Fig. 2: Relationship between RT–PCR Ct values, viral load, timing of observations and viral detection.
From: Evolution and spillover dynamics of yellow fever at the forest–urban interface in Brazil
a, Scatterplot of RT–PCR Ct values versus YFV mapped RPM for each sample group (Group I: H. leucocelaenus, Group II: PEAL NHPs, Group III: background NHPs), illustrating the inverse relationship between Ct values and viral abundance (Spearman’s r, two-sided). Fitted line and shaded band show linear trend and 95% confidence interval. b, Density ridge plot displaying the distributions of Ct values, viral load (RPM) and N50 among the different sample groups. c, Empirical and estimated distributions of the delay between A. guariba death and notification. The black line shows the fitted probability density (gamma distribution). Bars indicate the empirical distribution of days from death to observation, coloured by decomposition stage: green for intact or recently dead animals (0–2 days post death) and purple for medium or advanced decomposition (≥3 days post death) (see Methods). d, YFV genome coverage (% of reference) across 89 samples for which viral metagenomics sequencing was attempted (35 from intact or recently dead NHPs; 12 from NHPs found at medium or advanced decomposition; and 43 NHPs for which stage of decomposition was unknown). Samples were grouped by decomposition stage. The horizontal dashed red line marks the 70% whole-genome coverage threshold used for inclusion in phylogenetic analyses. Spearman’s correlations and Wilcoxon tests were two‑sided; exact P values are reported in main text.
