HIV subtype C diversity: analysis of the relationship of sequence diversity to proposed epitope locations

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dc.contributor.advisorHide, Winston
dc.contributor.advisorSeoighe, Cathal
dc.contributor.authorErnstoff, Elana Ann
dc.contributor.otherSouth African National Bioinformatics Institute (SANBI)
dc.contributor.otherFaculty of Science
dc.date.accessioned2013-08-27T13:50:14Z
dc.date.accessioned2024-05-17T07:20:11Z
dc.date.available2007/07/26 11:15
dc.date.available2007/07/26
dc.date.available2013-08-27T13:50:14Z
dc.date.available2024-05-17T07:20:11Z
dc.date.issued2002
dc.descriptionMagister Scientiae - MScen_US
dc.description.abstractSouthern Africa is facing one of the most serious HIV epidemics. This project contributes to the HIVNET, Network for Prevention Trials cohort for vaccine development. HIVÂ’s biology and rapid mutation rate have made vaccine design difficult. We examined HIV-1 subtype C diversity and how it relates to CTL epitope location along viral gag sequences. We found a negative correlation between codon sites under positive selection and epitope regions; suggesting epitope regions are evolutionarily conserved. It is possible that epitopes exist in non-conserved regions, yet fail to be detected due to the reference strain diverging from the circulating viral population. To test if CTL clustering is an artifact of the reference strain, we calculated differences between the gag codons and the reference strain. We found a weak negative correlation, suggesting epitopes in less conserved regions maybe evading detection. Locating conserved and optimal epitopes that can be recognized by CTLs is essential for the design of vaccine reagents.en_US
dc.description.countrySouth Africa
dc.identifier.urihttps://hdl.handle.net/10566/15241
dc.language.isoenen_US
dc.publisherUniversity of the Western Capeen_US
dc.rights.holderUniversity of the Western Capeen_US
dc.subjectHIV Subtype Cen_US
dc.subjectCytotoxic T Lymphoctyes (CTL)en_US
dc.subjectHuman Leukocyte Antigen (HLA)en_US
dc.titleHIV subtype C diversity: analysis of the relationship of sequence diversity to proposed epitope locationsen_US
dc.typeThesisen_US

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