Hepatitis C Viruses

472 Pages·2006·4.35 MB·English

by  Seng-Lai Tan

Contributors
Glen N. Barber* Jean Dubuisson*
Room 511 Papanicolau Building CNRS-UPR2511
1550 NW 10th Ave [M710] Institut de Biologie de Lille - Institut Pasteur
University of Miami School of Medicine de Lille
Miami Lille
FL 33136 France
USA
David N. Frick*
Keril J. Blight* Department of Biochemistry and Molecular
Department of Molecular Microbiology Biology
Center for Infectious Disease Research New York Medical College
Washington University School of Medicine Valhalla
660 South Euclid Ave NY 10595
Campus Box 8230 USA
St. Louis
MO 63110-1093 Jeffrey S. Glenn*
USA Division of Gastroenterology and Hepatology
Stanford University School of Medicine
D. Spencer Carney CCSR Building
Department of Digestive and Liver Diseases Room 3115
University of Texas Southwestern Medical 269 Campus Drive
Center Palo Alto
5323 Harry Hines Blvd. CA 94305-5187
Dallas TX USA
75390-9048
USA Anne Goffard
CNRS-UPR2511
Stéphane Chevaliez Institut de Biologie de Lille - Institut Pasteur
Department of Virology de Lille
INSERM U635 Lille
Henri Mondor Hospital France
University of Paris 12
Créteil David R. Gretch*
France Laboratory Medicine
Virology
Linda B. Couto Box 359690
Benitec LLC 325 9th Ave
2375 Garcia Ave Seattle
Mountain View WA 98104-2499
CA 94043 USA
USA
Xiao-Song He*
Michael Gale Jr.* VA Medical Center 154C
Department of Microbiology Building 101
University of Texas Room C4-171
Southwestern Medical Center 3801 Miranda Ave. Palo Alto
5323 Harry Hines Blvd. CA94304
Dallas TX USA
75390-9048
USA
v
Yupeng He Chao Lin*
Abbott Laboratories Department of Infectious Diseases
Abbott Park Vertex Pharmaceuticals Incorporated
IL 60064 130 Waverly Street
USA Cambridge
Massachusetts 02139
Cheng Kao USA
Department of Biochemistry and Biophysics
Texas A&M University Jaisri R. Lingappa
College Station Department of Pathobiology
TX 77843 University of Washington
USA Seattle
WA
Takanobu Kato USA
Liver Diseases Branch
NIDDK Ayaz M. Majid
National Institute of Health Department of Microbiology and Immunology
Bethesda University of Miami School of Medicine and
Maryland 20892 Sylvester Comprenhensive Cancer Center
USA Miami
Florida
Kevin C. Klein USA
Department of Pathobiology
University of Washington Tatsuo Miyamura
Seattle Department of Virology II
WA National Institute of Infectious Diseases
USA 1-23-1 Toyama
Shinjuku-ku
Alexander A. Kolykhalov* Tokyo 162-8640
Benitec LLC Japan
2375 Garcia Ave
Mountain View Elizabeth A. Norgard
CA 94043 Department of Molecular Microbiology
USA Center for Infectious Disease Research
Washington University School of Medicine
Michael M. C. Lai* 660 South Euclid Ave
University of Southern California Campus Box 8230
Keck School of Medicine St. Louis
2011 Zonal Avenue MO 63110-1093
Los Angeles USA
CA 90033
USA Arnim Pause*
McGill Cancer Center and Department of
Muriel Lavie Biochemistry
CNRS-UPR2511 McGill University
Institut de Biologie de Lille Montreal
Institut Pasteur de Lille Quebec
Lille H3G 1Y6
France Canada
vi
Jean-Michel Pawlotsky* Ella H. Sklan
Department of Virology Division of Gastroenterology and Hepatology
INSERM U635 Stanford University School of Medicine
Henri Mondor Hospital CCSR Building
University of Paris 12 Room 3115
Créteil 269 Campus Drive
France Palo Alto
CA 94305-5187
Stephen J. Polyak* USA
Department of Laboratory Medicine
Virology Division Kirk A. Staschke
Box 359690 Lilly Research Laboratories
325 9th Ave. Indianapolis
Seattle IN 46285
WA 98104-2499 USA
USA
Seng-Lai Tan*
C. T. Ranjith-Kumar* Lilly Research Laboratories
Department of Biochemistry and Biophysics Indianapolis
Texas A&M University IN 46285
College Station USA
TX 77843
USA Takaji Wakita*
Department of Microbiology
Stephanie T. Shi Tokyo Metropolitan Institute for Neuroscience
Department of Virology 2-6 Musashidai
Pfizer Inc. Fuchu
San Diego Tokyo 183-8526
CA 92121 Japan
USA
Sarah Welbourn
Ikuo Shoji McGill Cancer Center and Department of
Department of Virology II Biochemistry
National Institute of Infectious Diseases McGill University
1-23-1 Toyama Montreal
Shinjuku-ku Quebec
Tokyo 162-8640 H3G 1Y6
Japan Canada
* Corresponding author
vii
Preface
Chronic hepatitis C is a serious public health problem and a disease burden in
many parts of the world. The discovery of the causative agent, hepatitis C virus
