Global Alert and Response (GAR)

Hepatitis C

The hepatitis C virus

- Morphology and physicochemical properties
- Genome and proteins
- Stability

Although its means of transmission are well documented, the hepatitis C virus itself still remains an enigma.

The hepatitis C virus is an enveloped RNA virus with a diameter of about 50 nm, classified as a separate genus (Hepacivirus) within the Flaviviridae family. The genomic organization and sequence of HCV resembles that of the pestiviruses and flaviviruses.39, 52, 74, 97

The reservoir of HCV is man, but the virus has been transmitted experimentally to chimpanzees.39, 41, 52, 74, 97

The genome of HCV is highly mutable. Because HCV is an RNA virus and lacks efficient proofreading ability as it replicates, virions infecting humans undergo evolution with time, giving rise to the notion that HCV persists as a collection of virus quasispecies. By constant mutation, HCV may be able to escape host immunologic detection and elimination.41, 52, 74, 97

HCV undergoes rapid mutation in a hypervariable region of the genome coding for the envelope proteins and escapes immune surveillance by the host. As a consequence, most HCV-infected people develop chronic infection.

HCV also knocks out the host’s Innate Immunity.30

Mutations are not randomly distributed along the genome, but are most pronounced within a hypervariable region located near the N-terminus of E2. This region maps at a surface loop of the E2 protein containing a B-cell epitope that undergoes antigenic evolution over time.52, 74, 97

HCV is highly heterogeneous. Eleven HCV genotypes with several distinct subtypes have been identified throughout the world. These diversities have distinct consequences: although different strains have not been shown to differ dramatically in their virulence or pathogenicity, different genotypes vary in their responsiveness to interferon/ribavirin combination therapy. Moreover, such heterogeneity hinders the development of vaccines, since vaccine antigens from multiple serotypes will probably be necessary for global protection.39, 41, 52, 68, 74, 97

Click here for: Electron Microscopy (EM) picture of the hepatitis C virion
Click here for: The hepatitis C virus life cycle
Click here for: HCV genotypes

Morphology and physicochemical properties
HCV particles have a buoyant density of 1.24 g/cm3 in CsCl, and a sedimentation coefficient of 200 S in sucrose gradients.74

The density of HCV in sucrose gradients has been measured between 1.08 and 1.11 g/ml. A lighter fraction of 1.04 to 1.06 g/ml appears to be due to the association of HCV with serum beta-lipoprotein. A denser fraction of about 1.17 g/ml in sucrose appears to correspond with noninfectious immune complexes of virus and antibody. The nucleocapsid of the virus was found to have a density in sucrose of 1.25 g/cm3.39, 74

Genome and proteins
HCV contains a single-stranded, positive-sense RNA molecule of 9.6 kb with one long open reading frame coding for a large polyprotein of about 3000 amino acids which undergoes co- and post translational cleavage by host and viral proteases to yield individual viral proteins.23, 39, 41, 52, 74, 97

The HCV genome has been cloned in 1989.19

A highly conserved, 5'-untranslated region of about 340 nucleotides precedes the translation initiation codon. There is also a 3'-untranslated region of variable length (consisting of a short, poorly conserved sequence (28-42 nucleotides), a poly(u)/polypyrimidine tract and a highly conserved 98-base element).39, 41, 52

The N-terminal quarter of the genome encodes the core and structural proteins. These consist of a non-glycosylated nucleic acid-binding nucleocapsid protein (C) of about 190 amino acids (about 21 kD) and one or possibly two membrane-associated glycoproteins (E1 and E2/NS1) of about 190, respectively 370 amino acids respectively (33 and 70 kD when glycosylated).41, 52, 74, 97

The glycosylated E1 and E2 molecules are anchored inside the lumen of the endoplasmic reticulum (ER). The C protein remains on the cytosol side.39

The rest of the genome encodes the nonstructural proteins NS2-NS5.

