Thesis (MSc (Medical Virology )--University of Stellenbosch, 2004. / 150 leaves printed on single pages, preliminary pages i-vii and numberd pages 1-143. Includes bibliography and figures digitized at 300 dpi grayscale and 300 dpi 24-bit Color to pdf format (OCR), using a Hp Scanjet 8250 Scanner and digitized at 600 dpi grayscale to pdf format (OCR), using a Bizhub 250 Konica Minolta Scanner. / ENGLISH ABSTRACT: The first episode of HIV-1 in South Africa was documented in 1982.
Homosexual transmission of the virus was the predominate mode of
transmission in an epidemic of mainly HIV-1 subtype Band D infections. To
date, no full-length sequences of Subtype D strains from South Africa has been
reported. Here we describe the characterization and some of the unique
features of the Tygerberg HIV-1 subtype D strains.
A near full-length 9 kb fragment was obtained through a one step PCR using
high molecular weight DNA. Cloning was done successfully with the pCR-XLTapa
cloning kit. Large quantities of plasmid DNA was grown and sequenced
on both strands of the DNA. ORF determination and subtyping was followed by
standard phylogenetic methods to construct evolutionary phylogenetic trees.
Subtyping and similarity plots revealed that the sequences from Tygerberg are
pure subtype D. All the Tygerberg strains had intact genes with no premature
stop codons. At the tip of the V3 loop, the Tygerberg strains have the GOGO
motif. R214 has a more variable vpu gene than the rest of the Tygerberg
strains, but is still subtype D in this region. No premature stop codons have
been observed in the tat gene and the glycosilation of the strains are less than
the subtype D consensus.
We are the first to report full-length sequences of HIV-1 subtype D strains from
South Africa. The sequences represent non-mosaic genomes of subtype D. Our
results confirm that the subtype D sequences from the beginning of the HIV-1
epidemic differ from the Subtype D sequences from recent isolates. / AFRIKAANSE OPSOMMING: Die eerste episode van HIV-1 infeksie in Suid Afrika is in 1982 gedokumenteer.
Die epidemie het hoofsaaklik uit subtipe B en D bestaan en was deur
homoseksuele kontak oorgedra. Geen vollengte subtipe D DNS volgordes van
Suid-Afrika is tans beskryf nie. Hier beskryf ons die karakterisering van
vollengte subtipe D stamme asook sommige van die unieke eienskappe van die
virusse.
Die vollengte 9 kb genoom volgorde was verkry deur 'n eenstap PKR reaksie
met hoë molekulêre gewig DNS uit te voer. Die 9 kb fragment was suksesvol
gekloneer met behulp van die peR-Xl-TOPO klonerings toetsstel. Groot
hoeveelhede plasmied DNS was opgegroei en die nukleotied volgorde bepaal
op beide stringe van die genoom. Die stamme was gesubtipeer en filogenetiese
analise was uitgevoer met standaard metodes.
Die volledige DNS volgordes was bepaal en subtipering het daarop gedui dat
die stamme van Tygerberg suiwer subtipe D is. Geen premature stop kodons is
in die nukleotied volgordes van die Tygerberg stamme gevind nie. By die draai
van die varieerbare deel (V3) het al die Tygerberg stamme die GQGQ motief
gehad. R214 het 'n meer varieerbare vpu geen, maar behoort steeds tot die
subtipe D groep in die gedeelte. Daar was geen premature stop kodons in die
tat geen gevind nie en die glikosilasie van die stamme is minder as die van die
konsensus subtipe D stam.
Ons is die eerste groep om vollengte subtipe D stamme van Suid-Afrika te
karakteriseer. Die DNS volgordes verteenwoordig suiwer subtipe D genome.
Ons resultate bevestig die van ander dat die nukleotied volgordes van die ouer
subtipe D stamme verskil van die nuwer stamme.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/3266 |
| Date | 12 1900 |
| Creators | Loxton, Andre Gareth, Janse van Rensburg, E., Engelbrecht, S. |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | Unknown |
| Type | Thesis |
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