Background: The rapid identification of emerging transmission clusters could help reach the 2030 goal of halting transmission of HIV in Switzerland. We characterised the size, structure, and growth of recent HIV-1 transmission clusters in the Swiss HIV Cohort Study (SHCS).

Methods: In this retrospective molecular epidemiology analysis in Switzerland, we analysed 32 294 HIV-1 pol sequences from 16 428 SHCS participants, enrolled between Aug 14, 1984, and May 19, 2025. Sequences were aligned and clustered using a 0·01 Tamura-Nei 93 distance threshold, and networks were constructed at the participant level to identify clusters and their growth. We defined and described a set of fast-growing clusters of HIV in Switzerland. Associations between clustering, demographic and clinical characteristics, and viral suppression were assessed.

Findings: 7387 (45·0%) participants were part of 1131 clusters. Cluster size distribution was highly skewed: 62% contained only two individuals, whereas a few large clusters accounted for thousands of participants. The epidemic fragmented from a single dominant cluster of people who inject drugs in the 1990s into numerous smaller clusters, predominantly among gay, bisexual, and other men who have sex with men (MSM). Since 2016, 32·6% of the total cluster growth was concentrated in a set of 23 fast-growing clusters. These fast-growing clusters mostly comprised western European MSM with high rates of condomless sex. Cluster growth was strongly associated with viraemia among connected participants.

Interpretation: The Swiss HIV epidemic has evolved into fragmented, short transmission chains, with a small number of fast-growing clusters sustaining ongoing transmission. Molecular surveillance can identify such clusters, enabling tailored interventions that complement treatment as prevention. Achieving zero HIV transmission in Switzerland will require integration of molecular epidemiology into routine prevention.