The frequency at which sites in NS2A were estimated to have nonzero effects appeared bimodal, either showing effects in <1% of the number of times sampled or >99%, Fig 5C. and without effects by whether or not they are part of known epitopes. Odds ratios were calculated by either considering epitopes of both human-derived monoclonal antibodies (hmAb) Eicosapentaenoic Acid and murine-derived monoclonal antibodies (mmAb) and when only restricted to hmAb epitopes. Defining neighborhoods of known epitopes as positions within N sites away (linear distance), the probability of nonzero effect sites being within the neighborhood at random (red) are contrasted against the proportion of variable TNFSF13 sites that were within the neighborhood (gray): b) known epitopes for either hmAb or mmAb, c) known epitopes for hmAb, and d) known epitopes for mmAb outside of hmAb epitopes. N = 0 was when the neighborhood was exactly at the Eicosapentaenoic Acid reported epitope positions. e, f, g) Respective analogous analysis but with neighborhoods defined as being within X angstroms away from known epitopes (3-dimensional spatial distance). X = 0 was when the neighborhood was exactly at the reported epitope positions.(PDF) ppat.1010500.s004.pdf (49K) GUID:?D21064C8-930D-4636-93E5-1B8637C5A447 S5 Fig: Proportion of estimations in which substitutions showed nonzero effect. a) Substitutions in envelope protein (E) only, ordered by the proportion at which substitutions showed nonzero effect across the 100 estimations. Substitutions identified by our threshold of 95% was highly similar to the maximum stringency of 100%; 372/394 substitutions (94.4%). Involvement was retained in 76/77 (99%) of the sites. b) In the analysis where E was concatenated to the 62 nonstructural protein 2A (NS2A) sites which consistently showed nonzero effects in our site sampling analysis, 292/304 substitutions (96.1%) in the NS2A sites remained nonzero at a threshold of 100%. Involvement was retained in 62/62 (100%) of the sites. Proportions corresponding to nonzero effect substitutions reported in our study (threshold of 95%) are colored red.(PDF) ppat.1010500.s005.pdf (37K) GUID:?573EE88E-F44C-4EA2-9FCE-577F37708F1C S6 Fig: Substitutions with non-zero effect sizes in NS2A. Median effect size of substitutions across the 100-fold Monte Carlo cross-validations shown as points, 95% interquartile range as whiskers. Points are colored by locations of the sites: ER lumen (green), transmembrane (yellow), or cytosol (blue). Locations of the sites and domain annotations were taken from [34].(PDF) ppat.1010500.s006.pdf (24K) GUID:?CCC45442-8AB1-4E5A-AD18-B5102C0BE400 S7 Fig: Distribution of nonzero effect sites across NS2A segments. a) Total number of sites in each segment (hollow), number of variable sites (filled black), and number of sites estimated to have nonzero effects (filled red). b) Probability that at least these number of nonzero effect sites were associated with the segments at random. Amino acid positions of the segments shown in parentheses.(PDF) ppat.1010500.s007.pdf (5.7K) GUID:?FDE55E18-7A2E-4361-8A53-00115ABB61CD S8 Fig: Density of coevolving residue Eicosapentaenoic Acid pairs detected by percentile of MI values between pairs throughout the DENV genome. Density scaled to maximum value of one. Thin rectangle corresponds to coevolution relationship between E gene (y-axis) and sites throughout the genome. Thick rectangle highlights relationship between E gene and NS2A gene. b) Density plot expanding the highlighted region in panel (a).(PDF) ppat.1010500.s009.pdf (87K) GUID:?F39DC724-B70E-4685-96D4-79A54B793EE4 S10 Fig: Relationship between difference in antigenic distance observed in Eicosapentaenoic Acid virus triplets and effect size estimates from the substitution model. Shown separately for substitutions located in epitopes of human-derived monoclonal antibodies (hmAb), E domain I/II/III but outside of known epitopes (EDI/II/III), E stem/anchor domain, and nonstructural protein 2A (NS2A). Points are the medians of the observations/estimates. Lines are 95% interquartile ranges.(PDF) ppat.1010500.s010.pdf (7.7K) GUID:?BE084F48-F07F-41DC-8DE7-A579391B9689 S11 Fig: Effects of substitutions in footprints of human-derived mAb (hmAb). Difference in antigenic distance observed between pairs of Eicosapentaenoic Acid viruses separated by the specific substitution and antigenic distance observed in respective effectively identical viruses without the substitution (control viruses). Thick lines show median and 95% interquartile range (IQR) for triplets of all serotype.