaction between Virus and Host towards Treatment Outcome. PLoS ONE, 8, e62393.
[22] Kamila Caraballo-Cortés, K., Zagordi O., Laskus , T., Poski R.,Bukowska-Osko, I., Pawelczyk, A. et al.(2013) Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis. BioMed Research International, 2013, 626083.
[23] Barzon, L., Lavezzo, E., Militello, V., Toppo, S. and Palu, G. (2011) Applications of Next-Generation Sequencing Technologies to Diagnostic Virology. International Journal of Molecular Sciences, 12, 7861-7884.
[24] Beerenwinkel, N. (2011) Ultra-Deep Sequencing for the Analysis of Viral Populations. Current Opinion in Virology, 1, 413-418.
[25] Gregori, J., Esteban, J.I, Cubero, M., Garcia-Cehic, D., Perales, C., Casillas, R., et al. (2013) Ultra-Deep Pyrosequencing (UDPS) Data Treatment to Study Amplicon HCV Minor Variants. PLoS ONE, 8, e83361.
[26] Di Lorenzo,C., Angus, A.G. and Patel, A.H. (2011) Hepatitis C Virus Evasion Mechanisms from Neutralizing Antibodies. Viruses, 3, 2280-2300.
[27] Guglietta, S., Garbuglia, A.R., Pacciani, V., Scotta, C., Perrone, M.P., Laurenti, L., et al. (2005) Positive Selection of Cytotoxic T Lymphocyte Escape Variants during Acute Hepatitis C Virus Infection. European Journal of Immunology, 35, 2627-2637.
[28] Zagordi, O., Bhattacharya, A., Eriksson, N. and Beerenwinkel, N. (2011) ShoRAH: Estimating the Genetic Diversity of a Mixed Sample from Next-Generation Sequencing Data. BMC Bioinformatics, 12, 119.
[29] 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. Molecular Biology and Evolution, 28, 2731-2739.
[30] Delport, W., Poon, A.F., Frost, S.D. and Kosakovsky-Pond, S.L. (2010) Datamonkey 2010: A Suite of Phylogenetic Analysis Tools for Evolutionary Biology. Bioinformatics, 26, 2455-2457.
[31] Drummond, A.J., Rambaut, A., Shapiro, B. and Pybus, O.G. (2005) Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences. Molecular Biology and Evolution, 22, 1185-1192.
[32] Drummond, A.J. and Rambaut, A. (2007) BEAST: Bayesian Evolutionary Analysis by Sampling Trees. BMC Evolutionary Biology, 7, 214.
[33] Stadler, T., Kühnert, D., Bonhoeffer, S. and Drummond, A.J. (2013) Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV).Proceedings of the National Academy of Science USA, 110, 228-233.
[34] Stadler, T. (2011) Mammalian phylogeny reveals recent diversification rate shifts. Proceedings of the National Academy of Science USA, 108, 6187-6192.
[35] Stadler, T. (2010) Sampling-Through-Time in Birth-Death Trees. Journal of Theoretical Biology, 267, 396-404.
[36] Stadler, T., Kouyos, R., von Wyl, V., Yerly, S., Boni, J., Burgisser, P., et al. (2012) Estimating the Basic Reproductive Number from Viral Sequence Data. Molecular Biology and Evolution, 29, 347-357.
[37] Bouckaert, R. (2010) DensiTree: Making Sense of Sets of Phylogenetic Trees. Bioinformatics, 26, 1372-1373.
[38] Bandelt, H.J., Forster, P. and Rohl, A. (1999) Median-Joining Networks for Inferring Intraspecific Phylogenies. Molecular Biology and Evolution, 16, 37-48.
[39] Poon, A.F.Y., Lewis, F.I., Kosakovsky-Pond, S.L. and Frost, S.D.W. (2007) An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope. PLOS Computational Biology, 3, e231.
[40] Offman, M.N., Tournier, A.L. and Bates, P.A. (2008) Alternating Evolutionary Pressure in a Genetic Algorithm Facilities Protein Model Selection. BMC Structural Biology, 8, 34.
[41] Hanson, R.M. (2010) Jmol—A Paradigm Shift in Crystallographic Visualization. Journal of Applied Crystallography, 43, 1250-1260.
[42] Drummond, A.J., Ho, S.Y.W., Phillips, M.J. and Rambaut, A. (2006) Relaxed Phylogenetics and Dating with Confindence. PLoS Biology, 4, e88.
[43] Guan, M., Wang, W., Lui, X., Tong, Y., Liu, Y., Ren, H., et al. (2012) Three Different Functional Microdomains in the Hepatitis C Virus Hypervariable Region 1 (HVR1) Mediate Entry and Immune Evasion. The Journal of Biological Chemistry, 287, 35631-35645.
