Variability and Signatures of RNase-H Amino Acid Domain and Central Polypurine Tract of HIV-1 B-Subtype from Drug-Naive Individuals

Background: The conversion to HIV-1 single-stranded RNA into double-stranded DNA for nuclear integration is an essential viral step in replication: this process is mediated by Reverse-Transcriptase (RT) and by central polypurine tract (cPPT), a domain where the plus-strand synthesis requires viral primers produced by RNase-H cleavage. Recent studies highlighted the need of investigating the role of RNase-H in RT nucleoside-inhibitors-resistance, because specific mutation(s) could affect cPPT removal and RNase-H cleavage specificity. Thus, the variability of RNase-H and cPPT were studied. Methods: HIV-1 subtype-B sequences from 746 drug-naive and 806 antiretroviral-(ARV)-treated patients were used and analysed. Results: In drug-naive patients, among 54 RNase-H variable residues, 25 were mutated in >5% of patients, and 7 of them were highly variable (>25%), whilst in ARV-treated individuals, 53 RNase-H variable residues were observed, which 24 were mutated in >5% of patients and 6 of them were highly variable (>25%). Differently, a high conservation was observed in cPPT-area, with no statistically significant differences observed between the two datasets analysed. Nevertheless, in ARV-treated patients the variability of cPPT nucleotide at position 6 was found three times higher with respect to the drug-naive dataset. The topology of the dendrogram has revealed the existence of a cluster (boostrap=0.98) grouping the A6G(cPPT) with V531I and S519N RNase-H signatures. Conclusion: These signatures observed within cPPT and mostly in RNase-H, warrant advanced structural analysis to delineate their potential roles in the affinity/recognition of RT and the cleavage capacity of RNase-H. Exploring further the implications such changes may have on drug-resistance may be relevant.