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Respirology pp 11–23Cite as

Next-Generation Sequencing of 5′ Untranslated Region of Hepatitis C Virus in Search of Minor Viral Variant in a Patient Who Revealed New Genotype While on Antiviral Treatment

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Part of the book series: Advances in Experimental Medicine and Biology ((NR,volume 885))

Abstract

The role of mixed infections with different hepatitis C virus (HCV) genotypes in viral persistence, treatment effects, and tissue tropism is unclear. Next-generation sequencing (NGS), which is suitable for analysis of large, genetically diverse populations offers unparalleled advantages for the study of mixed infections. The aim of the study was to determine, using two different deep sequencing strategies (pyrosequencing – 454 Life Sciences/Roche and reversible terminator sequencing-by-synthesis by Illumina), the origin of a novel HCV genotype transiently detectable during antiviral therapy (pre-existing minor population vs. de novo superinfection). Secondly, we compared 5′ untranslated region (5′-UTR) variants obtained by the two NGS approaches. 5′ UTR amplification products from 9 samples collected from genotype 1b infected patient before, during, and after treatment (4 serum and 5 peripheral blood mononuclear cell – PBMC – samples) were subjected to the next-generation sequencing. The sequencing revealed the presence of two (454/Roche) and one (Illumina) genotype 4 variants in PBMC at Week 16. None of these variants were present either in the preceding or following samples as revealed by both platforms. 454/Roche sequencing detected 24 different 5’-UTR variants: 8 were present in serum and PBMC, 4 only in serum and 12 only in PBMC. Illumina sequencing detected 11 different 5’-UTR variants: 5 in serum and PBMC, 4 only in serum and 2 only in PBMC. Six variants were identical for both sequencing platforms. The difference in variants number was primarily due to variability in two 5’-UTR homopolymeric regions. In conclusion, longitudinal analysis of HCV variants, employing two independent deep sequencing methods, suggests that the transient presence of a different genotype strain in PBMC was a result of superinfection and not a selection of pre-existing minor variant.

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Acknowledgements

This work was supported by the projects from Polish National Science Center NN 401646740 and 1 M24/PM12/12.

Conflicts of Interest

The authors declare no conflicts of interest in relation to this article.

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Authors and Affiliations

  1. Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3c Pawińskiego St., 02-106, Warsaw, Poland

    Kamila Caraballo Cortes, Iwona Bukowska-Ośko, Agnieszka Pawełczyk, Karol Perlejewski, Tomasz Laskus & Marek Radkowski

  2. Department of Medical Genetics, Warsaw Medical University, 3c Pawińskiego St., 02-106, Warsaw, Poland

    Rafał Płoski

  3. Department of Genetics, Institute of Physiology and Pathology of Hearing, 10 Mochnackiego St., 02-042, Warsaw, Poland

    Urszula Lechowicz & Piotr Stawiński

  4. Department of Laboratory Medicine and Clinical Immunology of Developmental Age, Warsaw Medical University, 24 Marszałkowska St., 00-576, Warsaw, Poland

    Urszula Demkow

Authors
  1. Kamila Caraballo Cortes
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  2. Iwona Bukowska-Ośko
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  3. Agnieszka Pawełczyk
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  5. Rafał Płoski
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  6. Urszula Lechowicz
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  7. Piotr Stawiński
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  8. Urszula Demkow
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  9. Tomasz Laskus
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  10. Marek Radkowski
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Correspondence to Iwona Bukowska-Ośko .

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Editors and Affiliations

  1. Institute of Nursing, Public Higher Medical Professional Schoo, Opole, Poland

    Mieczyslaw Pokorski

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© 2015 Springer International Publishing Switzerland

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Caraballo Cortes, K. et al. (2015). Next-Generation Sequencing of 5′ Untranslated Region of Hepatitis C Virus in Search of Minor Viral Variant in a Patient Who Revealed New Genotype While on Antiviral Treatment. In: Pokorski, M. (eds) Respirology. Advances in Experimental Medicine and Biology(), vol 885. Springer, Cham. https://doi.org/10.1007/5584_2015_186

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