LAMP-Seq: Population-Scale COVID-19 Diagnostics Using a Compressed Barcode Space

Jonathan L Schmid-Burgk; David Li; David Feldman; Mikolaj Slabicki; Jacob Borrajo; Jonathan Strecker; Brian Cleary; Aviv Regev; Feng Zhang

Barcodes were made robust to sequencing errors by ensuring a minimum Levenshtein edit distance between any barcode pair sufficient to detect either one (10,000 barcode set) or two (1,000 barcode set) insertion, deletion or substitution errors (Suppl. Comparing barcoded LAMP reactions to non-barcoded controls using a dsDNA surrogate template for SARS-CoV-2, we confirmed that the presence of a 10-nt barcode within the FIP primer does not affect LAMP sensitivity, product amounts, or downstream PCR amplification ( Fig. 1D ). Templating two individually barcoded LAMP reactions with 100-fold differing amounts of dsDNA template, combining them for PCR amplification, and sequencing the products resulted in read numbers within two-fold between the two samples ( Fig. 1E ), indicating that LAMP saturation can effectively compress the dynamic range of input viral loads.