title: Phylogenetic diversity and low level antiretroviral resistance mutations in HIV type 1 treatment-naive patients from Cape Town, South Africa.
abstract: We analyzed the HIV-1 pol gene from patients in Cape Town to determine the genetic diversity of HIV-1 in the region and to assess the baseline HIV-1 resistance level of treatment-naive patients. Plasma was collected prior to the national antiretroviral therapy (ART) program. RNA was extracted, followed by RT-PCR and automated DNA sequencing of the viral protease (PR) and reverse transcriptase (RT) coding region. Genotyping was done through phylogenetic analysis. The sequences were inspected for resistance-associated mutations against PR and RT inhibitors. A total of 140 pol sequences were analyzed, of which 133 (95%) belong to HIV-1 subtype C, five (3.6%) were subtype B, and one each was subtype G and CRF02_AG. Five sequences (3.6%) had resistance-associated mutations. These include three (2.1%) NNRTI mutations. With the progression of the national ART program, it is important to monitor the resistance profile of naive and treatment-experienced patients.
authors.affiliation: Division of Medical Virology, National Health Laboratory Service (NHLS) and University of Stellenbosch, Tygerberg 7505, Cape Town, South Africa.
authors.forename: Graeme B
authors.initials: GB
authors.lastname: Jacobs
authors.forename: Annette
authors.initials: A
authors.lastname: Laten
authors.forename: Estrelita Janse
authors.initials: EJ
authors.lastname: van Rensburg
authors.forename: Jochen
authors.initials: J
authors.lastname: Bodem
authors.forename: Benedikt
authors.initials: B
authors.lastname: Weissbrich
authors.forename: Axel
authors.initials: A
authors.lastname: Rethwilm
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Preiser
authors.forename: Susan
authors.initials: S
authors.lastname: Engelbrecht
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology*; D044966:Anti-Retroviral Agents; D024882:Drug Resistance, Viral / Q000235:genetics; D005260:Female; D015751:Genes, pol / Q000235:genetics; D014644:Genetic Variation; D015658:HIV Infections / Q000821:virology*; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009154:Mutation; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D011480:Protease Inhibitors / Q000494:pharmacology; D018894:Reverse Transcriptase Inhibitors / Q000494:pharmacology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013019:South Africa
chemical_list: D019380:Anti-HIV Agents; D044966:Anti-Retroviral Agents; D011480:Protease Inhibitors; D018894:Reverse Transcriptase Inhibitors; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D016333:HIV Protease