4 ms·

I have a couple of questions that I hope you would have insight in to. * Why did the CDC decide to develop their own diagnostic? Was there some issue with the

by anitil 7y ago

I have a couple of questions that I hope you would have insight in to. * Why did the CDC decide to develop their own diagnostic? Was there some issue with the WHO test that they were trying to avoid? Or just internal politics * What was the core issue with the CDC's tests? (It's possible that I'm not equipped to understand this, but an ELI5 would be great) (Edit - I have tried to research this, but for #1 it seemed kind of murky and #2 looks like either poor quality control or poor design - https://www.vice.com/en_us/article/y3mkpx/how-the-cdc-botched-basic-science-in-its-attempt-to-make-a-coronavirus-test https://www.vice.com/en_us/article/y3mkpx/how-the-cdc-botche.... I'm hoping for some clarity on these)

vikramkr 7y ago
1) No idea 2) You found the article I was about to link actually. Basically, for a PCR test, what you're doing is making a lot of a particular sequence of DNA if it's present. You set up the reaction conditions so that if a particular sequence of DNA is present in your test tube (actually a plate but same difference), that sequence of DNA will make a lot more of itself. If there isn't that sequence of DNA, nothing will happen. You don't get to pick the entire sequence youa re looking for. You basically hae to pick a start region and and end region for the piece of DNA you want to amplify. So if the nucleotide sequence for a coronavirus gene was atcgctatagc, and you are using 3 letter long end regions (in reality you use longer length sequences and regions), you might pick your targets as atc and agc from each end. Therefore, any sequence of dna in your sample with atg and agc will get amplified and you will get a signal telling you that a dna sequence that starts with that first target sequence and ends with that second target sequence is there. If you don't get a signal, that means no coronavirus. When picking that sequence (known as a primer sequences since it primes the replication reaction), you have to be careful. Lets say that in your body you have a gene that goes gtcatcagctga or something. Inside of that sequence, your primer sequences are present. If you run a test for your desired sequence, you're going to get signal from non-coronavirus DNA. In order to make sure there are no overlaps in your primers, you, well, this is the part that's hard to believe. You type in your sequences in to a website and hit a button. Hence the following excerpt from the article you found: “I just put the primers as input into this program and within seconds it tells you there’s problems with it,” Altman said. “It’s freely available. It’s not hard to use at all. It’s one of those things you’d do as a basic quality control check. It seems like they hand-designed these primers and it seems like they didn’t use computer tools to check it.” So, yeah. Everyone's still having a hard time wrapping their head around it. All it boils down to is that you want to find sequences of dna that are present in coronavirus but not in humans (and also maybe the reverse for some types of controls). It's, I mean. I don't have words for it. Designing primers is like the first thing an undergrad who joins a lab for a research project or internship is taught. And I had it rough when I was designing primers like 3 years ago. In those ancient times, I had to design the primer by opening a whole new tab and going to a whole new website! (The site is https://www.ncbi.nlm.nih.gov/tools/primer-blast/ https://www.ncbi.nlm.nih.gov/tools/primer-blast/). So much work. Thankfully the lab I was working in implemented an electronic lab notebook (I think it was benchling?) that had the feature built in. Now i don't have to open another tab. I'm being flippant but also, common, this is the CDC. The WHO had no problem doing it. Private labs had no problem doing it. It's not something weird about this virus. It's just, i don't know. There must have been deeper issues.
- anitil 7y ago
  Great reply, thank you. I feel like this filled the gap I was missing. Sounds like we're in regular expression territory, and the rest falls in to place in my mind. I think I was expecting the error to be somehow more technical or down in the weeds somehow.
dirtyid 7y ago
From my understanding the US policy is to always use kits developed in domestically. The problem with the test was one of the reagents for negative control was contaminated so it could not distinguish between positive and negative tests. This component of the test was suppose to be an extremely basic process, so much so that none of the epidemiological response plans ever accounted for this possible failure mode.
unishark 7y ago
Not only is it standard procedure in recent pandemics for the US to make their own kits as the pother poster noted, but other developed countries do the same thing. China, Japan, Korea, and the UK all made their own kits too. These are just the countries I checked into. The WHO kit by the way is the one made by Germany, not some grand international super-kit. Imagine if it had been the faulty one. And developed countries wouldn't actually use WHO kits, just the protocol to manufacture their own tests. The WHO distributes kits only to poor countries. Everyone still runs into the same issues ramping up production.
- jobigoud 7y ago
  This makes it even stranger that of all developped nations only the US didn't manage to get this right.
  - deleted 7y ago
    [deleted]
- anitil 7y ago
  Ah yes I had missed that. Thanks

