Sequencing data from samples with known viral infection that were sequenced using different RNA-seq technologies were aligned to the PalmDB using kallisto translated search. Viral loads obtained through alternative methods, such as RNA in situ hybridization (RNA ISH) and qPCR, are plotted against the target virus counts returned by kallisto. Correlations were tested using Pearson’s r . From left to right: first panel, RNA ISH over total raw kallisto counts for SARS-CoV for 23 lung autopsy samples from patients with COVID-19, obtained by bulk RNA-seq. Error bars show minimum and maximum values for each read in a pair; the dot shows the mean; P = 2.13 x 10 −6. Second panel, SARS-CoV-2 viral load by RT–qPCR over total raw kallisto counts for SARS-CoV species obtained by bulk RNA-seq of 16 saliva, nasal swab and throat swab specimens from patients with acute SARS-CoV-2 infection. Points indicate the mean among paired reads and duplicates; error bars show minimum and maximum values; P = 1.85 x 10 −6. Third panel, total raw kallisto counts for SARS-CoV for three human induced pluripotent stem (iPS) cell-derived cardiomyocytes infected with SARS-CoV-2 and three control samples obtained by SMART-Seq. Last panel, RT–qPCR over total raw kallisto counts for EBOV for 19 macaque blood samples obtained during different stages of infection with EBOV and sequenced with Seq-Well.
