A phylogenetic assessment of HIV-1 transmission trends among people who inject drugs from Coastal and Nairobi, Kenya.

Although recent modeling suggests that needle-syringe programs (NSPs) have reduced parenteral HIV transmission among people who inject drugs (PWID) in Kenya, the prevalence in this population remains high (∼14-20%, compared to ∼4% in the larger population). Reducing transmission or acquisition requires understanding historic and modern transmission trends, but the relationship between the PWID HIV-1 sub-epidemic and the general epidemic in Kenya is not well understood. We incorporated 303 new (2018-21) HIV-1 sequences from PWID and their sexual and injecting partners with 2666 previously published Kenyan HIV-1 sequences to quantify relative rates and direction of HIV-1 transmissions involving PWID from the coast and Nairobi regions of Kenya. We used genetic similarity cluster analysis (thresholds: patristic distance <0.045 and <0.015) and maximum likelihood and Bayesian ancestral state reconstruction to estimate transmission histories at the population group (female sex workers, men who have sex with men, PWID, or general population) and regional (coast or Nairobi) levels. Of 1081 participants living with HIV-1, 274 (25%) were not virally suppressed and 303 (28%) had sequences available. Of new sequences from PWID, 58% were in phylogenetic clusters at distance threshold <0.045. Only 21% of clusters containing sequences from PWID included a second PWID sequence. Sequences from PWID were similarly likely to cluster with sequences from female sex workers, men who have sex with men, and the general population. Ancestral state reconstruction suggested that transmission to PWID from other populations was more common than from PWID to other populations. This study expands our understanding of the HIV-1 sub-epidemic among PWID in Kenya by incorporating four times more HIV-1 sequences from this population than prior studies. Despite recruiting many PWID from local sexual and injecting networks, we found low levels of linked transmission in this population. This may suggest lower relative levels of parenteral transmission in recent years and supports maintaining NSPs among PWID, while also strengthening interventions to reduce HIV-1 sexual acquisition and transmission for this population.