With Western Australia’s (WA) close proximity to countries with high a prevalence of HIV-1 and with the increase of 457, student and spouse visa holders, WA is facing a change in HIV-1 diversity. In this study we aim to monitor HIV-1 mobility in WA and to determine whether direct transmission events occur.
1183 HIV-1 sequences from 2000-2012 underwent HIV-1 subtype identification based on sequencing the protease and reverse transcriptase gene and submission to Stanford HIV drug resistant database. BIOEDIT and MEGA 5.1 software were used for phylogenetic analysis. Maximum likelihood was inferred with +100 bootstrap trees, General Time Reversible (GTR) model with gamma distributed rate of heterogeneity with invariant sites (G+I). Evidence of direct transmission was identified with a genetic distance of <1.5% and a bootstrap value of ≥98%. To determine the robustness of this framework we included multiple time point sequences, unrelated B cohort and deleted drug resistant sites.
There was limited HIV-1 diversification in WA in 2000-2005. Since 2005 we have identified an increase in C and CRF01_ AE subtypes, to the point where B subtypes marginally dominate non B subtypes 52% to 48% by 2012. We identified 27 non B (11 C, 14 CRF01_AE, 1 CRF02_AG and 1 A subtype) and 45 B clusters. Many Non B clusters appear as pairs (93%) whilst only 56% of B subtype clusters were paired. We identified 2 B-subtype clusters with 11 and 15 patients. Interestingly, one large B-subtype cluster, with known contacts, was not identified by using the analysis framework. Also interestingly, utilising unrelated B subtype sequences or deleting drug resistant sites had little impact on phylogenetic tree construction.
This study provided an insight into HIV-1 transmission dynamics in WA with the results suggesting new intervention strategies are required focusing on visa holders, travelers, MSM and heterosexuals.
