Each polygon represents a patient, with larger polygons representing two or more patients with identical sequences. The patient details are written inside the polygon: F = female, M = male. The number is the year of the start of the disease episode. The shapes describe drug resistance of the strain: squares = drug sensitive, circles = drug resistant, octagons = unknown. The colour of the polygon refers to HIV status of the patient: red = positive, blue = negative, grey = unknown. The colour of the edge refers to the lineage: Lineage 1 (Indo Oceanic) dark blue, Lineage 2 (Beijing/East Asian) light blue, Lineage 3 (East African Indian) green, and Lineage 4 (Europe American) red. The numbers on the arrows between the polygons are the number of SNPs between them.