by anitil 7y ago

vikramkr 7y ago

1) No idea 2) You found the article I was about to link actually. Basically, for a PCR test, what you're doing is making a lot of a particular sequence of DNA if it's present. You set up the reaction conditions so that if a particular sequence of DNA is present in your test tube (actually a plate but same difference), that sequence of DNA will make a lot more of itself. If there isn't that sequence of DNA, nothing will happen. You don't get to pick the entire sequence youa re looking for. You basically hae to pick a start region and and end region for the piece of DNA you want to amplify. So if the nucleotide sequence for a coronavirus gene was atcgctatagc, and you are using 3 letter long end regions (in reality you use longer length sequences and regions), you might pick your targets as atc and agc from each end. Therefore, any sequence of dna in your sample with atg and agc will get amplified and you will get a signal telling you that a dna sequence that starts with that first target sequence and ends with that second target sequence is there. If you don't get a signal, that means no coronavirus. When picking that sequence (known as a primer sequences since it primes the replication reaction), you have to be careful. Lets say that in your body you have a gene that goes gtcatcagctga or something. Inside of that sequence, your primer sequences are present. If you run a test for your desired sequence, you're going to get signal from non-coronavirus DNA. In order to make sure there are no overlaps in your primers, you, well, this is the part that's hard to believe. You type in your sequences in to a website and hit a button. Hence the following excerpt from the article you found: “I just put the primers as input into this program and within seconds it tells you there’s problems with it,” Altman said. “It’s freely available. It’s not hard to use at all. It’s one of those things you’d do as a basic quality control check. It seems like they hand-designed these primers and it seems like they didn’t use computer tools to check it.” So, yeah. Everyone's still having a hard time wrapping their head around it. All it boils down to is that you want to find sequences of dna that are present in coronavirus but not in humans (and also maybe the reverse for some types of controls). It's, I mean. I don't have words for it. Designing primers is like the first thing an undergrad who joins a lab for a research project or internship is taught. And I had it rough when I was designing primers like 3 years ago. In those ancient times, I had to design the primer by opening a whole new tab and going to a whole new website! (The site is https://www.ncbi.nlm.nih.gov/tools/primer-blast/ https://www.ncbi.nlm.nih.gov/tools/primer-blast/). So much work. Thankfully the lab I was working in implemented an electronic lab notebook (I think it was benchling?) that had the feature built in. Now i don't have to open another tab. I'm being flippant but also, common, this is the CDC. The WHO had no problem doing it. Private labs had no problem doing it. It's not something weird about this virus. It's just, i don't know. There must have been deeper issues.

anitil 7y ago
Great reply, thank you. I feel like this filled the gap I was missing. Sounds like we're in regular expression territory, and the rest falls in to place in my mind. I think I was expecting the error to be somehow more technical or down in the weeds somehow.

dirtyid 7y ago

From my understanding the US policy is to always use kits developed in domestically. The problem with the test was one of the reagents for negative control was contaminated so it could not distinguish between positive and negative tests. This component of the test was suppose to be an extremely basic process, so much so that none of the epidemiological response plans ever accounted for this possible failure mode.

unishark 7y ago

Not only is it standard procedure in recent pandemics for the US to make their own kits as the pother poster noted, but other developed countries do the same thing. China, Japan, Korea, and the UK all made their own kits too. These are just the countries I checked into. The WHO kit by the way is the one made by Germany, not some grand international super-kit. Imagine if it had been the faulty one. And developed countries wouldn't actually use WHO kits, just the protocol to manufacture their own tests. The WHO distributes kits only to poor countries. Everyone still runs into the same issues ramping up production.

jobigoud 7y ago
This makes it even stranger that of all developped nations only the US didn't manage to get this right.
- deleted 7y ago
  [deleted]
anitil 7y ago
Ah yes I had missed that. Thanks