title: Analysis of HCV quasispecies dynamic under selective pressure of combined therapy.
abstract: BACKGROUND
  The quasispecies composition of Hepatitis C virus (HCV) could have important implications with regard to viral persistence and response to interferon-based therapy. The complete NS5A was analyzed to evaluate whether the composition of NS5A quasispecies of HCV 1a/1b is related to responsiveness to combined interferon pegylated (PEG-IFN) and ribavirin therapy.
  
  
  METHODS
  Viral RNA was isolated from serum samples collected before, during and after treatment from virological sustained responder (SVR), non-responder (NR) and the end-of-treatment responder patients (ETR). NS5A region was amplified, cloned and sequenced. Six hundred and ninety full-length NS5A sequences were analyzed.
  
  
  RESULTS
  This study provides evidence that lower nucleotide diversity of the NS5A region pre-therapy is associated with viral clearance. Analysis of samples of NRs and the ETRs time points showed that genetic diversity of populations tend to decrease over time. Post-therapy population of ETRs presented higher genetic distance from baseline probably due to the bottleneck phenomenon observed for those patients in the end of treatment. The viral effective population of those patients also showed a strong decrease after therapy. Otherwise, NRs demonstrated a continuous variation or stability of effective populations and genetic diversity over time that did not seem to be related to therapy. Phylogenetic relationships concerning complete NS5A sequences obtained from patients did not demonstrate clustering associated with specific response patterns. However, distinctive clustering of pre/post-therapy sequences was observed. In addition, the evolution of quasispecies over time was subjected to purifying or relaxed purifying selection. Codons 157 (P03), 182 and 440 (P42), 62 and 404 (P44) were found to be under positive selective pressure but it failed to be related to the therapy.
  
