The evolution of subtype B HIV-1 tat in the Netherlands during 1985–2012

• Published in: Virus research 2018-05, Vol.250, p.51-64
• Main Authors: van der Kuyl, Antoinette C., Vink, Monique, Zorgdrager, Fokla, Bakker, Margreet, Wymant, Chris, Hall, Matthew, Gall, Astrid, Blanquart, François, Berkhout, Ben, Fraser, Christophe, Cornelissen, Marion
• Format: Article
• Language: English
• Subjects: Codon - genetics; Evolution, Molecular; Gene Expression Regulation, Viral; Genome, Viral; HIV Infections - epidemiology; HIV Infections - virology; HIV Long Terminal Repeat; HIV-1; HIV-1 - classification; HIV-1 - genetics; Humans; Life Sciences; LTR; Luciferase; Luciferases; Netherlands - epidemiology; Open Reading Frames; RNA, Viral; Subtype B; Tat; tat Gene Products, Human Immunodeficiency Virus - genetics; The Netherlands; Transcription, Genetic; Transcriptional Activation; Viral Load
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2018.04.008

•The encoded Tat protein of Dutch HIV-1 subtype B genomes varies in length over time.•Before 1995, 101 codons was the standard size of all tat ORFs.•From 1995–2012, tat genes varied increasingly in length, ranging from 86 to 124 codons.•Tat size was not associated with clinical parameters or transcription induction.•Longer Tat variants were somewhat improved in complementing a tat-defective virus. For the production of viral genomic RNA, HIV-1 is dependent on an early viral protein, Tat, which is required for high-level transcription. The quantity of viral RNA detectable in blood of HIV-1 infected individuals varies dramatically, and a factor involved could be the efficiency of Tat protein variants to stimulate RNA transcription. HIV-1 virulence, measured by set-point viral load, has been observed to increase over time in the Netherlands and elsewhere. Investigation of tat gene evolution in clinical isolates could discover a role of Tat in this changing virulence. A dataset of 291 Dutch HIV-1 subtype B tat genes, derived from full-length HIV-1 genome sequences from samples obtained between 1985–2012, was used to analyse the evolution of Tat. Twenty-two patient-derived tat genes, and the control TatHXB2 were analysed for their capacity to stimulate expression of an LTR-luciferase reporter gene construct in diverse cell lines, as well as for their ability to complement a tat-defective HIV-1LAI clone. Analysis of 291 historical tat sequences from the Netherlands showed ample amino acid (aa) variation between isolates, although no specific mutations were selected for over time. Of note, however, the encoded protein varied its length over the years through the loss or gain of stop codons in the second exon. In transmission clusters, a selection against the shorter Tat86 ORF was apparent in favour of the more common Tat101 version, likely due to negative selection against Tat86 itself, although random drift, transmission bottlenecks, or linkage to other variants could also explain the observation. There was no correlation between Tat length and set-point viral load; however, the number of non-intermediate variants in our study was small. In addition, variation in the length of Tat did not significantly change its capacity to stimulate transcription. From 1985 till 2012, variation in the length of the HIV-1 subtype B tat gene is increasingly found in the Dutch epidemic. However, as Tat proteins did not differ significantly in their capacity to stimulate transcrip