[44] van Doorn, L. J., Capriles, I., Maertens, G., DeLeys, R., Murray, K., Kos, T., Schellekens, H. and Quint, W. (1995) Sequence Evolution of the Hypervariable Region in the Putative Envelope Region E2/NS1 of Hepatitis C Virus Is Correlated with Specific Humoral Immune Responses. Journal of Virology, 69, 773-778.
[45] Dowd, K.A., Netski, D.M., Wang, X.H., Cox, A.L. and Ray, S.C. (2009) Selection Pressure from Neutralizing Antibodies Drives Sequence Evolution during Acute Infection with Hepatitis C Virus. Gastroenterology, 136, 2377-2386.
[46] Liu, L., Fisher, B.E., Dowd, K.A., Astemborski, J., Cox, A.L. and Ray, S.C. (2010) Acceleration of Hepatitis C Virus Envelope Evolution in Humans Is Consistent with Progressive Humoral Immune Selection during the Transition from Acute to Chronic Infection. Journal of Virology, 84, 5067-5077.
[47] Domingo, E. (2007) Virus Evolution. In: Knipe, D.M. and Howley, P.M., Eds., Fields Virology, 5th Edition, Lippincott Williams & Wilkins, Philadelphia, 389-421.
[48] Lutchman, G., Danehower, S., Song, B.C., Liang, T.J., Hoofnagle, J.H., et al. (2007) Mutation Rate of the Hepatitis C Virus NS5B in Patients Undergoing Treatment with Ribavirin Monotherapy. Gastroenterology, 132, 1757-1766.
[49] Abe, H., Hayes, C.N., Hiraga, N., Imamura, M., Tsuge, M., et al.(2013) A Translational Study of the Resistance Emergence Using Sequenctial Direct-Acting Antiviral Agents for Hepatitis C Using Ultra-Deep Sequencing. American Journal of Gastroenterology, 108, 1464-1472.
[50] Jackowiak, P., Kuls, K., Budzko, L., Mania, A., Figlerowicz, M., et al. (2014) Phylogeny and Molecular Evolution of Hepatitis C Virus. Infection, Genetics and Evolution, 21, 67-82.
[51] Drummond, A.J., Suchard, M.A., Xie, D. and Rambaut, A. (2012) Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969-1973.
[52] Gray, R.R., Parker, J., Lemey, P., Salemi, M., Katzourakis, A., et al. (2011) The Mode and Tempo of Hepatitis C Virus Evolution within and among Hosts. BMC Evolutionary Biology, 11, 131.
[53] Campo, D.S., Dimitrova, Z., Mitchell, R.J., Lara, J. and Khudyakov, Y. (2008) Coordinated Evolution of the Hepatitis C Virus. Proceedings of the National Academy of Science USA, 105, 9685-9690.
[54] Ramachandran, S., Campo, D.S., Dimitrova, Z.E., Xia, G.L., Purdy, M.A. and Khudyakov, Y.E. (2011) Temporal Variations in the Hepatitis C Virus Intrahost Population during Chronic Infection. Journal of Virology, 85, 6369-6380.
[55] Domingo, E., Sheldon, J. and Perales, C. (2012) Viralquasispecies Evolution. Microbiology and Molecular Biology Review, 76, 159-216.
[56] Escobar-Gutierrez, A., Soudeyns, H., Larouche, A., Carpio-Pedroza, J., Martinez-Gaurneros, A., et al.(2013) Vertical Transmission of Hepatitis C Virus: A Tale of Multiple Outcomes. Infection, Genetics and Evolution, 20, 465-470.
[57] Poon, A.F.Y., Lewis, F., Frost, S.D.W. and Kosakovsky-Pond, S.L. (2008) Spidermonkey: Rapid Detection of CoEvolving Sites Using Bayesian Graphical Models. Bioinformatics, 24, 1949-1950.
[58] Bankwitz, D., Steinmann, E., Bitzegeio, J., Ciesek, S., Friesland, M., et al. (2010) Hepatitis C Virus Hypervariableregion 1 Modulates Receptor Interactions, Conceals the CD81-Binding Site, and Protects Conserved Neutralizing Epitopes. Journal of Virology, 84, 5751-5763.
[59] Kwong, A.D., Najera, I., Bechtel, J., Bowden, S., Fitzgibbon, J., et al. (2011) Sequence and Phenotypic Analysis for Resistance Monitoring in Hepatitis C Virus Drug Development: Recommendations from the HCV DRAG. Gastroenterology, 140, 755-760.

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