Fig. 1

DeepSARS enables simultaneous diagnostic testing and genomic surveillance of SARS-CoV-2. A DeepSARS workflow consists of patient sample collection from nasopharyngeal swab or saliva (without RNA extraction) followed by targeted and multiplexed library preparation for deep sequencing. The multiplexing strategy uses well-specific primers to introduce a patient-barcode during reverse transcription. Samples are then pooled and multiplexed PCR is performed with a plate-specific barcode. Overview created using Biorender.com. B SARS-CoV-2 sequence diversity for each nucleotide based on whole genome sequencing data from 2825 samples collected between December 2019 and March 2020. Red points indicate regions covered by the site-13 primer set in DeepSARS. C Colored lines represent sites of the SARS-CoV-2 genome targeted by the three primer sets of DeepSARS tested in this study: site-13, alpha-15 and spike-16. D Maximum likelihood trees generated on 100 samples from previous study that profiled an Austrian outbreak [14]; trees are inferred using either WGS or the sites targeted by DeepSARS. Color corresponds to variant classification (based on characteristic mutation profiles) and tip name corresponds to the individual sequence. Tree was rooted using a reference sequence recovered from Wuhan (NCBI: MN908947). E Phylodynamic estimates of the effective reproductive number (R_e) using either WGS or the sites covered by DeepSARS. For each tree, 30 sequences were sampled from Italy at two different time points (prior to March 8, 2020) or at a later time point where the majority of sequences correspond to the alpha variant (between February 1, 2021 to March 15, 2021). Dotted line indicates the prior distribution. F Phylodynamic estimates using the same sequences in (E) but depicting the inferred origin date of the outbreak using WGS or sites covered by DeepSARS