We’re working on 1M Covid-19 testing capacity per day

I'm the co-founder and CTO at BillionToOne. I'm happy to answer any questions here. I've also posted a slightly more technical explanation of how the test works and why it can scale here: https://twitter.com/dtsao/status/1247642005510873088?s=21

Edit: Since our site seems to be overwhelmed at the moment, here's a recap:

We’ve been working hard at BillionToOne on a new COVID-19 test that scales testing to everyone in the US. Our test (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, per capita (https://www.washingtonpost.com/world/2020/04/02/free-coronav...).

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 protocol so COVID-19 could be detected from sequencing data using linear regression. 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.

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 we can skip RNA extraction entirely without affecting test sensitivity and limit of detection.

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

A distributed system is often the only way 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 Distributed testing could scale from 200k to >1 million tests per day, but would require a change in regulations that currently prohibit it.

Thanks to the BillionToOne team for pulling this work together! Next step is to start manufacturing test kits and obtain Emergency Use Authorization from the FDA. We’re eager to work with clinical Lab Directors and contract kit manufacturers.

Edit 2: Link to scientific manuscript: https://www.dropbox.com/s/07esyehsvfpmllc/A%20Highly%20Scala...

Hmm... website seems overloaded atm.

LMK if you need help making your site work.

Can someone here explain in a couple of points what the idea is? While the site is overwhelmed?

Edit, is the idea (for the non-expert):

1) Repurposing idle gene sequencing equipment left over from Human Genome project

2) Reducing / removing the step of having to extract the RNA of the virus as the marker

3) Making these tests / machines available widely across the country so that the delay to getting a result is minimized ?

Thanks for your efforts! Inspiring to see our broader community spring into action.

I was part of a volunteer team that tested 3400 people on Friday/Saturday in Santa Clara country for COVID-19 antibodies [1]. It took a team of 100+ volunteers 10 hours / day just to collect samples.

Stanford, for example, has plenty of automated testing capacity, and even reagents. IMHO, the limiting factors are not that we need new tests, but rather we need (1) lighter regulations (2) funding to buy supplies and (3) massive manpower to scale-up drive through testing

[1] https://www.stanforddaily.com/2020/04/04/stanford-researcher...