  
  CONCLUSIONS
  These results confirm the hypothesis that a relationship exists between NS5A heterogeneity and response to therapy in patients infected with chronic hepatitis C.
authors: Departament of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University, São José do Rio Preto, SP, Brazil.
authors: Ana C G
authors: AC
authors: Jardim
authors: Cíntia
authors: C
authors: Bittar
authors: Renata P A
authors: RP
authors: Matos
authors: Lílian H T
authors: LH
authors: Yamasaki
authors: Rafael A
authors: RA
authors: Silva
authors: João R R
authors: JR
authors: Pinho
authors: Roberta M
authors: RM
authors: Fachini
authors: Claudia M A
authors: CM
authors: Carareto
authors: Isabel M V G
authors: IM
authors: de Carvalho-Mello
authors: Paula
authors: P
authors: Rahal
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D000998:Antiviral Agents / Q000627:therapeutic use*; D016000:Cluster Analysis; D019143:Evolution, Molecular; D005260:Female; D016174:Hepacivirus / Q000145:classification / Q000187:drug effects* / Q000235:genetics; D019698:Hepatitis C, Chronic / Q000097:blood / Q000188:drug therapy / Q000821:virology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008954:Models, Biological; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D012367:RNA, Viral / Q000097:blood; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D017361:Viral Nonstructural Proteins / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
chemical_list: D000998:Antiviral Agents; D012367:RNA, Viral; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase
references: Dig Dis Sci. 2006 May;51(5):960-7
references: 16758308
references: J Virol. 1999 Apr;73(4):2938-46
references: 10074143
references: Semin Liver Dis. 2005 Feb;25(1):72-83
references: 15731999
references: J Infect Dis. 2009 Sep 15;200(6):866-76
references: 19673650
references: J Gen Virol. 2005 Apr;86(Pt 4):1067-1075
references: 15784900
references: Trends Microbiol. 1999 Oct;7(10):402-10
references: 10498948
references: J Gen Virol. 2010 May;91(Pt 5):1183-8
references: 20089799
references: J Virol. 2004 Jul;78(14):7400-9
references: 15220413
references: Curr Opin Genet Dev. 2002 Dec;12(6):688-94
references: 12433583
references: J Med Virol. 1998 Apr;54(4):256-64
references: 9557291
references: Hepatol Res. 2004 Jun;29(2):89-96
references: 15163430
references: J Gen Virol. 1998 Jun;79 ( Pt 6):1373-81
references: 9634077
references: PLoS One. 2010 Nov 30;5(11):e14132
references: 21152430
references: J Virol. 2008 Oct;82(19):9417-24
references: 18667493
references: World J Gastroenterol. 2007 May 7;13(17):2416-26
references: 17552024
references: J Virol. 2005 Mar;79(5):3187-94
references: 15709040
references: Genome Res. 1998 Mar;8(3):195-202
references: 9521923
references: BMC Infect Dis. 2010 Feb 23;10:36
references: 20178583
references: J Med Virol. 2001 Jan;63(1):8-16
references: 11130893
references: J Virol. 1998 Apr;72(4):2795-805
references: 9525599
references: PLoS Pathog. 2008 Mar 28;4(3):e1000035
references: 18369481
references: J Hepatol. 1997 Jan;26(1):6-13
references: 9148023
references: J Clin Invest. 1995 Jul;96(1):224-30
references: 7542279
references: Infect Genet Evol. 2009 Jul;9(4):689-98
references: 19063998
references: BMC Evol Biol. 2007 Nov 08;7:214
references: 17996036
references: J Biol Chem. 2004 Nov 19;279(47):48576-87
references: 15339921
references: Proc Natl Acad Sci U S A. 1990 Sep;87(17):6547-9
references: 2168552
references: Clin Liver Dis. 1999 Nov;3(4):693-716, vii
references: 11291246
references: J Clin Microbiol. 2007 Apr;45(4):1102-12
references: 17287328
references: Hepatology. 2005 Oct;42(4):962-73
references: 16149085
references: J Virol. 2000 Oct;74(19):9028-38
references: 10982347
references: J Biol Chem. 2004 Sep 24;279(39):40835-43
references: 15247283
references: Lancet. 2001 Sep 22;358(9286):958-65
references: 11583749
references: Genome Res. 1998 Mar;8(3):186-94
references: 9521922
references: Gene. 1996 Dec 5;182(1-2):203-11
references: 8982089
references: J Virol. 2004 May;78(9):4617-27
references: 15078944
references: Arch Virol. 2010 Dec;155(12):1977-87
references: 20842394
references: Genet Mol Res. 2008 Sep 30;7(3):970-81
references: 18949714
references: Mol Biol Evol. 1998 May;15(5):568-73
references: 9580986
references: J Hepatol. 2009 May;50(5):861-71
references: 19307038
references: World J Gastroenterol. 2007 May 7;13(17):2461-6
references: 17552030
references: J Clin Microbiol. 2005 Feb;43(2):750-4
references: 15695675
references: Bioinformatics. 1998;14(9):817-8
references: 9918953
references: Comput Appl Biosci. 1997 Oct;13(5):555-6
references: 9367129
references: Gut. 2004 Sep;53(9):1345-51
references: 15306598
references: Clin Liver Dis. 2003 Feb;7(1):45-66
references: 12691458
references: J Viral Hepat. 1999 Sep;6(5):343-56
references: 10607250
references: Virology. 2000 May 10;270(2):476-87
references: 10793006
references: J Virol. 1992 May;66(5):3225-9
references: 1313927
references: Mol Biol Evol. 2007 Aug;24(8):1596-9
references: 17488738
references: Curr Top Microbiol Immunol. 2006;299:51-82
references: 16568896
references: Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):3081-6
references: 11880647
references: Gastroenterology. 2000 Dec;119(6):1649-55
references: 11113086
references: N Engl J Med. 2002 Sep 26;347(13):975-82
references: 12324553
references: N Engl J Med. 1996 Jan 11;334(2):77-81
references: 8531962
references: Rev Med Virol. 2002 Jul-Aug;12(4):221-38
references: 12125014
references: J Clin Pharmacol. 2004 Jan;44(1):20-9
references: 14681338
references: Genome Res. 1998 Mar;8(3):175-85
references: 9521921
references: Bioinformatics. 2005 Mar 1;21(5):676-9
references: 15509596
references: Virol J. 2007 Feb 14;4:16
references: 17300723
references: Antiviral Res. 2003 Jun;59(1):1-11
references: 12834855
references: Science. 1989 Apr 21;244(4902):359-62
references: 2523562
references: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references: 9396791
references: PLoS One. 2008 Aug 26;3(8):e3058
references: 18725975
references: J Gastroenterol. 2005 Jan;40(1):43-51
references: 15692788
references: J Biol Chem. 2002 Mar 8;277(10):8130-9
references: 11744739