Within-host dynamics of the hepatitis C virus quasispecies population in HIV-1/HCV coinfected patients

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Bernini, Flavia ^a   Ebranati, Erika ^a   De Maddalena, Chiara ^a   Shkjezi, Renata ^a   Milazzo, Laura ^a   Presti, Alessandra Lo ^b   Ciccozzi, Massimo ^b   Galli, Massimo ^a   Zehender, Gianguglielmo ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; GLYCOPROTEIN E1; GLYCOPROTEIN E2;

ADULT; ARTICLE; CD4 LYMPHOCYTE COUNT; CLINICAL ARTICLE; CONTROLLED STUDY; EVOLUTIONARY ADAPTATION; FEMALE; GENE SEQUENCE; GENOTYPE; HEPATITIS C; HEPATITIS C VIRUS; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOREACTIVITY; MALE; MICROBIAL POPULATION DYNAMICS; MIXED INFECTION; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROBABILITY; PROSPECTIVE STUDY; SEQUENCE ANALYSIS; VIRUS CELL INTERACTION; VIRUS REPLICATION; BAYES THEOREM; COMORBIDITY; DRUG EFFECT; EVOLUTION; GENETIC SELECTION; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNE SYSTEM; IMMUNOLOGY;

HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; BAYES THEOREM; BIOLOGICAL EVOLUTION; COMORBIDITY; HEPACIVIRUS; HEPATITIS C; HIV INFECTIONS; HIV-1; HUMANS; IMMUNE SYSTEM; PHYLOGENY; PROSPECTIVE STUDIES; SELECTION, GENETIC;

EID: 79551617719     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016551     Document Type: Article

References (57)

