Masters Degrees (Medical Virology)

Permanent URI for this collection

https://scholar.sun.ac.za/handle/10019.1/3155

Browse

Browsing Masters Degrees (Medical Virology) by Author "Engelbrecht, S."

Now showing 1 - 1 of 1
  • Thumbnail Image
    Item
    Characterisation of new full-length HIV-1 subtype D viruses from South Africa
    (2004-12) Loxton, Andre Gareth; Janse van Rensburg, E.; Engelbrecht, S.
    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.