Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis
Cluster types within the phylogenetic tree are defined as follows. Singletons (in blue) are clusters of size 1, or cases whose sequence solely clustered with sequences from the Los Alamos HIV Sequence Database. Small clusters (in green) comprise sequences from 2–9 ATHENA patients. Large clusters comprise sequences from ten or more patients in the ATHENA cohort. Amongst those, non-MSM-dominant clusters (in brown) contain a majority of sequences from non-MSM patients, whilst MSM-majority clusters contain a majority of sequences from MSM patients. Among large MSM-majority clusters, pre-1996 clusters (in dark orange) are defined as those in which the first diagnosed patient in the cluster was diagnosed before 1996, and post-1996 clusters are defined as those in which all patients in the cluster were diagnosed in or after 1996. Large MSM-majority post-1996 clusters are stratified as “time of MRCA pre-1996” (in light orange) when the estimated time of the MRCA is before 1996, and “time of MRCA post-1996” (in purple) when the estimated time of the MRCA is in or after 1996. (A) Number of MSM registered in the ATHENA cohort in the Netherlands with a sequence in this study by year of diagnosis and by cluster type. (B) Number of clusters of each type by year of first diagnosed case in each cluster.