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Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response

Cíntia Bittar1, Ana Carolina G Jardim1, Lilian HT Yamasaki1, Artur TL de Queiróz2, Claudia MA Carareto1, João Renato R Pinho34, Isabel Maria VG de Carvalho-Mello5* and Paula Rahal1

Author Affiliations

1 UNESP, São Paulo State University, IBILCE, Institute of Bioscience, Language & Literature and Exact Science, Department of Biology, Rua Cristóvão Colombo, 2265 , Bairro Jardim Nazareth, CEP 15054-010, São José do Rio Preto, São Paulo, Brazil

2 USP, São Paulo University, Rua do Matão, trav 14, n° 321, Cidade Universitária, CEP 05508-900, São Paulo, São Paulo, Brazil

3 USP, São Paulo University, Faculty of Medicine, Department of Gastroenterology, Laboratory of Hepatology and Gastroenterology from Institute of Tropical Medicine, Av Dr Arnaldo, 455, Cerqueira César, CEP: 01246903, São Paulo, SP, Brazil

4 Albert Einstein Israeli Hospital, Department of Clinical Pathology, Av Albert Einstein, 627/701, CEP 05652-000São Paulo, SP, Brazil

5 Butantan Institute, Viral Immunology Laboratory, Av Vital Brasil n° 1500, CEP 05503-900, Butantã, São Paulo, SP, Brazil

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BMC Infectious Diseases 2010, 10:36  doi:10.1186/1471-2334-10-36

Published: 23 February 2010



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.


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.


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.


Our study provides an overview of the genetic variability of complete NS5A protein in HCV genotype 3a.