Thesis Topic Details

Topic ID:
3291
Title:
Deep sequencing analysis of the early infection phase of hepatitis C virus
Supervisor:
Fabio Luciani
Research Area:
Virology- immunology, Bioinformatics, Health informatics
Associated Staff
Assessor:
Bruno Gaeta
Topic Details
Status:
Active
Type:
R & D
Programs:
CS CE BIOM BINF SE
Group Suitable:
No
Industrial:
No
Pre-requisites:
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Description:
Hepatitis C virus is a pathogen that affects humans and monkey, with a prevalence of 2-3% among the Worldwide human population. The disease can be resolved by the host immune response in 40-60% of the cases, while for the other cases the infection results in a chronic disease, such as hepatitis, and sometimes cancer (hepatocellular carcinoma). A major obstacle in designing a vaccine against HCV is the tremendous rapidity at which the virus evolves. HCV mutates very rapidly its genome, at rate that the immune system cannot cope with. The result is a distribution of mutants that escape the immune response. A question that should be answered is how often mutants arise and how fast mutants grow within the host.

The project seeks to investigate the quasi-species distribution of the virus HCV during the early phase of the infection. The study will be based on deep sequencing analysis performed with next generation sequencing methodology. This technique allows to identifying viral mutants present in the infected host at frequencies below 1%. The student will actively analyse the sequence data obtained from the deep sequencing and identify true sequence variations as opposed to artifacts arising from the technique. Softwares are available to perform this analysis.

The experimental data consist of blood samples taken from HCV infected individual within the first 2-3 months of infection. These data are unique because HCV is often asymptomatic in the early phase, thus making almost impossible to detect. Our early infected cases have been found through an intensive study performed within prisons of NSW among injecting drug users.
The results are foundamental to understand how HCV evolve in the early phase of infection, where critical events occur that will affect the outcome of the disease.
Comments:
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Past Student Reports
  Preston LEUNG in s2, 2012
Deep sequencing analysis of the early infection phase of hepatitis C virus
  Luke MANNING in s1, 2013
Deep sequencing analysis of the early infection phase of hepatitis C virus
 

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