title: Viral diversity and diversification of major non-structural genes vif, vpr, vpu, tat exon 1 and rev exon 1 during primary HIV-1 subtype C infection.
abstract: To assess the level of intra-patient diversity and evolution of HIV-1C non-structural genes in primary infection, viral quasispecies obtained by single genome amplification (SGA) at multiple sampling timepoints up to 500 days post-seroconversion (p/s) were analyzed. The mean intra-patient diversity was 0.11% (95% CI; 0.02 to 0.20) for vif, 0.23% (95% CI; 0.08 to 0.38) for vpr, 0.35% (95% CI; -0.05 to 0.75) for vpu, 0.18% (95% CI; 0.01 to 0.35) for tat exon 1 and 0.30% (95% CI; 0.02 to 0.58) for rev exon 1 during the time period 0 to 90 days p/s. The intra-patient diversity increased gradually in all non-structural genes over the first year of HIV-1 infection, which was evident from the vif mean intra-patient diversity of 0.46% (95% CI; 0.28 to 0.64), vpr 0.44% (95% CI; 0.24 to 0.64), vpu 0.84% (95% CI; 0.55 to 1.13), tat exon 1 0.35% (95% CI; 0.14 to 0.56 ) and rev exon 1 0.42% (95% CI; 0.18 to 0.66) during the time period of 181 to 500 days p/s. There was a statistically significant increase in viral diversity for vif (p = 0.013) and vpu (p = 0.002). No associations between levels of viral diversity within the non-structural genes and HIV-1 RNA load during primary infection were found. The study details the dynamics of the non-structural viral genes during the early stages of HIV-1C infection.
authors.affiliation: Department of Biological Sciences, University of Botswana, Gaborone, Botswana.
authors.forename: Raabya
authors.initials: R
authors.lastname: Rossenkhan
authors.forename: Vladimir
authors.initials: V
authors.lastname: Novitsky
authors.forename: Theresa K
authors.initials: TK
authors.lastname: Sebunya
authors.forename: Rosemary
authors.initials: R
authors.lastname: Musonda
authors.forename: Berhanu A
authors.initials: BA
authors.lastname: Gashe
authors.forename: M
authors.initials: M
authors.lastname: Essex
mesh_terms: D000328:Adult; D019143:Evolution, Molecular; D005091:Exons; D005260:Female; D005500:Follow-Up Studies; D014644:Genetic Variation; D015658:HIV Infections / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D054298:Human Immunodeficiency Virus Proteins / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D013997:Time Factors; D054334:Viral Regulatory and Accessory Proteins / Q000235:genetics*; D054321:rev Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D054320:vif Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D054325:vpr Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D054334:Viral Regulatory and Accessory Proteins; D054321:rev Gene Products, Human Immunodeficiency Virus; D054322:tat Gene Products, Human Immunodeficiency Virus; D054320:vif Gene Products, Human Immunodeficiency Virus; D054325:vpr Gene Products, Human Immunodeficiency Virus; C514860:rev protein, Human Immunodeficiency Virus-1; C514847:vif protein, Human immunodeficiency virus 1; C514912:vpr protein, Human immunodeficiency virus 1; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins