Extended Data Fig. 10. Examples of clonal lineages with unique features.
a, A clonal lineage where a substantial fraction of early BGC cells did not bind Env trimer by flow cytometry. Clone 5491: H-CDR3 15 AAs in length, >2 N additions, found in one LN. b, Another clonal lineage with a substantial fraction of BGC cells that did not detectable bind Env trimer by flow cytometry. Clone 29183: H-CDR3 8 AA in length, >2 N additions, >10 cells per LN. This clone was excluded from LN migration quantitation analysis as it did not meet the required H-CDR3 length criteria. c, An example of a clonal lineage that was almost exclusively IgM. Clone 29183: H-CDR3 14 AA in length, >2 N additions,>10 cells per LN. In (a), (b) and (c), each B cell is labeled according to observed time point (left column), Env-binding by flow cytometry (center column), and anatomical sampling location (right column). d, Lineage tree 21094 shown in Fig. 4j by anatomical sampling location. Clone 21094: H-CDR3 14 AAs in length, >2 N additions, >10 cells per LN. e, Lineage tree 29121 shown in Fig. 4j by sampling location. Clone 29121: H-CDR3 18 AAs in length, >2 N additions, found in one LN. f, H-CDR3 length distribution of clones found in one or both ILNs using a broader definition of clonal lineages (H-CDR3 length > 10 AA, > 5 cells in lineage). Lineages found in a single LN and two distal LNs exhibited similar H-CDR3 length distributions. One hypothetical concern about the definition of clonality was the possibility of two independent naïve B cells having identical H-CDR3 and L-CDR3 recombination events. If that were the driving phenomenon behind the observation of matching BGC cells in distant LNs, based on recombination event likelihoods it would be expected that length distributions would be skewed towards shorter lengths and no N-additions would be observed. g, iNext42 plots showing the results of rarefaction analysis to determine the extent of sequence coverage from the Env+/+ LN FNA and PBMC VDJ sequence data.