5 ms·

I’d be curious to the answer to that too. I can think of quite a few reasons, but I’m sure there are nuances that are completely unknown to me. I’m more intere

I’d be curious to the answer to that too. I can think of quite a few reasons, but I’m sure there are nuances that are completely unknown to me. I’m more interested in the parent question at the moment. I know almost nothing about the subject matter. What are the blockers for deploying a simple virus test at the scale we need?

bhaumik 7y ago
Supply chain issues, for one. Eg. Not enough cotton swabs: https://www.politico.com/news/2020/03/16/coronavirus-testing-glitch-cotton-swabs-132692 https://www.politico.com/news/2020/03/16/coronavirus-testing...
- hcknwscommenter 7y ago
  Seriously? There are approximately 1 Billion cotton swabs in this country (U.S.). This is not the issue. The issue is gross federal gov't incompetence.
  - Reelin 7y ago
    It's somewhat more nuanced than that. The currently approved swabs have limited availability, and indeed there are others (unapproved) that would work. However it seems you can't use just any - they have to consist of synthetic fiber, can't have a wooden shaft, and can't contain calcium alginate. This rules out many of the swabs that a healthcare facility might have on hand. (https://khn.org/news/as-coronavirus-testing-gears-up-specialized-swabs-running-out/ https://khn.org/news/as-coronavirus-testing-gears-up-special...)
- makomk 7y ago
  Yeah, by a bit of absolutely terrible luck, the preferred swabs for this are produced by a factory in Lombardy, Italy. There are other manufacturers of swabs that could be used but they don't seem to have the production capacity.
nkrumm 7y ago
It boils down to people, logistics, and efficiency: Yes, we can produce the primers, develop the tests, ramp up the supply of RNA extraction kits, swabs, tips, etc. Individually easy, but together more challenging, especially when the entire world is also trying to acquire the same products. Yes, large, fast and high-scale instruments exist. But, they need to be set up and calibrated. They need adequate power, cooling, water, space, etc. The technicians need training. They need network interfaces, etc. Yes, it's a simple test. But there are still SO MANY steps needed to generate a result from a sample, and those take people. Just looking at the laboratory workflow: 1) Sample received in shipment -- unbox, scan manifest (if provided) 2) Unbag sample + requisition 3) Check sample label (usually handwritten) and verify accuracy to requisition (possibly handwritten). In an ideal case, orders are coming in as "interfaced orders" (meaning electronically) but many smaller clinics/hospitals will not have this. 4) Enter all demographics of the patient into laboratory system 5) Have second person verify the information 6) Re-bag and send sample to location in lab with test instrumentation 7) Technicians unbag, verify label + order accuracy 8) Decant sample from non-standardized tube sent to lab to standard tube used in lab 9) Scan into liquid handling robot... ...et cetera, et cetera As I will probably find out in the replies there are "solutions" to all of these problems, and many labs utilize them. However, to scale such a complex system so quickly means that there is no room for a "test environment", and all changes have to be made "in production". Even simple changes to the workflow require days of prep to communicate to all of the staff across three daily shifts-- you get the idea. source: i'm a laboratory medicine resident at the UW lab. We scaled from 0 to 3000 tests in 2 weeks and it's been an incredible all-hands effort.
- deleted 7y ago
  [deleted]
- Reelin 7y ago
  I appreciate what's going on at UW regarding this and realize that it must have been a huge amount of work to say the least. However, I'd like to point out that most of what you've described is related to the bureaucracy and paperwork of certified medical procedures. Under ordinary circumstances that's all well and good, but given the severity of the situation it seems like it would have been better to eliminate much of that at least a month ago. Put another way, combat medics don't let someone die just because they're short some official FDA approved widget. Why keep such detailed records? Barcode it on the way in, run the test, and report the result - forget demographic data and any other paperwork, whoever ordered the test can deal with that. The supplies for RNA extraction are common and readily available (I think all the raw components are mass produced?), but only specific kits are FDA approved. Only specific swabs are FDA approved. (https://khn.org/news/as-coronavirus-testing-gears-up-specialized-swabs-running-out/ https://khn.org/news/as-coronavirus-testing-gears-up-special...) > the government is considering expanding its recommended testing material options to allow for more general nasal swabs to keep up with the increased testing demand Standard qPCR machines are incredibly common in both academia and industry and have 96 wells at minimum. The protocol published by the CDC has an 80 minute runtime. That's 1000 tests per day for a _single_ low-end machine. The US response has been an absolute shitshow of bureaucratic dysfunction as far as I'm concerned, and people will likely end up dead as a direct result.

