We’re working on 1M Covid-19 testing capacity per day • Hacker News Board

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

#151

Post by fragmede » Wed, Apr 08, 2020, 6:39 AM UTC

buzzkillington wrote: post #60

tbenst wrote: post #10

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…

I find it incredible that no one has done these studies before issuing the lock down orders. Without knowing what the proportion of people who have been exposed but aren't sick any response is the wrong response. If it turns out that it's already spread to most everybody lock downs are just a way to create more homelessness. If it turns out that the only people with the antibodies are the ones in the hospitals we nee…

The lock-downs are because we don't have the tests and we don't have these studies, and still won't, for weeks or months to come. They're being run as fast as possible but there's a lot we don't know about this disease. In the meanwhile, people are getting sick and dying.

We can disagree on whether a lockdown causes the least amount of societal distress compared to some of the other options, we can argue on when we would personally chose to enact lockdown. We could even try and work out what it would take to prevent people losing their homes and dying. $2000/month UBI seems like it might help.

But seriously, doing anything at all is wrong? And the only right response is to do nothing? No ordering more PPE, no preparing for a surge, no rebalancing shifts so the contagion doesn't take out the police force/navy/healthcare workers/etc?

Saying that any possible response is wrong seems like pretending the problem will go away if we pretend it doesn't exist. Which is really hard to do while people are dying.

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

#152

Post by meheleventyone » Wed, Apr 08, 2020, 6:40 AM UTC

I’d like to point out that schools are not open in the normal sense in Iceland. All the older kids school is stopped and Universities are shut. Our youngest is three and is in her leikskoli on alternate days so they can maintain small group sizes with no contact between them. Our eldest is six and only in school for a few hours in the morning, skips a bunch of more risky activities and is again segregated from other classes. As many businesses are working from home or shut completely a lot of parents have also opted to have their kids at home.

We’re currently in a better situation than a lot of places but it’s by no means without significant changes to daily life. It’s also a lot to do with the early response.

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

#153

Post by raspasov » Wed, Apr 08, 2020, 6:41 AM UTC

mjul wrote: post #147

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…

The RNA extraction can also be done without reagents by using a heat reaction on the sample similar to boiling an egg. It is a 5-minute process. According to an older scientist, Anders Fomsgaard at the Danish Serum Institute, this is how they did it ”in the old days”. He is the father of one of the authors. This eliminates supply chain problems for reagents and was shared quickly to help in Spain. Preprint by Fomsgaa…

This is amazing.

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

#154

Post by cyrux004 » Wed, Apr 08, 2020, 6:45 AM UTC

phantom0308 wrote: post #141

s_y_n_t_a_x wrote: post #94

Earlier quoted context omitted.

Testing has been ramping up https://covidtracking.com/data/us-daily

It's plateaued and has been hovering around 100k per day for 2 weeks (outside California clearing its backlog on 4/4). The White House promised 27M by 3/31 and we were at 1M. It doesn't look like it's ramping up.

I WA we were doing around 7k-8k tests/day 2 weeks back, now its between 4-5k

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

#155

Post by zmmmmm » Wed, Apr 08, 2020, 6:59 AM UTC

dvdt wrote: post #130

zmmmmm wrote: post #123

Earlier quoted context omitted.

All the material on your page talks about throughput but not turnaround time which makes me quite suspicious that it's not very good. Obviously, however, if it takes 2 weeks to do the test then it has very limited utility as the person will have recovered (or had an adverse outcome) anyway. Since it cannot be administered at the point of care I am imagining that you are already up against a day or so of logistics jus…

A turn around time of 24-36 hours should be easily achievable for the performing lab, depending on the time of day the specimen arrives (morning vs afternoon). It takes about 1 hour for the initial RT-PCR amplification, and sequencing takes about 12 hours.

Thanks - that's not too bad.

If people can sort out logistics well enough then it sounds like it could be extremely helpful for implementing broad scale testing.

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

#156

Post by poarneemn123 » Wed, Apr 08, 2020, 7:13 AM UTC

'Machine learning algorithms'

Nothing to see here, just trying to make a quick buck using the pandemic

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

#157

Post by zelphirkalt » Wed, Apr 08, 2020, 7:21 AM UTC

You can test all you want, with a spread like in the USA, there will be trouble to have proper treatment for all the cases. If such testing had begun earlier, then maybe lock down or near lock down scenarios could have been avoided. I see little chance, even with such 1 mio tests, to get it back under control without some kind of lock down or similar restriction to slow the spread. Where do you put all the infected people without locking down? If everyone infected is just told to stay at home, even if everyone complies, it is like a self quaranteen, like a lock down for those people.

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

#158

Post by somberi » Wed, Apr 08, 2020, 7:36 AM UTC

On a separate note - DVDT and billiontoone (David and Bobby) - you guys have been impressive on how you have handled the conversation in this thread. You are polite, informative and a template for me to follow. In addition to what you guys are doing, kudos on your PR skills.

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

#159

Post by ars » Wed, Apr 08, 2020, 7:51 AM UTC

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…

Why not use pooling? You can test 64 samples at once and use a binary search if the pool is positive.

See: https://www.medrxiv.org/content/10.1101/2020.03.26.20039438v...

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

#160

Post by aurelwu » Wed, Apr 08, 2020, 7:56 AM UTC

Great work, a friend of mine is molecular biologist and she is furious about how in germany they don't use alternative methods for RNA Extraction like Phenol/Chloroform (labor intensive but no shortage of material) / SPRI (with magnetic beads) or skipping it altogether.