Thesis (MScMedSc (Pathology. Medical Virology))--University of Stellenbosch, 2005. / There are currently an estimated 5.3 million people infected with human
immunodeficiency virus / acquired immunodeficiency syndrome (HIV/AIDS) in
South Africa. HIV-1 group M Subtype C is currently responsible for the majority of
HIV infections in sub-Saharan Africa (56% worldwide). The Khayelitsha informal
settlement, located 30 km outside Cape Town, has one of the highest HIV prevalence
rates in the Western Cape. The objective of this study was to investigate the
molecular epidemiology of HIV-1 in Khayelitsha using serotyping and genotyping
techniques.
Patient samples were received from the Matthew Goniwe general health clinic located
at site C in Khayelitsha. Serotyping was performed through a competitive enzymelinked
immunosorbent assay (cPEIA). RNA was isolated from patient plasma and a
two step RT-PCR amplification of the gag p24, env gp41 IDR, env gp120 V3 and pol
genome regions performed. Sequences obtained were used for detailed sequence and
phylogenetic analysis. Neighbour-joining and maximum likelihood phylogenetic
trees were drawn to assess the relationship between the Khayelitsha sequences
obtained and a set of reference sequences obtained from the Los Alamos National
Library (LANL) HIV database (http://www.hiv.lanl.gov/).
Through serotyping and genotyping the majority of HIV strains were characterised as
HIV-1 group M subtype C. One sample (1154) was characterised as a possible C / D
recombinant strain. In 9 other samples HIV-1 recombination cannot be excluded, as
only one of the gene regions investigated could be amplified and characterised in
these samples. The gag p24 genome region was found to be more conserved than the
env gp41 IDR, with the env gp41 IDR more conserved than the env gp120 V3. The
variability of the env gp120 V3 region indicates that patients might be dually infected
with variant HIV-1 subtype C strains or quasispecies. Conserved regions identified in
the Khayelitsha sequences can induce CD4+ T-cell responses and are important
antibody recognition target sites. These conserved regions can play a key role in the
development of an effective HIV-1 immunogen reactive against all HIV-1 subtypes.
The majority of subtype C viruses were predicted to use CCR5 as their major chemokine co-receptor. The pol sequences analysed indicate that mutations
associated with minor resistance to Protease Inhibitors (PIs) might be present in the
Khayelitsha community. The identification of resistant mutations is vital for people
receiving antiretroviral treatment (ART). It can influence the success of their
treatment and delay the onset of AIDS.
Serotyping is a quick characterisation method, but not always accurate. With
genotyping detailed molecular analysis can be performed. However, with genotyping
the success of amplification often depends on viral load. In Southern Africa a subtype
C candidate vaccine appears to be the best option for future vaccine considerations.
The sporadic detection of non-subtype C and recombinant subtype C viruses remains
a concern and will thus have to be closely monitored. Phylogenetic analysis can help
to classify and monitor the spread and evolution of these viruses.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/2196 |
| Date | 12 1900 |
| Creators | Jacobs, Graeme Brendon |
| Contributors | Engelbrecht, Susan, De Beer, Corena, University of Stellenbosch. Faculty of Health Sciences. Dept. of Pathology. Medical Virology. |
| Publisher | Stellenbosch : University of Stellenbosch |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Rights | University of Stellenbosch |
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