Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response.
BACKGROUND
The quasispecies nature of HCV may have important implications for viral persistence, pathogenicity and resistance to antiviral agents. The variability of one of the viral proteins, NS5A, is believed to be related to the response to IFN therapy, the standard treatment for infection. In this study we analyzed the quasispecies composition of NS5A protein in patients infected with HCV genotype 3a, before IFN therapy.


METHODS
Viral RNA was isolated from samples of 12 patients: four sustained virological responders (SVR), four non-responders (NR), and four end-of-treatment responders (ETR). cDNA was synthesized, the NS5A region was amplified and the fragments obtained were cloned. Fifteen clones from each patient were sequenced with eight primers, generating 179 contigs.


RESULTS
Higher values for substitution (either synonymous or non-synonymous) and for distance were found in the SVR group. However, the NR group showed relatively more non-synonymous mutations than the other groups, owing to the higher values of dN/dS in complete NS5A and most specific regions. Overall, NS5A protein is undergoing purifying selection, since all dN/dS ratios values are below 0.5.


CONCLUSIONS
Our study provides an overview of the genetic variability of complete NS5A protein in HCV genotype 3a.
Bittar
Cíntia
C
Butantan Institute, Viral Immunology Laboratory, Av Vital Brasil n degrees 1500, CEP 05503-900, Butantã, São Paulo, SP, Brazil.
Jardim
Ana Carolina G
AC
Yamasaki
Lilian H T
LH
de Queiróz
Artur T L
AT
Carareto
Claudia M A
CM
Pinho
João Renato R
JR
de Carvalho-Mello
Isabel Maria V G
IM
Rahal
Paula
P
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics; D000998:Antiviral Agents / Q000627:therapeutic use*; D016000:Cluster Analysis; D014644:Genetic Variation; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D019698:Hepatitis C, Chronic / Q000188:drug therapy* / Q000821:virology*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D017354:Point Mutation; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D016896:Treatment Outcome; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase
D000998:Antiviral Agents; D012367:RNA, Viral; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase