Central Asia is among the few regions where the HIV epidemic is still on the rise. It is imperative to investigate the ‘hotspots’ of rapid HIV transmission and the means to curtail its spread. HIV prevalence is high among people who inject drugs (PWID), but is growing through heterosexual- , men who have sex with men (MSM)-, and cross-border migrant-associated transmissions. Since the HIV epidemic in Kazakhstan among PWID is still a major driver of HIV spread, there is an opportunity for prevention through the provision of targeted programs. It is important to understand the status of the HIV epidemic among PWID in Kazakhstan who are exposed to multiple adverse risk environments that contribute to rapid HIV transmission. Additionally, it is imperative to determine the high-risk groups where transmission is now bridging to and from PWID populations. To curtail further transmission, we need to identify the characteristics of the social/sexual networks responsible for the current/emerging transmission clusters. Our objective is to characterize HIV phylogenetic transmission clusters among PWID and other at risk populations. Knowledge of transmission dynamics is critical to understanding the network structure and the influences that sustain HIV transmission, informed by viral phylogenetics linked to epidemiological data. Phylodynamic analysis of HIV gene sequences can reveal information of public health relevance, including transmission of drug-resistant virus, hotspots of recently emerging HIV infections, and transmission bridging across demographics and behavioural subgroups.