Hepatitis C Virus: Structure, Pathogenesis, and Diagnosis

Hepatitis C virus, an RNA virus, belongs to the hepacivirus genus of the family Flaviviridae. It is the most important cause of parenteral non-A, non-B hepatitis (NANBH). Most patients with hepatitis C infection develop chronic liver diseases, progressing into hepatocellular carcinoma and cirrhosis.

According to ICTV (international committee on taxonomy of viruses), hepatitis C has eight genotypes and 93 subtypes.

Structure of Hepatitis C

Hepatitis C belongs to the genus hepacivirus of the family Flaviviridae. It has a close resemblance to hepatitis D virus, yellow fever virus, and dengue virus. The general structure of the hepatitis C virus has the following features:

  • It is a spherical, enveloped virus with a diameter of 55 nm (approximately).
  • Positive sense, Single-stranded RNA of 9.6 kb is the genetic material of the virus.
  • The genomic material encodes for ten structural and regulatory proteins.
  • The structural proteins involve a core protein, and two envelop proteins (E1 and E2). 
  • The two envelop proteins undergo variation because of the hypervariable regions within the gene.

Genomic arrangement of Hepatitis C virus

  • HCV has plus-strand single-stranded RNA of 9.6 kb.
  • The genome has a long open reading frame (ORF) that encodes polyprotein precursors. The protein has 3010 amino acids.
  • The HCV has a 341 nucleotides long 5′ untranslated region (UTR) located upstream of the ORF in the RNA. The 5′ UTR consists of 4 highly structured domains, I to IV. 
  • Domains II, III, and IV of 5′ UTR with the first 12 to 30 nucleotides of the core-coding region make up IRES (internal ribosome entry site).
  • The IRES can directly bind to the ribosome and start the translation process.
  • The virus produces polyprotein after translation cleaves during and after translation. Thus forming ten proteins; core proteins, envelope proteins (E1 and E2), and non-structural proteins (NS1 or p7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B).
Genomic structure of HCV

Replication of Hepatitis C virus

The replication of the hepatitis C virus takes place in hepatocytes, and sometimes the replication may occur in monocytes, dendritic cells, and B and T lymphocytes. The steps involved in the replication are as follows:

Replication of HCV


While circulating in the bloodstream, the viral particles bind to lipoprotein. Viral cell surrounded by lipoprotein attaches to various cell receptors like CD81, SR-B1, LDL-R, EGFR, and EphA2. 


After attachment, the entry of the viral particle is facilitated by clathrin-mediated endocytosis. 


After the fusion with the cell membrane, the virus’s capsid breaks down by the mechanism triggered by the low pH of the endosome. The uncoating of the capsid releases the viral genome into the host cell cytoplasm.


The RNA translates a polyprotein precursor, cleaved into angle protein by the enzyme proteases. The translation occurs in RER (rough endoplasmic reticulum).


A replication complex is formed by non-structural and host proteins, which synthesize multiple copies of the HCV RNA genome with the help of a minus-strand RNA as a template.

Maturation and Assembly

The virus acquires E1 and E2 glycoprotein from the host cell’s ER (endoplasmic reticulum). The assembly also takes place in the ER. Lipoviral particle is formed as soon as the maturation and just before release.


The release of the viral particles takes place by exocytosis. However, transmission to other cells takes place by a cell-free mechanism. 

Pathogenesis of Hepatitis C

HCV is carried in the bloodstream of the infected person. Even though its natural target cells are hepatocytes, they can also target B lymphocytes. 50% of the hepatocytes may be infected during chronic hepatitis. Almost all the infected people develop persisting viremia, which is associated with a different degree of inflammation and fibrosis. Typical histopathological details in chronic hepatitis are portal inflammation, interphase hepatitis, and lobular necrosis.  

Virulence factor

Hepatitis C has different factors which help the virus infect human hepatocytes and develop persistence. They are as follows:

  • E2 glycoprotein initiates the attachment of the virus.
  • E1 glycoprotein is thought to play a role in intra-cytoplasmic virus membrane fusion.
  • It is challenging to produce vaccines against HCV because of its highly diverse but closely related genomic structures within an infected individual.
  • NS5A non-structural protein produced by the HCV genome is resistant to interferon, so interferon cannot be used to treat hepatitis C infection.

