[AR] Re: wakeup call, courtesy of COVID-19
- From: Norman Yarvin <yarvin@xxxxxxxxxxxx>
- To: arocket@xxxxxxxxxxxxx
- Date: Wed, 25 Mar 2020 17:12:54 -0400
On Wed, Mar 25, 2020 at 03:20:20PM -0400, Norman Yarvin wrote:
For background on the US testing fiasco, see:
https://thedispatch.com/p/timeline-the-regulationsand-regulatorsthat
What that article doesn't go into, by the way, is the technology of
the test in question. It's ordinary quantitative RT-PCR, such as is
routinely used in labs. For those who aren't up to speed on the
jargon: PCR amplifies DNA, but only the parts of it that are between
two matches to primers that you use, which are short pieces of DNA.
"RT-" means that reverse transcriptase is used: the coronavirus is an
RNA virus, and reverse transcriptase converts it into DNA first.
"Quantitative" means that you add something to the reaction tube which
changes color or something when enough DNA is amplified, and you keep
watching for that change, so you know roughly how much RNA was in the
original sample: each round of PCR doubles the amount of DNA, and you
count how many rounds it takes. The primers are normally something
that one orders from a DNA company rather than making them oneself:
you tell them what DNA sequences you want, and get them in the mail.
Anyway, quite a lot of labs (both academic and clinical) routinely do
this. All they need to be told is what primers to use, and they don't
even necessarily need to be told that, since the Chinese published the
sequence of the virus fairly early on, and primer design is not all
that hard; there are even web tools for it:
https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Besides, primers were already designed by the Chinese and by others:
http://virological.org/t/initial-assessment-of-the-ability-of-published-coronavirus-primers-sets-to-detect-the-wuhan-coronavirus/321
Still, as that link shows, it can be a bit tricky, and other things
being equal it's easier to monitor the epidemic if everyone is using
the same, good, primers. But "other things being equal" does not
include weeks of delay; and the CDC insisted not only that they be the
ones to design the primers, but that they be the ones actually
physically providing the primers. And then they botched one of those.
(They didn't just design one set of primers, but four sets, three with
varying specificity for the coronavirus and a fourth as a control: I
forget exactly what it detected, but it was something that should be
in every normal sample. Anyway, there was something bad about one of
the first three, which wouldn't really have been a problem except that
it took time to realize that, and then more time to change the rules
so that labs could just ignore it.)
Anyway, not content with this screwup, the FDA recently banned home
test kits, where people would swab themselves at home and then send
the sample in to a lab:
https://www.statnews.com/2020/03/21/fda-warns-new-home-coronavirus-tests-unauthorized/
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