[Goose]

I think this is potentially an issue, but six months in to the outbreak, you would expect the testing supply chain pipeline to be full by now. The purchasing people also should know what the lead times are, and I would expect the lead times should be going down, not up. Independent of the cause, if I am a lab who can't test because I don't have a reagent (for whatever reason), I would be screaming to the press and the public about it. We aren't seeing that.



I think it more probable that there are administrative delays that make the process take more time than it should. There are lots of "steps" in getting a sample from the test subject to the remote lab and back, and each one of those steps probably isn't optimized for speed. Nobody has analyzed the system from the point of view of minimizing the delay. Each step may not take real long, but is death by 1000 cuts. Several different organizations are involved in each step. Tests are probably marshaled several different times in the process. Each time one waits for "enough" tests to accumulate, there is a delay. Obviously, I don't know this for a fact. However, given it is a system that has been created basically from nothing in the last 5 or 6 months, it is unlikely it is well optimized.

This is incorrect. There are real delays in reagent supply chain. Our hospital recently had to add a new type of testing machine, not cheap. We could have bought more of the other testing machines we already have that functions very well, but by diversifying we can ensure more backup capability, and use different types of reagents because we couldn't get enough from what we had to return labs quick enough. We needed 48 hour turnaround but were starting to come up to 72 hrs.

It sounds to me like your lab had a capacity issue due to the increase in cases. When you are running at 100% of capacity and have any delay in your supply chain, you can't ever recover. Thus testing becomes permanently delayed. The increase in cases also probably increased consumption of everything, making it necessary to order more supplies earlier than expected. The new machine will increase capacity, and it probably does make sense to order from another manufacturer to reduce dependence on single-source materials. It also may be you could get that machine faster.

This is pretty unusual- normally there is one type of lab you can order for any particular lab. Now there's three, two in house and one send out (Quest, which takes the longest, and only used for low priority tests now).
[/quest]
Yes, these are the marshaling delays I referred to.

[quote]

This is not including rapid tests, only PCR.



Now, different orgs have different throughput and needs. My wife's practice uses a more smaller, perhaps more boutique, lab without big numbers and bought a lot of reagents when able. They can turn around a test in 6 hours.

They may have some capacity that lies unused most of the time. They probably doing the test the "manual" PCR way. Morel labor intensive, but  more responsive. You don't need to fill up the machine, etc.

The main issue again is our prevalence. If this thing wasn't raging everywhere we'd surely have results uniformly in less than 24 hrs.



Here's NYT on this-

https://www.nytimes.com/2020/07/23/healt...rtage.html

For sure the prevalence has really upped the need for testing, and it would appear the suppliers haven't expanded as fast as it requires. Thanks for the link. The NYT article seems to say it is random shortages of everything that is limiting testing throughput.

I read an article recently (can't seem to find it now) that said the issue was that we were too reliant on the more automated testing machines.  One where you could just put it in and it'd do everything for you.  And unfortunately, while we have a ton of these machines.  We don't have whatever it was that was needed for these machines to process these tests (I'll call them test kits).  These companies all had their own proprietary kits.  The lack of a common standard means that if you are using company ABC's most prolific machine that can process 6k tests a day.  You're in a bind because that company has 100k such machines out there, but can only produce 1 million test kits  a day, so you're still short 5 million from maxing out those machines.

I'm making up the numbers, but the testing crunch, at least for the US, was attributed to the preference for these more automated machines, each with their own proprietary test kits.

And so like dabigv13 said hospitals are resorting to have to buy multiple brands so that they won't be hamstrung by one company running out of test supplies.  Unfortunately, that likely means that the hospitals are running way under capacity considering all the machines they have.

I doubt that. They are running all the tests that they can. Their "capacity" may be reduced by the lack of custom plastic or the lack of primer kits. Quoting how many tests per day your machines can run as your capacity is an error that has been prevalent during this whole epidemic. Your capacity can be limited by lack of technical staff, lack of reagents, or lack of people to do the paperwork. At one time or another all of these have been cited as a reason for delays in testing.

Edit:
Found the article:
https://www.reuters.com/article/health-c...SL2N2EV01Z

Good article. Thanks for the link. It does contain some real examples of limitations due to insufficient reagent supplies. This has been absent in most of what I had seen previously.
However, I think the Reuters article leaves the impression that using the "old style" method of testing was an option to deliver adequate testing in the USA. It isn't. The article does point out that it is labor-intensive, but it doesn't point out adequately that it is SKILLED labor intensive. Training people takes just as long or longer than increasing supply from sole-source vendors does, assuming you can even find the people qualified to do the work. The impression is also given that you can just order a "generic" reagent and all will be well. It is not that simple.The reagent has to be validated for that test. It can be done by the vendor, or by the user, but it has to be done. There are approved protocols that must be followed. For example, the CDC test cited in the article was only approved with certain lots of reagents from two vendors. Others may have been added later, but it isn't a free-for-all. The USA is doing it mostly using high-throughput machines because with our population automation is the only way we can come close to doing the number of tests required. Nothing is stopping hospitals (and State labs) from doing it the "old" way. If it were viable, it would be done that way.

