Low-level alternative tRNA priming of reverse transcription of HIV-1 and SIV in vivo

BACKGROUND: Reverse transcription (RT) of HIV and SIV is initiated by the binding of the acceptor stem of tRNA(Lys3) to the primer binding site (PBS) of the viral RNA genome. Previous studies have suggested that this tRNA(Lys3) is not the only molecule capable of priming reverse transcription, and that at least one other lysyl tRNA, tRNA(Lys5), which has an acceptor stem sequence varying from tRNA(Lys3) by only a single transition mutation resulting in the integration of a thymine (T) at position 8 of the PBS in the viral genome, can prime reverse transcription. RESULTS: We undertook an unbiased approach, evaluating the primer binding site by deep-sequencing of HIV and SIV directly from the plasma of 15 humans and 11 macaques. We found that in humans there are low but measurable levels of viral RNA genomes harboring a PBS containing the noncanonical T at position 8 (PBS-Lys5) corresponding to the tRNA(lys5) sequence and representing an average of 0.52% (range 0.07–1.6%) of the total viral population. This value is remarkably consistent with the proportion of PBS-Lys5 we identified in a cross-sectional assessment of the LANL HIV database (0.51%). In macaques chronically infected with SIVmac239, the PBS-Lys5 was also detected but at a frequency 1-log less than seen for HIV, with an average of 0.056% (range 0.01–0.09%). At this proportion, PBS-Lys5 was comparable to other transition mutations, making it impossible to determine whether the mutation observed is a result of use of tRNA(Lys5) as an RT primer at very low levels or merely the product of in vitro cDNA synthesis/PCR error. We also identified two novel PBS sequences in HIV and SIV at low levels in vivo corresponding to tRNA(Lys6) and tRNA(Lys1,2), suggesting that these tRNAs may rarely also be used to prime RT. In vivo reversion of the PBS-Lys5 found in SIVmac239 was rapid and reached background levels by 30 days post-infection. CONCLUSIONS: We conclude that while alternative tRNAs can initiate reverse transcription of HIV and SIV in vivo, their overall contributions to the replicating viral population are small. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12977-019-0473-2) contains supplementary material, which is available to authorized users.