[HN Gopher] Show HN: We're unlocking 1M Covid-19 testing capacit...
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Show HN: We're unlocking 1M Covid-19 testing capacity per day
Author : dvdt
Score : 38 points
Date : 2020-04-07 22:37 UTC (22 minutes ago)
(HTM) web link (www.billiontoone.com)
(TXT) w3m dump (www.billiontoone.com)
| voz_ wrote:
| LMK if you need help making your site work.
| supernova87a wrote:
| 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 ?
| tbenst wrote:
| 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.
| 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
| dang wrote:
| While waiting for the site to come back: Internet archive has a
| version from earlier today.
|
| https://web.archive.org/web/20200407224229/https://www.billi...
| dvdt wrote:
| 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, I'm
| posting here 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 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.
|
| 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 <24 hour turnaround, there is an opportunity to
| further scale up testing by distributing the work to their
| (currently) idle sequencers.
|
| 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.
| [deleted]
| thelean12 wrote:
| Your site seems to be getting hugged to death. Can you answer a
| few questions here:
|
| - Is this test to see if someone currently has it, or if they
| have the anti-bodies and are (presumably) immune?
|
| - What are the false-positive/false-negative rates? How does this
| compare to current leading tests?
|
| - What's the cost per test? How does this compare to current
| leading tests?
| dvdt wrote:
| Thanks for letting me know about the site!
|
| This is a test to see if someone has a current COVID-19
| infection. The antibody tests (serological) tests are also
| important, but since it is estimated that only ~1% of the US
| has previously contracted COVID-19, it will be a while before
| serological testing becomes useful at a population level.
|
| Our initial data show no false-positives and no false-negatives
| out of all specimens assayed. However, it is early days still
| and _none_ of the leading tests have real-world data on false-
| positive and false-negative rates. The crucial parameter here
| to compare test performance is limit of detection (LOD). We
| showed we could detect as few as 10 molecules of virus, which
| is on par with the best RT-qPCR tests.
|
| Cost is definitely an important consideration for roll-out of a
| widespread test. We anticipate that the cost will be about $15
| per test.
| bb88 wrote:
| Hmm... website seems overloaded atm.
| Turukawa wrote:
| Why advertise before you've got FDA approval?
| nomel wrote:
| The FDA _is_ the lock.
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(page generated 2020-04-07 23:00 UTC)