Extended Data Fig. 5: Within-pair similarity of neutralization and binding responses remains significant for transmission pairs with lower genetic distance.

a–c, As a sensitivity analysis for Fig. 1b, the average similarity of neutralization and antibody-binding responses was determined for those transmission pairs with a genetic distance <0.03 (a, n = 280), <0.02 (b, n = 243) or <0.01 (c, n = 148), and compared to two alternative scenarios: (1) completely random reassignment of recipients to transmitters and (2) random reassignment of recipients to transmitters with same demographics (subtype, ethnicity and untreated infection length). One-sided P values were derived from comparison with 1,000 reassignments. Each violin plot is smoothed using a normal kernel, and its width represents the likelihood of a certain average correlation in the respective alternative scenario. The medians are shown (white dots), each box spans the IQR and each whisker extends to the most extreme value no more than 1.5× IQR from the box. d, e, As a sensitivity analysis for Fig. 1c, the proportion of variability in responses explained by the infecting virus, determined using unadjusted (d) and fully adjusted (e) (adjusted for duration of infection, subtype, ethnicity, log viral load and diversity) mixed-effect Tobit regression models is shown when restricting the analysis to closely related pairs (threshold on the x axis).