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Next-Generation Sequencing of Hepatitis C Virus (HCV) Mixed-Genotype Infections in Anti-HCV-Negative Blood Donors

  • Maciej Janiak
  • Kamila Caraballo Cortés
  • Karol Perlejewski
  • Dorota Kubicka-Russel
  • Piotr Grabarczyk
  • Urszula Demkow
  • Marek Radkowski
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1096)

Abstract

The infection with more than one hepatitis C virus (HCV) genotype especially in subjects with a high risk of multiple HCV exposures has been demonstrated. The role of HCV mixed-genotype infection in viral persistence and treatment effect is not fully understood. The prevalence of such infection varies greatly depending on the technique used for genotype determination and studied population. Next-generation sequencing (NGS) which is suitable for extensive analysis of complex viral populations is a method of choice for studying mixed infections. The aim of the present study was to determine the prevalence of mixed-genotype HCV infections in the Polish seronegative, HCV-RNA-positive blood donors (n = 76). Two-step PCR was used for amplification of 5′-UTR of HCV. Using pyrosequencing altogether, 381,063 reads were obtained. The raw reads were trimmed and subjected to similarity analysis against the entire unfiltered NCBI nt database. Results obtained from NGS were compared with the standard genotyping. One (1.3%) mixed-genotype [3a, 2989 reads (94.8%); 1b, 164 reads (5.2%)] infection was found in a sample diagnosed as genotype 3a only by routine testing. Two samples were identified with different genotypes, compared to routine testing. In conclusion, NGS is a sensitive method for HCV genotyping. The prevalence of mixed-genotype HCV infections in blood donors is low.

Keywords

Blood donors HCV genotyping HCV mixed-genotype infections Hepatitis C virus Next-generation sequencing Pyrosequencing 

Notes

Acknowledgments

The study was supported by National Science Center grant No. 238240.

Conflicts of Interest

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

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Maciej Janiak
    • 1
  • Kamila Caraballo Cortés
    • 1
  • Karol Perlejewski
    • 1
  • Dorota Kubicka-Russel
    • 2
  • Piotr Grabarczyk
    • 2
  • Urszula Demkow
    • 3
  • Marek Radkowski
    • 1
  1. 1.Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
  2. 2.Department of VirologyInstitute of Hematology and Transfusion MedicineWarsawPoland
  3. 3.Department of Laboratory Medicine and Clinical Immunology of Developmental AgeMedical University of WarsawWarsawPoland

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