Phylogenetic relationship between samples from individuals with persistent SARS-CoV-2 RNA (hereafter referred to as persistent infections) (top), and reinfections with a representative background population of Alpha (B.1.1.7; see Extended Data Fig. 2 for the analysis on the other three major lineages) (bottom). The dashed lines connect every pair of sequences from the same individual. Pairs from individuals with persistent infections cluster closely together, whereas reinfections do not. All sequences from the same individual are given the same colour.
