Fig. 4: Evolution and positive selection of SARS-CoV-2 spike in PWH with CD4 counts < 200 cells/ μL.

Maximum-likelihood phylogenetic trees rooted on Hu-1 for all haplotypes from each PWH with CD4 counts < 200 cells/μL. Participants S006-001 and S074-001 were infected with multiple founders and are shown separately in Supplementary Fig. 7a. Clades with bootstrap support < 50% are indicated with dashed lines. Sites detected under positive selection within each participant (see “Methods”) are shown at their inferred location on the tree with numbered symbols; mutations corresponding to each number are listed beside each participant’s tree. Symbol shapes are coded by spike protein domain (see legend, center bottom). The frequency of each haplotype detected at each sample time point (days post symptom onset) in each participant is indicated to the right of the tree via the dot plot. SARS-CoV-2 RNA levels (rRT-PCR Ct values) and serum antibody binding to spike protein (optical density, 450 nm [OD450]) are shown above the dot plot for each participant. The positivity cutoff index (COI) of 0.4 for serum antibody binding to spike protein is indicated.