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J Infect Dis DOI:10.1093/infdis/jis679

Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.

Publication TypeJournal Article
Year of Publication2013
AuthorsNewman, RM, Kuntzen, T, Weiner, B, Berical, A, Charlebois, P, Kuiken, C, Murphy, DG, Simmonds, P, Bennett, P, Lennon, NJ, Birren, BW, Zody, MC, Allen, TM, Henn, MR
JournalJ Infect Dis
Date Published2013 Jul
KeywordsAntiviral Agents, Base Sequence, Drug Resistance, Viral, Genetic Variation, Genome, Viral, Genotype, Hepacivirus, Hepatitis C, Humans, Molecular Sequence Data, Phylogeny

BACKGROUND:  Infection with hepatitis C virus (HCV) is a burgeoning worldwide public health problem, with 170 million infected individuals and an estimated 20 million deaths in the coming decades. While 6 main genotypes generally distinguish the global geographic diversity of HCV, a multitude of closely related subtypes within these genotypes are poorly defined and may influence clinical outcome and treatment options. Unfortunately, the paucity of genetic data from many of these subtypes makes time-consuming primer walking the limiting step for sequencing understudied subtypes.

METHODS:  Here we combined long-range polymerase chain reaction amplification with pyrosequencing for a rapid approach to generate the complete viral coding region of 31 samples representing poorly defined HCV subtypes.

RESULTS:  Phylogenetic classification based on full genome sequences validated previously identified HCV subtypes, identified a recombinant sequence, and identified a new distinct subtype of genotype 4. Unlike conventional sequencing methods, use of deep sequencing also facilitated characterization of minor drug resistance variants within these uncommon or, in some cases, previously uncharacterized HCV subtypes.

CONCLUSIONS:  These data aid in the classification of uncommon HCV subtypes while also providing a high-resolution view of viral diversity within infected patients, which may be relevant to the development of therapeutic regimens to minimize drug resistance.


Alternate JournalJ. Infect. Dis.
PubMed ID23136221
PubMed Central IDPMC3666132
Grant ListHHSN272200900018C / AI / NIAID NIH HHS / United States
U19-AI082630 / AI / NIAID NIH HHS / United States
R01 AI067926 / AI / NIAID NIH HHS / United States
U19 AI082630 / AI / NIAID NIH HHS / United States
HHSN272200900006C / AI / NIAID NIH HHS / United States
R01-AI067926 / AI / NIAID NIH HHS / United States