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

J Infect Dis
Authors
Keywords
Abstract

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.

Year of Publication
2013
Journal
J Infect Dis
Volume
208
Issue
1
Pages
17-31
Date Published
2013 Jul
ISSN
1537-6613
URL
DOI
10.1093/infdis/jis679
PubMed ID
23136221
PubMed Central ID
PMC3666132
Links
Grant list
HHSN272200900018C / 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