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Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants

Newman, Ruchi M. ; Kuntzen, Thomas ; Weiner, Brian ; Berical, Andrew ; Charlebois, Patrick ; Kuiken, Carla ; Murphy, Donald G. ; Simmonds, Peter ; Bennett, Phil ; Lennon, Niall J. ; Birren, Bruce W. ; Zody, Michael C. ; Allen, Todd M. ; Henn, Matthew R.

In: The Journal of Infectious Diseases, 2013, vol. 208, no. 1, p. 17-31

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    Title
    • Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants
    Author
    • Newman, Ruchi M.. Broad Institute of MIT and Harvard, Cambridge
    • Kuntzen, Thomas. Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts
    • Weiner, Brian. Broad Institute of MIT and Harvard, Cambridge
    • Berical, Andrew. Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts
    • Charlebois, Patrick. Broad Institute of MIT and Harvard, Cambridge
    • Kuiken, Carla. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico
    • Murphy, Donald G.. Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Canada
    • Simmonds, Peter. Centre for Infectious Diseases, University of Edinburgh
    • Bennett, Phil. Micropathology, University of Warwick Science Park, Coventry, United Kingdom
    • Lennon, Niall J.. Broad Institute of MIT and Harvard, Cambridge
    • Birren, Bruce W.. Broad Institute of MIT and Harvard, Cambridge
    • Zody, Michael C.. Broad Institute of MIT and Harvard, Cambridge
    • Allen, Todd M.. Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts
    • Henn, Matthew R.. Broad Institute of MIT and Harvard, Cambridge
    Document Type
    • Postprint
    Language
    • English
    Published in
    • The Journal of Infectious Diseases, 2013, vol. 208, no. 1, p. 17-31. Oxford University Press
    Other Version
    OAI-PMH Identifier
    • oai:doc.rero.ch:294416
    Summary
    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