The NS2 (250 amino acids), NS3 (500 amino acids), and NS4a proteins interact to mediate the processing of the presumed NS region of the polyprotein. NS3 (500 amino acids) is both a proteolytic cleavage enzyme and a helicase, to facilitate unwinding of the viral genome for replication. NS5b is the RNA-dependent RNA polymerase needed for viral replication.39, 41, 52, 74, 97

NS proteins have been localized to the membrane of the ER, suggesting that it is the site of polyprotein maturation and viral particle assembly.39, 97

Little is known about the three dimensional structure of the HCV proteins.74

Click here for: HCV coding organization

HCV is inactivated by:74
- exposure to lipid solvents or detergents
- heating at 60°C for 10 h or 100°C for 2 min in aqueous solution
- formaldehyde (1:2000) at 37°C for 72 h
- ß-propriolactone
- UV irradiation

HCV is relatively unstable to:
- storage at room temperature
- repeated freezing and thawing


Electron Microscopy (EM) picture of the hepatitis C virion


From: "Copyright 1998 Trustees of Dartmouth College. All rights reserved. The C. Everett Koop Institute at Dartmouth documents available from this web site are protected by the copyright laws of the United States and international treaties."

The hepatitis C virus life cycle
Very little is known about the replication cycle of HCV, because there is no in vitro cell culture system that is permissive for virus replication.74 However, progress has been made.5, 39, 52

HCV probably follows the replication strategy of other positive-strand RNA viruses. The virus enters the cell and is uncoated in the cytoplasm. The viral genome is transcribed to form a complementary negative-sense RNA molecule, which, in turn, serves as a template for the synthesis of progeny positive-strand RNA molecules. The newly translated polyprotein is cleared by a host-cell signalase as well as virus-specific non-structural proteins, NS-2 and NS-3. The enzyme capable of performing both steps of RNA synthesis is the virally encoded RNA-dependent RNA polymerase NS5b.23 The NS-3 of HCV also has helicase (unwindase) activity.

HCV replicates by a negative-strand RNA intermediate and has no reverse transcriptase activity.41, 97

HCV genotypes

HCV is classified into eleven major genotypes (designated 1-11), many subtypes (designated a, b, c, etc.), and about 100 different strains (numbered 1,2,3, etc.) based on the genomic sequence heterogeneity.89

The variability is distributed throughout the genome. However, the non-coding regions at either end of the genome (5'-UTR and 3'-UTR; UTR-untranslated region) are more conserved and suitable for virus detection by PCR.89

The genes coding for the envelope E1 and E2 glycoproteins are the most variable. Amino acid changes may alter the antigenic properties of the proteins, thus allowing the virus to escape neutralizing antibodies.89

Genotypes 1-3 have a worldwide distribution. Types 1a and 1b are the most common, accounting for about 60% of global infections. They predominate in Northern Europe and North America, and in Southern and Eastern Europe and Japan, respectively. Type 2 is less frequently represented than type 1. Type 3 is endemic in south-east Asia and is variably distributed in different countries. Genotype 4 is principally found in the Middle East, Egypt, and central Africa. Type 5 is almost exclusively found in South Africa, and genotypes 6-11 are distributed in Asia.39, 58, 94, 103

The influence of viral genotype in the pathogenesis of liver disease is still controversial. Environmental, genetic, and immunological factors may contribute to the differences in disease progression, so characteristic of HCV infection, observed among patients.58

The determination of the infecting genotype is however important for the prediction of response to antiviral treatment: genotype 1 is generally associated with a poor response to interferon alone, whereas genotypes 2 and 3 are associated with more favourable responses.58 The current gold standard of therapy - pegylated interferon-a in combination with ribavirin – significantly improves response for all genotypes. 65


HCV coding organization


From: Houghton M. Hepatitis C viruses. In: Fields BN, Knipe DM, Howley PM, eds. Fields Virology, 3rd ed. Philadelphia, Lippincott - Raven, 1996:1035-1058, with permission.

Genetic organization of HCV genome. Cleavage site coordinates in the putative structural regions of isolates HCV-J, HCV-1, HCV-H, and HCV-1b are shown along with those in the putative nonstructural regions on HCV-H and HCV-1.39