Transmission of Hepatitis C 

Hepatitis C infection occurs only in humans. The transmission occurs from an infected person to a healthy individual in the following ways:

Parenteral transmission

Parenteral transmission of HCV infections occurs in the following ways:

  • Blood transfusion is the most frequent reason for the information of hepatitis C infection. It appears in one case per 100,000 units of blood transfused. 
  • Needle sharing in intravenous drug users. It is the principal reason for parenteral transmission.
  • Organ transplantation 

Sexual Transmission

20% of the cases of HCV infection are considered to be transmitted sexually. Cross-infection with HIV is seen in most cases.

Incubation Period

The incubation period of HCV ranges from 2 weeks to 6 months. The average period is approximately eight weeks.


HCV is the causative agent of acute as well as chronic HCV infection. This lead to hepatitis-induced complications. The symptoms of hepatitis C infection are as follows:

Acute HCV infection

Most patients with acute infection are asymptomatic and do not progress to jaundice. The symptoms in those symptomatic patients are mild. The symptoms are as follows:

  • Fever
  • Fatigue
  • Decreased appetite 
  • Nausea
  • Vomiting 
  • Abdominal pain 
  • Dark urine
  • Joint pain
  • Less than 25% of symptomatic patients develop jaundice.

Chronic HCV infection

Most chronic cases are asymptomatic but can present non-specific symptoms like fatigue or malaise. 

Further Complications

Cirrhosis and hepatocellular carcinoma are the further complications of HCV infections. 

It takes up to 20 years for the infections to progress to cirrhosis. The progression occurs in approximately 20% of cases. Patients with cirrhosis risk developing secondary liver failure, portal hypertension, and other complications.

Hepatocellular carcinoma is another complication of HCV. It progresses after approximately 30 years of chronic HCV infection and cirrhosis. It occurs in 1-5% of people with cirrhosis. 

Diagnosis of Hepatitis C Infection

Sample collection and transport

Blood serum is the sample of choice. Collect 15ml blood in a vial free of the anticoagulant. Transport the sample as soon as possible. Once you receive the sample, allow it to clot and centrifuge it. It results in the separation of serum from the blood. 

In case of delay in transporting the sample, refrigerate it at 4℃.

Sample Processing 

There are multiple ways of processing serum samples. The conventional method of laboratory diagnosis of diseases is the observation of viruses by electron microscopy and the culture of viruses. However, culturing and electron microscopic observation are suitable only for research purposes.

Thus, the most convenient way to diagnose HCV infection is antigen, antibody, and nucleic acid detection.

Antigen Detection

Detection of the core antigen of HCV is done by using ELISA (enzyme-linked immunosorbent assay) and CLIA (chemiluminescence immunoassay).

Antibody Detection

Antibodies against core, envelope, NS3 and NS4 proteins are seen in acute infection only after 6-8 weeks of initial infection and persist throughout life. RDT (rapid detection test kit) kit, ELISA, and EIA are used to detect antibodies. But recombinant immunoblot assay that uses recombinant HCV antigen is the most specific test for detection.

Nucleic Acid Detection/ Molecular Diagnosis

PCR (polymerase chain reaction) detects HCV nucleic acid (RNA) from the serum sample. It is the most specific test for diagnosing acute HCV infection because it detects the presence of the virus, corrects false-positive cases, and identifies the genotype.

Other Tests

Before starting antiviral therapy, performing a liver biopsy is recommended. However, it is not applicable for laboratory diagnosis.

Treatment, Prevention, and Control of Hepatitis C Infection

Treatment of the symptoms is the only treatment necessary during acute infection. But chronic cases require treatment with PEGylated interferon and the antiviral agent ribavirin.

Vaccines are not available. Also, immunoglobulin does not help prevent transmission. Screening and preventing blood transfusion, organ transplantation, or sexual contact with HCV-positive individuals is the only way to prevent and control the infection.

PEGylated interferon (covalent conjugate of recombinant interferon-alpha and polyethylene glycol) is used to treat chronic cases because HCV can develop resistance to interferon.


Ashma Shrestha

Hello, I am Ashma Shrestha. I had recently completed my Masters degree in Medical Microbiology. Passionate about writing and blogging. Key interest in virology and molecular biology.

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