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

billiontoone.com

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

#101

Post by mrkurt »

zepto wrote: post #84
billiontoone wrote: post #35

Earlier quoted context omitted.

I don't think we are in any way undervaluing the serological tests. A great serological test would be very useful. However, because of the indirect measurement, they tend not to be very sensitive or specific, so it is fair to say that they become more important not at the peak of the pandemic but at the post-pandemic period. By the way, as a company, we really don't have much to gain from this test. If it does not ge…

You are downplaying the value by saying they will be useful in the future, rather than now. This is not so. They are valuable right now.

For what? "Google for answers" isn't very helpful. It sounds like they're saying serological tests are valuable, but not viable for immediately testing a large population.

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

#102

Post by kitteh »

loeg wrote: post #68
sgw928 wrote: post #48

Earlier quoted context omitted.

The situation is similar in WA state, where the current bottleneck is specimen collection, as there is a shortage of swabs, vials, PPE and personnel. This results in large amount of existing lab capacity, such as at UW Virology labs, not being used. Skipping RNA extraction definitely helps with expanding lab capacity in places where that's the current bottleneck, but isn't the most pressing thing in WA.

The other bottleneck in WA is that the state's multimillion dollar, IBM-contracted data collection program can't keep up ingesting a few thousand records a day.

Yes - this has been falling over for the past week.

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

#104

Post by mrkurt »

robomartin wrote: post #77

We are seeing example after example of the power of entrepreneurship and private enterprise. I hope we remember this going forward and weave it into our national culture deeper and wider than it already is.

What we're seeing is how agile a small, functional, and motivated group can be. Private enterprise as whole is every bit as f'd up as the government.

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

#105

Post by andrewon »

dvdt wrote: post #2

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…

Hi, I read through your paper. Interesting method.

In figure 1A, the workflow includes a standard PCR step before Sanger. Workflow-wise, wouldn't it still have the same bottleneck as qPCR test, i.e. limited by 96/384-well instrument runs?

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

#106

Post by andy_ppp »

I really think this explanation of how the number of people in the population who have the disease affects the chances of a positive test being incorrect, it is very unintuitive but look at the video as it explains that even very Sensitive and Specific tests can be problematic to see who in the population has a disease: https://www.instagram.com/tv/B-qZLJoAf3V/

Spreadsheet to play with is here: https://docs.google.com/spreadsheets/d/1IPcX2JYt9mXdaTvj-3mh...

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

#108

Post by t_serpico »

dvdt wrote: post #71
abhisuri97 wrote: post #53

Earlier quoted context omitted.

Hey, lowly Bio undergrad here, but how are you able to skip the RNA extraction step? I read the paper and you use the viral transport medium, but wouldn't you have to also purify RNA from that (or is it just much easier to extract RNA from that medium)? I also dived into the paper behind the "skip the RNA extraction step" methodology and it basically seems to swap out one RNA extraction kit for another (Qiagen RNeasy…

Thanks for the question! The goal of skipping RNA extraction is to decrease the amount of labor necessary for processing samples and also to eliminate a dependency on RNA extraction reagents that have recently become difficult to find. The FDA is very strict about the specific brand and model of kit you use, so showing that you can swap out one RNA kit for another is actually very useful because you will have allevia…

https://en.wikipedia.org/wiki/DNA_spiking -- this seems like an old idea, no?

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

#109

Post by andrewon »

dvdt wrote: post #44
Eridrus wrote: post #30

Earlier quoted context omitted.

Thank you for what seems to be a breakthrough with implications beyond even the current outbreak. I had a few questions though: How do you compare this test to the Abbott machines? Obviously that test is faster, but how does that impact what we can do with it? For 1m/day to be sufficient, do we need contact tracing programs to be able to find everybody who needs to be tested? How hard will it be to scale these progra…

The Abbott machines are point-of-care devices that typically sit in doctor's offices. One really interesting use case I've heard of for the Abbott machines is to test all OB patients who are coming in to the clinic for routine care to make sure that they are COVID-19 negative. This allows the clinical staff to conserve PPE and use less burdensome precautions. I think that where the Abbott machines might hit a wall is…

Abott's test is cartridge based, isothermal and modular. There should be no technical reason why they cannot build a high throughput, random access version.

Whether this is the direction the company wants to spend their resources is another story.

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

#110

Post by billiontoone »

andrewon wrote: post #105
dvdt wrote: post #2

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…

Hi, I read through your paper. Interesting method. In figure 1A, the workflow includes a standard PCR step before Sanger. Workflow-wise, wouldn't it still have the same bottleneck as qPCR test, i.e. limited by 96/384-well instrument runs?

Thanks; that is a good question. In our laboratory, we have a ratio of 10:1 for PCR to qPCR instruments. In the new laboratory that we are constructing, the ratio is 50:1. It was similar at Stanford academic laboratories during my PhD. Standard PCR instruments are inexpensive and very common. qPCR instruments are definitely not as common, as they are very specialized instruments for a few use-cases.

Most clinical laboratories would have 10 to 50 PCR instruments that they can use to run the initial amplification reaction in parallel before Sanger sequencing. Also, Sanger sequencing uses a plate feeder, so you can add new plates on top as the second round of PCR reactions finish.

But, more importantly, the qSanger can by-pass RNA extraction, which seems to be an important bottleneck in the RT-qPCR workflow.

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