Tracking viral transmissions using patterns of viral change during acute infection

Shruti Krishnan

    Research output: ThesisMaster's Thesis

    80 Downloads (Pure)


    [Truncated abstract] In this thesis the interaction between the immune response of the host and the corresponding viral adaptations occurring within the genome of the Hepatitis C virus (HCV) was examined in order to identify sites within HCV that could be used to track the direction of transmission. This information will be important in future criminal cases involving the intentional or negligent exposure of an infectious agent to another causing grievous harm. Phylogenetic analyses can be used to evaluate genetic relatedness between viruses to establish the relationship between any two viral species. This method has successfully been used to determine the likely transmission of HIV and HCV between individuals in criminal cases. However, typical phylogenetic analyses do not account for specific changes in the virus that may reflect the host or source of the virus. These host-related viral changes may be helpful in determining the direction of transmission along with overall genetic relatedness. Viruses such as HIV and HCV have a high replication and mutation rate resulting in many changes in their genome that may enable the virus to better adapt to a specific environment. Some of these changes may allow the virus to escape the immune pressure of the host. These changes are found in areas of the virus that are specifically targeted by the hosts immune response (epitopes) and mutations within these targets can abrogate T-cell recognition and accordingly affect the efficiency of the hosts defence against HCV or HIV. As the hosts Human Leucocyte Antigens (HLA) molecules regulate, to a certain extent, this T-cell response, these mutations can be observed at the population-level as HLA-associated viral mutations or adaptations. These viral adaptations are like footprints left in the viral genome and could be used in a forensic context to track the direction of transmission of the virus. These changes are thought to remain stable in the host while immune pressure is still acting on the virus. However, if the virus is transmitted to another individual with a different HLA type, the immune pressure is absent and it is thought that reversion to wild type (non-adapted form) would occur. In this study, viral adaptations that may be useful to track viral transmission were investigated in a cohort of acutely HCV infected subjects as most personal bio-crime cases would have sampling time-points in this phase. This study involved predominantly untreated acute and newly acquired HCV infected subjects in the ATAHC (Australian Trial of acute Hepatitis C) cohort. The cohort includes 138 longitudinal samples from 41 HCV-infected individuals from Sydney (n=20) and Melbourne (n=21). The study involved determining the HLA type of the subjects by performing high-resolution HLA Class I and II typing using direct DNA sequencing methods and obtaining the non-structural (NS) 3 and NS5B region sequences, as there are known immunodominant epitopes in these regions. Sequence analysis of the NS3 and NS5B regions confirmed the genotype of the main circulating virus at each time-point for the subjects and identified a potential transmission between two subjects 118 CRNE and 307 GAVE...
    Original languageEnglish
    Publication statusUnpublished - 2010


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