Characterisation of new full-length HIV-1 subtype D viruses from South Africa

[摘要] ENGLISH ABSTRACT: The first episode of HIV-1 in South Africa was documented in 1982.Homosexual transmission of the virus was the predominate mode oftransmission in an epidemic of mainly HIV-1 subtype Band D infections. Todate, no full-length sequences of Subtype D strains from South Africa has beenreported. Here we describe the characterization and some of the uniquefeatures of the Tygerberg HIV-1 subtype D strains.A near full-length 9 kb fragment was obtained through a one step PCR usinghigh molecular weight DNA. Cloning was done successfully with the pCR-XLTapacloning kit. Large quantities of plasmid DNA was grown and sequencedon both strands of the DNA. ORF determination and subtyping was followed bystandard phylogenetic methods to construct evolutionary phylogenetic trees.Subtyping and similarity plots revealed that the sequences from Tygerberg arepure subtype D. All the Tygerberg strains had intact genes with no prematurestop codons. At the tip of the V3 loop, the Tygerberg strains have the GOGOmotif. R214 has a more variable vpu gene than the rest of the Tygerbergstrains, but is still subtype D in this region. No premature stop codons havebeen observed in the tat gene and the glycosilation of the strains are less thanthe subtype D consensus.We are the first to report full-length sequences of HIV-1 subtype D strains fromSouth Africa. The sequences represent non-mosaic genomes of subtype D. Ourresults confirm that the subtype D sequences from the beginning of the HIV-1epidemic differ from the Subtype D sequences from recent isolates.

[发布机构] Stellenbosch University