[Goose]

I think this is potentially an issue, but six months in to the outbreak, you would expect the testing supply chain pipeline to be full by now. The purchasing people also should know what the lead times are, and I would expect the lead times should be going down, not up. Independent of the cause, if I am a lab who can't test because I don't have a reagent (for whatever reason), I would be screaming to the press and the public about it. We aren't seeing that.



I think it more probable that there are administrative delays that make the process take more time than it should. There are lots of "steps" in getting a sample from the test subject to the remote lab and back, and each one of those steps probably isn't optimized for speed. Nobody has analyzed the system from the point of view of minimizing the delay. Each step may not take real long, but is death by 1000 cuts. Several different organizations are involved in each step. Tests are probably marshaled several different times in the process. Each time one waits for "enough" tests to accumulate, there is a delay. Obviously, I don't know this for a fact. However, given it is a system that has been created basically from nothing in the last 5 or 6 months, it is unlikely it is well optimized.

This is incorrect. There are real delays in reagent supply chain. Our hospital recently had to add a new type of testing machine, not cheap. We could have bought more of the other testing machines we already have that functions very well, but by diversifying we can ensure more backup capability, and use different types of reagents because we couldn't get enough from what we had to return labs quick enough. We needed 48 hour turnaround but were starting to come up to 72 hrs.

It sounds to me like your lab had a capacity issue due to the increase in cases. When you are running at 100% of capacity and have any delay in your supply chain, you can't ever recover. Thus testing becomes permanently delayed. The increase in cases also probably increased consumption of everything, making it necessary to order more supplies earlier than expected. The new machine will increase capacity, and it probably does make sense to order from another manufacturer to reduce dependence on single-source materials. It also may be you could get that machine faster.

This is pretty unusual- normally there is one type of lab you can order for any particular lab. Now there's three, two in house and one send out (Quest, which takes the longest, and only used for low priority tests now).
[/quest]
Yes, these are the marshaling delays I referred to.

[quote]

This is not including rapid tests, only PCR.



Now, different orgs have different throughput and needs. My wife's practice uses a more smaller, perhaps more boutique, lab without big numbers and bought a lot of reagents when able. They can turn around a test in 6 hours.

They may have some capacity that lies unused most of the time. They probably doing the test the "manual" PCR way. Morel labor intensive, but  more responsive. You don't need to fill up the machine, etc.

The main issue again is our prevalence. If this thing wasn't raging everywhere we'd surely have results uniformly in less than 24 hrs.



Here's NYT on this-

https://www.nytimes.com/2020/07/23/healt...rtage.html

For sure the prevalence has really upped the need for testing, and it would appear the suppliers haven't expanded as fast as it requires. Thanks for the link. The NYT article seems to say it is random shortages of everything that is limiting testing throughput.

I read an article recently (can't seem to find it now) that said the issue was that we were too reliant on the more automated testing machines.  One where you could just put it in and it'd do everything for you.  And unfortunately, while we have a ton of these machines.  We don't have whatever it was that was needed for these machines to process these tests (I'll call them test kits).  These companies all had their own proprietary kits.  The lack of a common standard means that if you are using company ABC's most prolific machine that can process 6k tests a day.  You're in a bind because that company has 100k such machines out there, but can only produce 1 million test kits  a day, so you're still short 5 million from maxing out those machines.

I'm making up the numbers, but the testing crunch, at least for the US, was attributed to the preference for these more automated machines, each with their own proprietary test kits.

And so like dabigv13 said hospitals are resorting to have to buy multiple brands so that they won't be hamstrung by one company running out of test supplies.  Unfortunately, that likely means that the hospitals are running way under capacity considering all the machines they have.

I doubt that. They are running all the tests that they can. Their "capacity" may be reduced by the lack of custom plastic or the lack of primer kits. Quoting how many tests per day your machines can run as your capacity is an error that has been prevalent during this whole epidemic. Your capacity can be limited by lack of technical staff, lack of reagents, or lack of people to do the paperwork. At one time or another all of these have been cited as a reason for delays in testing.

Edit:
Found the article:
https://www.reuters.com/article/health-c...SL2N2EV01Z

Good article. Thanks for the link. It does contain some real examples of limitations due to insufficient reagent supplies. This has been absent in most of what I had seen previously.
However, I think the Reuters article leaves the impression that using the "old style" method of testing was an option to deliver adequate testing in the USA. It isn't. The article does point out that it is labor-intensive, but it doesn't point out adequately that it is SKILLED labor intensive. Training people takes just as long or longer than increasing supply from sole-source vendors does, assuming you can even find the people qualified to do the work. The impression is also given that you can just order a "generic" reagent and all will be well. It is not that simple.The reagent has to be validated for that test. It can be done by the vendor, or by the user, but it has to be done. There are approved protocols that must be followed. For example, the CDC test cited in the article was only approved with certain lots of reagents from two vendors. Others may have been added later, but it isn't a free-for-all. The USA is doing it mostly using high-throughput machines because with our population automation is the only way we can come close to doing the number of tests required. Nothing is stopping hospitals (and State labs) from doing it the "old" way. If it were viable, it would be done that way.