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A case of genotype-3b hepatitis C virus in which the whole genome was successfully analyzed using third-generation

Yoshihito Uchida1, Jun-Ichi Kouyama1, Kayoko Naiki1

  • 1Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan.

Hepatology Research : the Official Journal of the Japan Society of Hepatology
|March 30, 2019
PubMed

Insights

MinION nanopore sequencing successfully determined the whole genome of a difficult-to-classify hepatitis C virus (HCV) genotype 3b strain. This advanced sequencing method is valuable for HCV subtyping when standard methods fail.

Area of Science:

  • Virology
  • Genomics
  • Next-Generation Sequencing

Background:

  • Chronic hepatitis C virus (HCV) infection requires accurate genotyping for effective antiviral therapy.
  • Standard diagnostic kits sometimes fail to subtypify specific HCV genotypes, such as genotype 3.

Observation:

  • A 42-year-old Chinese male with chronic HCV infection presented challenges for subgenotype determination using conventional methods.
  • Whole-genome sequencing of the HCV strain was performed using the MinION nanopore sequencer.

Findings:

  • The MinION platform successfully sequenced 9442 bases of the HCV genome, classifying it as genotype 3b.
  • Sequence analysis revealed nucleotide identities of 87.6%–93.9% with known genotype 3b strains.
  • No known resistance-associated substitutions in NS3, NS5A, or NS5B were detected in this strain.

Implications:

  • The MinION nanopore sequencer offers a viable solution for comprehensive HCV genome analysis, particularly for challenging subgenotypes.
  • This technology can aid in understanding HCV diversity and guiding personalized antiviral treatment strategies.
  • Improved subtyping capabilities can enhance the management of hepatitis C virus infections globally.

Keywords:
genotype 3b HCVnanopore sequencingwhole-genome sequence

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