bhaumik 7y ago

Supply chain issues, for one. Eg. Not enough cotton swabs: https://www.politico.com/news/2020/03/16/coronavirus-testing-glitch-cotton-swabs-132692 https://www.politico.com/news/2020/03/16/coronavirus-testing...

hcknwscommenter 7y ago
Seriously? There are approximately 1 Billion cotton swabs in this country (U.S.). This is not the issue. The issue is gross federal gov't incompetence.
- Reelin 7y ago
  It's somewhat more nuanced than that. The currently approved swabs have limited availability, and indeed there are others (unapproved) that would work. However it seems you can't use just any - they have to consist of synthetic fiber, can't have a wooden shaft, and can't contain calcium alginate. This rules out many of the swabs that a healthcare facility might have on hand. (https://khn.org/news/as-coronavirus-testing-gears-up-specialized-swabs-running-out/ https://khn.org/news/as-coronavirus-testing-gears-up-special...)
makomk 7y ago
Yeah, by a bit of absolutely terrible luck, the preferred swabs for this are produced by a factory in Lombardy, Italy. There are other manufacturers of swabs that could be used but they don't seem to have the production capacity.

nkrumm 7y ago

It boils down to people, logistics, and efficiency: Yes, we can produce the primers, develop the tests, ramp up the supply of RNA extraction kits, swabs, tips, etc. Individually easy, but together more challenging, especially when the entire world is also trying to acquire the same products. Yes, large, fast and high-scale instruments exist. But, they need to be set up and calibrated. They need adequate power, cooling, water, space, etc. The technicians need training. They need network interfaces, etc. Yes, it's a simple test. But there are still SO MANY steps needed to generate a result from a sample, and those take people. Just looking at the laboratory workflow: 1) Sample received in shipment -- unbox, scan manifest (if provided) 2) Unbag sample + requisition 3) Check sample label (usually handwritten) and verify accuracy to requisition (possibly handwritten). In an ideal case, orders are coming in as "interfaced orders" (meaning electronically) but many smaller clinics/hospitals will not have this. 4) Enter all demographics of the patient into laboratory system 5) Have second person verify the information 6) Re-bag and send sample to location in lab with test instrumentation 7) Technicians unbag, verify label + order accuracy 8) Decant sample from non-standardized tube sent to lab to standard tube used in lab 9) Scan into liquid handling robot... ...et cetera, et cetera As I will probably find out in the replies there are "solutions" to all of these problems, and many labs utilize them. However, to scale such a complex system so quickly means that there is no room for a "test environment", and all changes have to be made "in production". Even simple changes to the workflow require days of prep to communicate to all of the staff across three daily shifts-- you get the idea. source: i'm a laboratory medicine resident at the UW lab. We scaled from 0 to 3000 tests in 2 weeks and it's been an incredible all-hands effort.

deleted 7y ago
[deleted]
Reelin 7y ago
I appreciate what's going on at UW regarding this and realize that it must have been a huge amount of work to say the least. However, I'd like to point out that most of what you've described is related to the bureaucracy and paperwork of certified medical procedures. Under ordinary circumstances that's all well and good, but given the severity of the situation it seems like it would have been better to eliminate much of that at least a month ago. Put another way, combat medics don't let someone die just because they're short some official FDA approved widget. Why keep such detailed records? Barcode it on the way in, run the test, and report the result - forget demographic data and any other paperwork, whoever ordered the test can deal with that. The supplies for RNA extraction are common and readily available (I think all the raw components are mass produced?), but only specific kits are FDA approved. Only specific swabs are FDA approved. (https://khn.org/news/as-coronavirus-testing-gears-up-specialized-swabs-running-out/ https://khn.org/news/as-coronavirus-testing-gears-up-special...) > the government is considering expanding its recommended testing material options to allow for more general nasal swabs to keep up with the increased testing demand Standard qPCR machines are incredibly common in both academia and industry and have 96 wells at minimum. The protocol published by the CDC has an 80 minute runtime. That's 1000 tests per day for a _single_ low-end machine. The US response has been an absolute shitshow of bureaucratic dysfunction as far as I'm concerned, and people will likely end up dead as a direct result.