1. Eigen M (1971) Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58: 465-523.
2. Farci P, Purcell RH (2000) Clinical significance of hepatitis C virus genotypes and quasispecies. Semin Liver Dis 20: 103-126.
3. Pawlotsky JM, Tsakiris L, Roudot-Thoraval F, Pellet C, Stuyver L, et al. (1995) Relationship between hepatitis C virus genotypes and sources of infection in patients with chronic hepatitis C. J Infect Dis 171: 1607-1610.
4. Ray SC, Wang YM, Laeyendecker O, Ticehurst JR, Villano SA, et al. (1999) Acute hepatitis C virus structural gene sequences as predictors of persistent viremia: hypervariable region 1 as a decoy. J Virol 73: 2938-2946.
5. Allain JP, Dong Y, Vandamme AM, Moulton V, Salemi M (2000) Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response: studies of infected donor-recipient clusters. J Virol 74: 2541-2549.
6. McAllister J, Casino C, Davidson F, Power J, Lawlor E, et al. (1998) Long-term evolution of the hypervariable region of hepatitis C virus in a common-sourceinfected cohort. J Virol 72: 4893-4905.
7. Booth JC, Kumar U, Webster D, Monjardino J, Thomas HC (1998) Comparison of the rate of sequence variation in the hypervariable region of E2/NS1 region of hepatitis C virus in normal and hypogammaglobulinemic patients. Hepatology 27: 223-227.
8. Toyoda H, Fukuda Y, Koyama Y, Takamatsu J, Saito H, et al. (1997) Effect of immunosuppression on composition of quasispecies population of hepatitis C virus in patients with chronic hepatitis C coinfected with human immunodeficiency virus. J Hepatol 26: 975-982.
9. Valdez H, Chowdhry TK, Asaad R, Woolley IJ, Davis T, et al. (2001) Changing spectrum of mortality due to human immunodeficiency virus: analysis of 260 deaths during 1995-1999. Clin Infect Dis 32: 1487-1493.
10. Babik JM, Holodniy M (2003) Impact of highly active antiretroviral therapy and immunologic status on hepatitis C virus quasispecies diversity in human immunodeficiency virus/hepatitis C virus-coinfected patients. J Virol 77: 1940-1950.
11. Blackard JT, Yang Y, Bordoni P, Sherman KE, Chung RT (2004) Hepatitis C virus (HCV) diversity in HIV-HCV-coinfected subjects initiating highly active antiretroviral therapy. J Infect Dis 189: 1472-1481.
12. Solmone M, Girardi E, Lalle E, Abbate I, D'Arminio Monforte A, et al. (2006) Evolution of HVR-1 quasispecies after 1-year treatment in HIV/HCVcoinfected patients according to the pattern of response to highly active antiretroviral therapy. Antivir Ther 11: 87-94.
13. Laskus T, Wilkinson J, Karim R, Mack W, Radkowski M, et al. (2007) Hepatitis C virus quasispecies in HIV-infected women: role of injecting drug use and highly active antiretroviral therapy (HAART). Hepatology 46: 359-370.
14. Shuhart MC, Sullivan DG, Bekele K, Harrington RD, Kitahata MM, et al. (2006) HIV infection and antiretroviral therapy: effect on hepatitis C virus quasispecies variability. J Infect Dis 193: 1211-1218.
15. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
16. Kingman JF (2000) Origins of the coalescent. 1974-1982. Genetics 156: 1461-1463.
17. Pybus OG, Rambaut A, Harvey PH (2000) An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155: 1429-1437.
18. Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, et al. (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303: 327-332.
19. Kosakovsky Pond SL, Frost SD (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22: 1208-1222.
20. Salemi M, Lamers SL, Huysentruyt LC, Galligan D, Gray RR, et al. (2009) Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma. PLoS One 4: e8153.
21. Salemi M, Lamers SL, Yu S, de Oliveira T, Fitch WM, et al. (2005) Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J Virol 79: 11343-11352.
22. Zehender G, Meroni L, De Maddalena C, Varchetta S, Monti G, et al. (1997) Detection of hepatitis C virus RNA in CD19 peripheral blood mononuclear cells of chronically infected patients. J Infect Dis 176: 1209-1214.
23. Zehender G, De Maddalena C, Bernini F, Ebranati E, Monti G, et al. (2005) Compartmentalization of hepatitis C virus quasispecies in blood mononuclear cells of patients with mixed cryoglobulinemic syndrome. J Virol 79: 9145-9156.
24. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
25. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
26. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
27. Kumar S, Tamura K, Nei M (1994) MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput Appl Biosci 10: 189-191.
28. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.
29. Suchard MA, Weiss RE, Sinsheimer JS (2001) Bayesian selection of continuoustime Markov chain evolutionary models. Mol Biol Evol 18: 1001-1013.
30. Pond SL, Frost SD, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
31. Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16: 1315-1328.
32. Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
33. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD (2006) GARD: a genetic algorithm for recombination detection. Bioinformatics 22: 3096-3098.
