A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing

Devon Chandler-Brown; Anna M. Bueno; Oguzhan Atay; David S. Tsao

More broadly, qSanger can enable an even higher volume of population-scale testing if clinical laboratories and Sanger sequencing centers are allowed to collaborate for COVID-19 testing. While Sanger sequencers exist in all molecular diagnostic laboratories, they are most commonly utilized in high volume in genome centers, academic sequencing core facilities, and commercial Sanger sequencing service laboratories. In this model, clinical laboratories could buy 96-well master-mix reaction plates that simply require the addition of each patient sample into a reaction well in a BioSafety Cabinet and PCR thermocycling, whereas the sequencing service laboratory would sequence the samples for next-day results. This would enable a rapidly deployed and distributed population-scale testing. qSanger also has a number of other advantages that may prove to be invaluable as we learn more information about SARS-CoV-2. Since SARS-CoV-2 mutates quickly, the availability of sequence information can be used to identify growing clusters of mutations and aid with contact tracing via phylogenetic analysis of the mutation data. Longer sequences can be designed to capture a wide range of mutations in the qSanger reaction, as the virus mutates and creates sub-strains with different clinical implications.