Fig. 2

DeepSARS performs highly sensitive detection and identifies mutations from synthetic RNA of SARS-CoV-2. A Samples with synthetic RNA templates of SARS-CoV-2 are mixed with human RNA and subjected to the DeepSARS library preparation protocol using site-13 primer set. Controls include human RNA only and no RNA. Bar graphs show the number of reads mapping to either viral or human genes (GAPDH, RNAP). Each read contained the correct patient barcode. B Synthetic RNA templates are titrated at different copy numbers in the absence (top) and presence (bottom) of human RNA and subjected to the DeepSARS library preparation protocol using site-13 primer set. Heatmaps and bar graphs show reads mapping to viral or human genes and their ratio. C Heatmaps and bar graphs show mapping reads following DeepSARS workflow with site-13 primers on synthetic RNA mixed with human RNA, including pooling samples post reverse transcription (RT). Each column corresponds to a distinct RT reaction. All RT reactions of a given viral copy number used a single patient barcode but a different plate barcode. D Following DeepSARS workflow described as in C but arranged that identical patient barcodes were used for each viral copy number dilution; box plots and heatmaps show the number of viral and human reads. Each column represents an individual RT reaction. Lines separating columns delineate different viral copy number dilutions. E Consensus sequences obtained using the site-13 primer set of DeepSARS on two SARS-CoV-2 synthetic RNA variants with defined mutational diversity. All bases in red indicate expected and recovered mutational divergence. F The fraction of aligned reads containing variant-defining mutations of either synthetic RNA control 4 or synthetic RNA control 14