34. Qurishi N, Kreuzberg C, Luchters G, Effenberger W, Kupfer B, et al. (2003) Effect of antiretroviral therapy on liver-related mortality in patients with HIV and hepatitis C virus coinfection. Lancet 362: 1708-1713.
35. Marine-Barjoan E, Saint-Paul MC, Pradier C, Chaillou S, Anty R, et al. (2004) Impact of antiretroviral treatment on progression of hepatic fibrosis in HIV/ hepatitis C virus co-infected patients. AIDS 18: 2163-2170.
36. Chung RT, Evans SR, Yang Y, Theodore D, Valdez H, et al. (2002) Immune recovery is associated with persistent rise in hepatitis C virus RNA, infrequent liver test flares, and is not impaired by hepatitis C virus in co-infected subjects. AIDS 16: 1915-1923.
37. Vento S, Garofano T, Renzini C, Casali F, Ferraro T, et al. (1998) Enhancement of hepatitis C virus replication and liver damage in HIVcoinfected patients on antiretroviral combination therapy. AIDS 12: 116-117.
38. Laskus T, Radkowski M, Wang LF, Vargas H, Rakela J (1998) The presence of active hepatitis C virus replication in lymphoid tissue in patients coinfected with human immunodeficiency virus type 1. J Infect Dis 178: 1189-1192.
39. Holmes EC (2008) Evolutionary history and phylogeography of human viruses. Annu Rev Microbiol 62: 307-328.
40. Abe K, Inchauspe G, Fujisawa K (1992) Genomic characterization and mutation rate of hepatitis C virus isolated from a patient who contracted hepatitis during an epidemic of non-A, non-B hepatitis in Japan. J Gen Virol 73(Pt 10): 2725-2729.
41. Brown RJ, Juttla VS, Tarr AW, Finnis R, Irving WL, et al. (2005) Evolutionary dynamics of hepatitis C virus envelope genes during chronic infection. J Gen Virol 86: 1931-1942.
42. Christie JM, Chapel H, Chapman RW, Rosenberg WM (1999) Immune selection and genetic sequence variation in core and envelope regions of hepatitis C virus. Hepatology 30: 1037-1044.
43. Curran R, Jameson CL, Craggs JK, Grabowska AM, Thomson BJ, et al. (2002) Evolutionary trends of the first hypervariable region of the hepatitis C virus E2 protein in individuals with differing liver disease severity. J Gen Virol 83: 11-23.
44. Kato N, Ootsuyama Y, Ohkoshi S, Nakazawa T, Sekiya H, et al. (1992) Characterization of hypervariable regions in the putative envelope protein of hepatitis C virus. Biochem Biophys Res Commun 189: 119-127.
45. Duffy M, Salemi M, Sheehy N, Vandamme AM, Hegarty J, et al. (2002) Comparative rates of nucleotide sequence variation in the hypervariable region of E1/E2 and the NS5b region of hepatitis C virus in patients with a spectrum of liver disease resulting from a common source of infection. Virology 301: 354-364.
46. Smith DB (1999) Evolution of the hypervariable region of hepatitis C virus. J Viral Hepat 6(Suppl 1): 41-46.
47. Zeisel MB, Fafi-Kremer S, Fofana I, Barth H, Stoll-Keller F, et al. (2007) Neutralizing antibodies in hepatitis C virus infection. World J Gastroenterol 13: 4824-4830.
48. Krey T, d'Alayer J, Kikuti CM, Saulnier A, Damier-Piolle L, et al. (2010) The disulfide bonds in glycoprotein E2 of hepatitis C virus reveal the tertiary organization of the molecule. PLoS Pathog 6: e1000762.
49. Rosa D, Campagnoli S, Moretto C, Guenzi E, Cousens L, et al. (1996) A quantitative test to estimate neutralizing antibodies to the hepatitis C virus: cytofluorimetric assessment of envelope glycoprotein 2 binding to target cells. Proc Natl Acad Sci U S A 93: 1759-1763.
50. Sheridan I, Pybus OG, Holmes EC, Klenerman P (2004) High-resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression. J Virol 78: 3447-3454.
51. Cuevas JM, Gonzalez M, Torres-Puente M, Jimenez-Hernandez N, Bracho MA, et al. (2009) The role of positive selection in hepatitis C virus. Infect Genet Evol 9: 860-866.
52. Dubuisson J (2007) Hepatitis C virus proteins. World J Gastroenterol 13: 2406-2415.
53. Callens N, Ciczora Y, Bartosch B, Vu-Dac N, Cosset FL, et al. (2005) Basic residues in hypervariable region 1 of hepatitis C virus envelope glycoprotein e2 contribute to virus entry. J Virol 79: 15331-15341.
54. Bartosch B, Verney G, Dreux M, Donot P, Morice Y, et al. (2005) An interplay between hypervariable region 1 of the hepatitis C virus E2 glycoprotein, the scavenger receptor BI, and high-density lipoprotein promotes both enhancement of infection and protection against neutralizing antibodies. J Virol 79: 8217-8229.
55. Bartosch B, Vitelli A, Granier C, Goujon C, Dubuisson J, et al. (2003) Cell entry of hepatitis C virus requires a set of co-receptors that include the CD81 tetraspanin and the SR-B1 scavenger receptor. J Biol Chem 278: 41624-41630.
56. Scarselli E, Ansuini H, Cerino R, Roccasecca RM, Acali S, et al. (2002) The human scavenger receptor class B type I is a novel candidate receptor for the hepatitis C virus. EMBO J 21: 5017-5025.
57. Felsenstein J (2006) Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Mol Biol Evol 23: 691-700.