Open Access Research article

Analysis of HCV quasispecies dynamic under selective pressure of combined therapy

Ana CG Jardim1, Cíntia Bittar1, Renata PA Matos1, Lílian HT Yamasaki1, Rafael A Silva2, João RR Pinho3, Roberta M Fachini4, Claudia MA Carareto1, Isabel MVG de Carvalho-Mello2* and Paula Rahal1

Author Affiliations

1 Departament of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University, São José do Rio Preto, SP, Brazil

2 Division of Gastroenterology Laboratory of Applied Molecular Hepatology, Hepatitis Section, Federal University of São Paulo, São Paulo, SP, Brazil

3 Departament of Gastroenterology, São Paulo Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, SP, Brazil

4 Department Hepatology, São José do Rio Preto School of Medicine, São Paulo, SP, Brazil

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BMC Infectious Diseases 2013, 13:61  doi:10.1186/1471-2334-13-61

Published: 1 February 2013

Additional files

Additional file 1:

Phylogenetic trees reconstructed from sequences obtained from patient P42 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples from patient P42 (ETR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red or pink. A sequence with nonsense mutation is colored in blue. The clade selected for selective pressure analysis is indicated by a gray line.

Format: TIFF Size: 182KB Download file

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Additional file 2:

Phylogenetic trees reconstructed from sequences obtained from patient P03 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P03 (ETR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. Sequence with nonsense mutation is colored in blue. The clade selected for selective pressure analysis is indicated by a gray line.

Format: TIFF Size: 234KB Download file

Open Data

Additional file 3:

Phylogenetic trees reconstructed from sequences obtained from patient P47 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P47 (ETR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. Sequence with nonsense mutation is colored in blue. The clades selected for selective pressure analysis are indicated by a gray line (clade 1, ω = 0.2487 and clade 2, ω = 0.7177).

Format: TIFF Size: 261KB Download file

Open Data

Additional file 4:

Phylogenetic trees reconstructed from sequences obtained from patient P37 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P37 (ETR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. Sequence with nonsense mutation is colored in blue.

Format: TIFF Size: 184KB Download file

Open Data

Additional file 5:

Phylogenetic trees reconstructed from sequences obtained from patient P11 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P11 (NR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. The clades selected for selective pressure analysis are indicated by a gray line (clade 1, ω = 0.5783 and clade 2, ω = 0.2685).

Format: TIFF Size: 215KB Download file

Open Data

Additional file 6:

Phylogenetic trees reconstructed from sequences obtained from patient P44 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P44 (NR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. Sequence with nonsense mutation is colored in blue. The clade selected for selective pressure analysis is indicated by a gray line.

Format: TIFF Size: 89KB Download file

Open Data

Additional file 7:

Phylogenetic trees reconstructed from sequences obtained from patient P146 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P146 (NR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. Sequence with nonsense mutation is colored in blue. The clade selected for selective pressure analysis is indicated by a gray line.

Format: TIFF Size: 237KB Download file

Open Data

Additional file 8:

Phylogenetic trees reconstructed from sequences obtained from patient P08 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P08 (NR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. The clade selected for selective pressure analysis is indicated by a gray line.

Format: TIFF Size: 227KB Download file

Open Data