(HCV), in 1989 has initiated an almost unparalleled research activity in academic
and pharmaceutical-industry laboratories over the ensuing years. This book aims to
provide a state-of-the-art account of recent advances in the molecular and cellular
biology, immunology and pathogenesis of HCV. It also aspires to discuss new
strategies as well as outstanding issues for future research.
Hepatitis C has been dubbed the "silent epidemic" because it is generally
asymptomatic for decades after infection; its victims often are unaware of the
infection until it is too late for therapy. What is the genetic makeup and molecular
features that make HCV such a "silent" yet deadly assassin? This question, in fact,
is the premise by which this monograph was prepared – it was an attempt to decode
the secrets of HCV, one viral gene at a time. To that end, we assembled a team of
highly regarded experts from different disciplines who have prepared 16 chapters
on various aspects of HCV, including the HCV genome and the role(s) of each
viral gene product within the context of the viral life cycle, host interactions, and
regulation of host antiviral defense and adaptive immunity.
This book can be divided into six main sections. The Introduction sets the stage by
providing an overview of the history and the significant hallmarks in the discovery,
diagnosis and initial treatments of HCV infection. In the first section, the authors
provide an overview of our present understanding of the HCV genome, the structure
and replication of these viruses (Chapter 1) and the role of the non-coding regions
of HCV in regulating HCV gene expression and RNA replication (Chapter 2).
The next two sections include in-depth reviews of the structural (Chapters 3 and
4) and nonstructural (Chapters 5-10) proteins of HCV. A major drawback in the
past has been the lack of a robust cell-culture and small-animal model system for
HCV infection and replication. However, substantial scientific progress has been
made in recent years (Chapters 11-12). Armed with these tools, we are beginning
to dissect the molecular mechanisms by which the virus disrupts the host innate
and adaptive immune response (Chapters 13 and 14), yielding novel insights into
the pathogenicity of HCV.
The final section covers the development of infectious HCV-like particle systems
(Chapter 15) and the recently developed robust in vitro HCV infection systems
based on the JFH-1strain (Chapter 16), which should greatly expedite our study
of the full viral life cycle, and our efforts to construct anti-viral strategies and
to develop effective immunization strategies with prophylactic and therapeutic
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potential. Needless to say, this is the Holy Grail of HCV research considering that
there is no vaccine available and current treatments fail in about half of HCV-
infected patients.
In the meantime, biotechnology and pharmaceutical companies are making
exciting progress in discovery and development of new drugs for HCV therapeutic
intervention. These have been the subject of many excellent recent reviews and thus
will not be covered in this book. Although it is likely to be several years before any
new drug candidate will be available as an anti-HCV agent, the clinical pipeline for
hepatitis C is starting to show promise for safer and more effective therapies.
Seng-Lai Tan, Ph.D.
Indianapolis, May 2006
x
Introduction

Introduction
David R. Gretch
When the term emerging infectious diseases is loosely applied, then chronic hepatitis
C is recognized as one of the most important new diseases afflicting man. The term
paradigm is useful when describing this disease, since the discovery, diagnosis
and initial treatments of hepatitis C virus infection are all perfect examples of the
increasing impact molecular biology is currently having on disease management
throughout the globe. The discovery of HCV in the late 1980s occurred without the
aid of conventional tissue culture or classical virological methods other than the
essential reliance of the chimpanzee model for propagation and initial definition
of the infectious agent as an enveloped RNA virus. Reverse transcription and PCR
amplification of a subgenomic fraction of the HCV genome not only lead to the
initial genetic characterization of HCV as a putative member of the Pestivirus family.
