Determining the origins of HIV-1 drug-resistant minority variants in people who are recently infected using phylogenetic reconstruction

Background: Drug-resistant minority variants (DRMinVs) detected in patients who recently acquired HIV-1 can be transmitted, generated de novo through virus replication, or technical errors. The first are likely to persist and result in treatment failure while the latter two could be stochastic and transient. Methods: Ultra-deep sequencing of plasma samples from 835 individuals with recent HIV-1 infection in the UK was performed to detect DRMinVs at mutation frequency between 2-20%. Sequence alignments including >110,000 HIV-1 partial pol consensus sequences from the UK HIV Drug Resistance Database (UK-HDRD) , linked to epidemiological and clinical data from the HIV and AIDS Reporting System (HARS),were used for transmission cluster analysis. Transmission clusters were identified using Cluster Picker with a clade support of >90% and maximum genetic distances of 4.5% or 1.5%, the latter to limit detection to likely direct transmission events. Results: Drug-resistant majority variants (DRMajVs) were detected in 66 (7.9%) and DRMinVs in 84 (10.1%) of the recently infected individuals. High levels of clustering to sequences in UK-HDRD were observed for both DRMajV (n=48; 72.7%) and DRMinV (n=63; 75.0%) sequences. Of these, 43 (65.2%) with DRMajVs were in a transmission cluster with sequences that harboured the same DR mutation compared to only 3 (3.6%) sequences with DRMinVs (p<0.00001; Fisher's exact test). Evidence of likely direct transmission of DRMajVs was observed for 25/66 (37.9%) whereas none was observed for the DRMinVs (p<0.00001). Conclusions: Using a densely sampled HIV-infected population we show no evidence of DRMajV-to-DRMinV transmission or vice versa among recently infected individuals.