CLOCK and HIV-1 infection: To obtain a GC clock rate estimate, we used previously identified measurably evolving B cell lineages from an HIV-1 infected donor sampled between 6–144 weeks after HIV-1 infection.49,56 We estimated the clock rate of each lineage using root-to-tip regression; i.e., slope of the linear regression of sample time vs genetic divergence from the MRCA.35 We used the mean rate of these 118 lineages (1×10−3 mut/site/week) as the mean of the normal prior clock rate for GC B cells in TyCHE and the fixed mean clock rate for SC and UCLD models (Fig. 4B).