Extended Data Fig. 6: Comparison of fitness model results with full data or disease only data.

(a-b) Results with the full data. (c-d) Results with the disease-only data. a and c present the model fits for the proportion of serotypes from non-vaccine type (NVT), PCV7 types, and additional PCV13 types not included in PCV7 from the years 2000 to 2014 in this study. Points represent data and line represent the model fit. b and d present the relative fitness estimates for all three groups of serotypes in each era. Pre-vaccine era is prior to 2009 for NVTs, prior to 2009 for PCV7 and prior to 2011 for PCV13. Post-vaccine era is post-2009 for NVTs, post-2009 for PCV7 and post-2011 for PCV13. Error bars represent 2.5 and 97.5 percentiles.