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

BMC Infectious Diseases

Marek Radkowski⁴  Andrzej Horban⁵  Hanna Berak¹  Rafał Płoski²  Agnieszka Pawełczyk⁴  Iwona Bukowska-Ośko⁴  Krzysztof Maroszek⁴  Tomasz Laskus⁴  Karol Perlejewski⁴  Osvaldo Zagordi³  Kamila Caraballo Cortés⁴ 

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

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

Others  :  1127366
DOI  :  10.1186/1471-2334-14-389

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

【 摘 要 】

Background

Hypervariable 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.

Methods

HVR1 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.

Results

Complexity, 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%.

Conclusions

While 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】

   
2014 Carabello Cortés et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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