Fig. 5: Rapid pathogen detection for sputum samples of patients with pneumonia or COVID-19.
From: Real-time and programmable transcriptome sequencing with PROFIT-seq
a, A schema of sample collection and target enrichment. Each flow cell was divided into two sections, where half of the pores were used to enrich target pathogens and the other half were sequenced without manipulation as a control. Adapted from Servier Medical Art by Servier under a Creative Commons license CC BY 4.0. b, The yield of total and on-target sequenced molecules in control and adaptive run. The y axis represents the number of raw reads or bases of all reads (top row) or target transcripts (bottom row). The bar colours represent control and adaptive runs, respectively. c, The coverage of SARS-CoV-2 genome during the sequencing process. The colours represent PROFIT-seq (red) or control runs (blue). The dashed lines indicate the time taken for adaptive sampling runs to achieve equivalent coverage as 24 h of control runs. d, The performance of PROFIT-seq in reducing elapsed time for SARS-CoV-2 detection. The points represent individual samples. The error bars indicate 95% confidence intervals (P = 0.0007, two-sided Wilcoxon rank sum test, n = 8 biological replicates). e, The performance of PROFIT-seq in increasing data yield for SARS-CoV-2 detection. The points represent individual samples. The error bars indicate 95% confidence intervals (P = 0.0007, two-sided Wilcoxon rank sum test, n = 8 biological replicates). f, The sensitivity of S-protein variant calling using PROFIT-seq (red) or control (blue) data. g, The composition of pathogenic bacteria in the S01 and S06 samples. h, The composition of detected pathogens in the sputum samples of patients with pneumonia using PROFIT-seq (top) and control data (bottom). The colours in g and h correspond to different target pathogens. Pneumonia and COVID-19 samples were named as P and S, respectively. Source numerical data are available in Source data.