It also paved the way for development of the first diagnostic test, an enzyme linked
immunoassay that utilized recombinant HCV protein fragments to capture HCV
antibodies from patient serum and thus provide serological evidence of infection.
This critical step was a major accomplishment for molecular medicine since it
provided the first opportunity to positively identify individuals with this highly
prevalent yet clinically silent disease.
Even though it was well established from epidemiological studies that non-A,
non-B (NANB) hepatitis was efficiently transmitted by blood transfusion, and that
screening blood products for anti-hepatitis B core antibody and ALT significantly
reduced the incidence of post-transfusion NANB hepatitis, development of the first
generation HCV antibody screening assay had an impact far greater than many
medical scientists in the field had anticipated. Results of early studies indicated
that up to 10% of all units of blood transfused in the U.S. prior to the discovery of
HCV had lead to transmission of the infectious agent to recipients, accounting for
the vast majority of cases of post-transfusion NANB hepatitis, a fact that may have
been as surprising as it was fortuitous. However, this was not the whole iceberg;
world wide population-based studies revealed a global seroprevalence of well over
100 million individuals, with current estimates being frequently quoted as 170
million HCV infections today. Initial studies reported that approximately 40% of
HCV infections in the U.S. were "community acquired", with no known risk factors
for acquisition. Subsequent epidemiological studies have suggested that many of
1
Gretch
these cases were actually associated with the most important risk factor for HCV
acquisition today, namely intravenous drug use. Such studies have also led to the
identification of other previously unknown risk factors, so the term community
acquired hepatitis C is no longer in vogue. Thus, cloning of a portion of the HCV
RNA genome and development of an effective diagnostic test for HCV antibodies
unveiled the insidious disease that is so heavily researched today; this would never
have occurred without the use of molecular tools.
A second major accomplishment of molecular medicine was development and
standardization of tests that efficiently detect and characterize HCV nucleic
acids in patient blood. Use of the reverse transcription polymerase chain reaction
(RT-PCR) assay in epidemiological studies revealed that of all patients acquiring
post-transfusion hepatitis C, over 80% became chronically infected with persistent
viremia for decades if not for life. Being able to define HCV viremia in a patient
with a risk factor for infection or an asymptomatic individual with serological
evidence of exposure to HCV has become a hallmark tool for hepatitis C
management in the clinical setting from several perspectives. Confirmation of
viremia equals confirmation of active disease. Since most patients with hepatitis
C are asymptomatic, a large percentage has normal ALT levels in the blood, and
up to 20% of infections spontaneously resolve, knowing HCV infection status is
critical for defining subsequent management. Determining whether the disease is
mild, moderate or severe still requires a liver biopsy unless the patient has clinical
evidence of liver decompensation.
The ability to detect, quantify and genetically characterize HCV RNA in patients
had an irreplaceable impact on our understanding of hepatitis C disease long
before the molecular studies described in the following chapters began to unravel
the complex mysteries associated with this truly unique virus-host relationship.
Studies of HCV molecular epidemiology indicated that six distinct genotypes have
evolved over centuries throughout the world. From clinical studies we learned
that HCV persistently replicates in humans for decades, maintaining remarkably
constant serum titers that often exceed 1 million viral genomes per milliliter of
serum. Pharmacodynamic studies indicated that the HCV production rate exceeds
one trillion new virions per day in the face of active immune responses, which is
remarkable because this level of virus production is often without overt detriment
to the infected host. However, HCV continuously evolves within the host as a
pool of genetic variants termed viral quasispecies, presumably as an adaptation to
host pressure. How host pressures shape these viral quasispecies without causing
significant perturbations in HCV RNA titers is also a mystery, as is the mechanistic
relationship between host pressure, viral evolution and disease progression. Again,
development of HCV nucleic acid-based assays was an essential contribution of
molecular medicine in terms of furthering our understanding of the fundamental
2