Deep sequencing of hepatitis C virus hypervariable region 1 reveals no correlation between genetic heterogeneity and antiviral treatment outcome

BMC Infectious Diseases

Research Article

Karol Perlejewski¹  Krzysztof Maroszek¹  Iwona Bukowska-Ośko¹  Marek Radkowski¹  Tomasz Laskus¹  Kamila Caraballo Cortés¹  Agnieszka Pawełczyk¹  Rafał Płoski²  Hanna Berak³  Andrzej Horban⁴  Osvaldo Zagordi⁵ 

[1] Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3c Pawińskiego Street, 02-106, Warsaw, Poland;Department of Medical Genetics, Medical University of Warsaw, 3c Pawińskiego Street, 02-106, Warsaw, Poland;Hospital for Infectious Diseases, 37 Wolska Street, 01-201, Warsaw, Poland;Hospital for Infectious Diseases, 37 Wolska Street, 01-201, Warsaw, Poland;Clinics of Infectious Diseases, Medical University of Warsaw, 37 Wolska Street, 01-201, Warsaw, Poland;Institute of Medical Virology, University of Zurich, Winterthurerstrasse, 190 8057, Zurich, Switzerland;

关键词: Hypervariable region 1;    Ultra-deep sequencing;    Treatment;    Genetic heterogeneity;    Hepatitis C virus;    Quasispecies;    Pyrosequencing;   

DOI  :  10.1186/1471-2334-14-389

 received in 2014-03-10, accepted in 2014-07-07,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundHypervariable region 1 (HVR1) contained within envelope protein 2 (E2) gene is the most variable part of HCV genome and its translation product is a major target for the host immune response. Variability within HVR1 may facilitate evasion of the immune response and could affect treatment outcome. The aim of the study was to analyze the impact of HVR1 heterogeneity employing sensitive ultra-deep sequencing, on the outcome of PEG-IFN-α (pegylated interferon α) and ribavirin treatment.MethodsHVR1 sequences were amplified from pretreatment serum samples of 25 patients infected with genotype 1b HCV (12 responders and 13 non-responders) and were subjected to pyrosequencing (GS Junior, 454/Roche). Reads were corrected for sequencing error using ShoRAH software, while population reconstruction was done using three different minimal variant frequency cut-offs of 1%, 2% and 5%. Statistical analysis was done using Mann–Whitney and Fisher’s exact tests.ResultsComplexity, Shannon entropy, nucleotide diversity per site, genetic distance and the number of genetic substitutions were not significantly different between responders and non-responders, when analyzing viral populations at any of the three frequencies (≥1%, ≥2% and ≥5%). When clonal sample was used to determine pyrosequencing error, 4% of reads were found to be incorrect and the most abundant variant was present at a frequency of 1.48%. Use of ShoRAH reduced the sequencing error to 1%, with the most abundant erroneous variant present at frequency of 0.5%.ConclusionsWhile deep sequencing revealed complex genetic heterogeneity of HVR1 in chronic hepatitis C patients, there was no correlation between treatment outcome and any of the analyzed quasispecies parameters.

【 授权许可】

Unknown   
© Carabello Cortés et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.