We’ve been working hard @BillionToOne on a new COVID-19 test that scales testing to everyone in the US https://www.billiontoone.com/covid-19 .
It (1) re-purposes existing infrastructure, (2) eliminates time-consuming RNA extraction, and (3) enables a distributed system for COVID-19 testing.

We need 1 million tests per day to end the stay-at-home orders. Schools are still open in Iceland because they test 15x more than the US does.

The first thing we figured out is how to run COVID-19 tests on existing automated Sanger sequencers. One sequencer can process up to 3840 samples per day. There are hundreds of sequencers of excess capacity because they were built for the Human Genome Project over 20 years ago.

It would take only 2 sequencers to surpass the current test capacity for all of California. There are far more than 2 sequencers in California (some individual labs have 10 or more).

We tweaked the lab protocol so that COVID-19 could be detected from sequencing data using machine learning. Basically, we add ~100 copies of a known DNA sequence to help us calculate how much virus nucleic acid is in the specimen. It works just as well as gold-standard RT-qPCR.

Clinical lab workflow for COVID-19 testing is traditionally (1) Specimen accessioning, (2) RNA extraction, (3) RT-qPCR (4) Reporting. RNA extraction in particular has been a huge bottleneck in terms of reagent shortages and labor-intensiveness.

We showed that our qSanger COVID-19 test can skip RNA extraction entirely without degrading sensitivity or limit of detection.

By skipping RNA extraction and using automated Sanger sequencers, we think the US can get to an additional 200,000 samples per day test capacity in existing clinical labs.

As Silicon Valley engineers know, you often need a distributed system to operate at massive scale. A fully distributed system could have different sites and labs responsible for each process and dynamically re-allocate resources based on availability and capacity.

The Broad Institute COVID-19 lab has already started doing this. They are asking for specimens to be submitted in a standardized tube format and pre-barcoded. They have essentially distributed the specimen accessioning work.

Because there is a highly developed service industry for Sanger sequencing with <24 hour turnaround, there is an opportunity to further scale up testing by distributing the work to their (currently) idle sequencers.

Distributed testing can scale to 1 million tests per day, but would require a change in regulations that currently prohibit it.

Thanks to the BillionToOne team for all the hard work pulling this together! Next step is to start manufacturing test kits and obtain Emergency Use Authorization from the FDA. If you're a Lab Director or contract kit manufacturer, we're looking for partners.