Fig. 1: SwabSeq diagnostic testing for COVID-19. | Nature Biomedical Engineering

Fig. 1: SwabSeq diagnostic testing for COVID-19.

From: Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples

Fig. 1

a, The workflow for SwabSeq is a five-step process that takes approximately 12 h from start to finish. b, In each well, we perform RT–PCR on clinical samples. Each well has two sets of indexed primers that generate cDNA and amplicons for the SARS-CoV-2 S gene and the human RPP30 gene. Each primer is synthesized with the P5 and P7 adaptors for Illumina sequencing, unique i7 and i5 molecular barcodes, and the unique primer pair. Importantly, every well has a synthetic in vitro S standard that is key to enabling the method to work at scale. c, The in vitro S standard differs from the virus S gene by 6 bp that are complementary (underlined). d, Read count at various viral concentrations. e, Ratiometric normalization enables in-well normalization for each amplicon. f, Every well has two internal well controls for amplification, the in vitro S standard and the human RPP30 standard. The RPP30 amplicon serves as a control for specimen collection. The in vitro S standard is critical for the ability of SwabSeq to distinguish true negatives.

Back to article page