Fig. 3

Detection of common respiratory viruses in NP metatranscriptomes. A Abundance heatmap for viruses detected in NP metatranscriptomes for 221 patients. For each virus, the qRT-PCR result is shown on the left of the column as a color gradient (negative—white, high to low cycle threshold values—light gray to black), and the estimated RNA-seq abundance is depicted on the right of the column as a color gradient (absent—white, low—yellow, high—dark blue). Each row in the heatmap and tip in the hierarchical tree corresponds to an individual patient sample. B qRT-PCR abundance (1/ cycle threshold) versus metatranscriptomic viral load (log₁₀ of the RPKM). The estimated viral load from RNA-seq is significantly correlated with 1/Ct value from qRT-PCR. C Metatranscriptomic abundance of respiratory viruses in negative ( −) versus positive ( +) samples (labelled on X axis) defined by qRT-PCR test result. The boxes show the interquartile range and median line, and the whiskers show the variability extending to the furthest data points within 1.5 times above and below the interquartile range. Outliers outside of these ranges are shown as data points. Two-tailed t-test p-values for positive versus negative samples are shown above each plot. Red dashed lines indicate the detection threshold equivalent to 1 RPM