Monitoring the HIV epidemic in Romania has proven challenging due to many factors, including the reluctance of newly diagnosed patients to disclose relevant epidemiological aspects during the clinical interview, such as sexual orientation or the existence of previous issues with injectable drug usage. We propose in this study a molecular approach to mitigate this problem with the help of bioinformatic tools, such as cluster analysis of phylogenetic trees. Both a maximum likelihood estimation, as implemented with FastTree, and a Bayesian approach, as used in BEAST, have been applied to our data set of 312 HIV subtype F1 pol gene sequences. ClusterPicker was used in order to identify groups of sequences and indicate similarities possibly related to the route of transmission. An important observation from this analysis is that transmission between men who have sex with men (MSM) is likely occurring in networks significantly larger than previously assessed by self-reported data (65% from the phylogenetic tree versus 37% from self-declared affiliation). Cluster analysis can help identify risk factors, reveal transmission trends, and, consequently, advise prevention programs.

The HIV epidemic in Romania started in the late eighties with a large cohort of children nosocomially infected with subtype F1 strains, in parallel with sexual transmission. The purpose of the present study was to investigate the transmitted drug resistance (TDR), subtype distribution, and transmission clusters among persons diagnosed with HIV between 2019 and 2022 in Romania. The prototype of a person recently diagnosed with HIV in Romania is male, 20–50 years old, a late presenter, infected with F1, B, or A subtype. The rate of TDR varied over time, from 5% in 2019 to 15% in 2022. TDR affected mainly the first generation of NNRTIs and the PI class. The rate of late presentation was almost 60%, with 35% of persons qualifying as very late presenters. Subtype F1 is still preponderant in Romania, whereas other subtypes (B, A) and recombinants account for a quarter of HIV-1 new cases. Several transmission networks were identified in the study population, two of them associated with TDR in subtypes F1 and A1. The largest cluster consisted of 26 sequences, originating from Western Romania and introduced around 2007. Molecular clock analysis indicated different origin time points for different clusters, with the most recent in subtypes A1 and B, and the oldest in subtype F1. In conclusion, the HIV-1 epidemic in Romania is currently driven by sexual transmission, with MSM contribution continuously rising in recent years; there are also increases in TDR and the circulation of HIV-1 strains other than F1 (subtype B, A, recombinants).