hpr-knowledge-base/hpr_transcripts/hpr3223.txt

Episode: 3223
Title: HPR3223: My COVID year summary
Source: https://hub.hackerpublicradio.org/ccdn.php?filename=/eps/hpr3223/hpr3223.mp3
Transcribed: 2025-10-24 19:07:06

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This is Haka Public Radio Episode 3223 for Wednesday 9th of December 2020.
Today's show is entitled, My Comedy Year Summary and In Part of the series, Health and Health Care.
It is hosted by B.E.M.I and in about 18 minutes long, and Karimma Clean Flag.
The Summary is, I summarise what I've been doing for the last year.
This episode of HPR is brought to you by archive.org.
Support universal access to all knowledge by heading over to archive.org forward slash donate.
Alright, this is B.E.M.I once again. It's been a long time. It's been a very busy year.
I'm sure there's been a little bit of interesting for everyone out there.
I'm on a walk up a mountain, so I'm a little out of breath, but it's quite up here,
and I figured it'd be a good place to have an episode, so here I am.
I just wanted to go into a little bit about what I've been up to for this past year.
I don't know if I've said it before, but I am a, for my day job, I'm a consultant.
I work with clinical laboratories in the US, and I do all types of stuff for them,
kind of a jack-of-all-trades, but I try to focus on quality management and regulatory
for one half of my business, and on the other half, I focus on laboratory informatics and software engineering.
And when, you know, in March, April, COVID really started cranking up, and there are a lot of different initiatives
in the US for incentives for companies to get into running SARS-CoV-2 PCR tests.
And, you know, my background is in molecular biology and bioinformatics.
And also, you know, I'm in the regulatory world for laboratories already, so
it was pretty natural that I started doing work in that area.
I wasn't expecting how busy I was going to get.
It's been quite a year, but a couple of things that I want to talk about are just kind of my own experiences
in dealing with this, and, you know, you can try to frame it.
I want to try to leave it as unbiased as I can, and you can put your own bias on top of it.
And I'm going to try to do my best to just say what my experience was.
So, like I was saying, there was a lot of focus on we need to ramp up testing.
And I don't like a lot of other countries where they have, like, a centralized government
and a centralized healthcare system that said, okay, well, once we have this test,
everybody has the same test, and we'll, you know, send it to everybody in the world, everybody in the country,
and then we'll have a test.
That's not the U.S. approach.
We had one test that was available for public health organizations, but public health organizations,
even in a pandemic, even in this pandemic, only tested about, no, less than 10% of all the tests
that were required.
It's the private industry, like you're questioning a lab course and your aeroves of the world
that do the most of the testing.
And then, you know, there obviously was an opportunity for smaller companies that were already
in molecular diagnostics or wanted to get into molecular diagnostics to come in.
And so, that's what they did.
They incentivized, they made some incentives for the big companies, but they also incentivized
smaller companies into the business.
And so, as a part of that, they had to, you know, it was kind of the wild, wild,
less were in the wild.
And a lot of companies that didn't know what they were doing, and thought it would be easy
and had no clue what their relative requirements were, and had no clue about the complexity.
They're like, oh, it's just like getting your blood, getting your cholesterol taken, right?
Well, it's not.
It's nothing like that.
It's complex steps, and there's a myriad of different tests that you can choose from
from different companies, and they have different pluses and minuses, some of them cost
more than others, some of them promise throughput that is unattainable by humans or by people
who have to deal with actual time.
So it's been quite a challenge, but some of the things I've been up to have to do with
bringing in, so first, helping some companies set up the test, you know, bring in my molecular
diagnostics experience and say, this is how you do it, helping them hire people who also
know how to do it, because I'm not going to sit there and run the test all day, but the
things do.
So between that and helping out on the, on the informatics side, which became the
majority of what I was doing, and then also helping out on the automation side, because
if you're going to do anything at scale, you're going to need advanced liquid handling
automation, another test of robotics to get you to the type of numbers that you really
need.
So for those who are unfamiliar with PCR, and what you have to do to get these tests, if
anyone's ever gotten the COVID test, you know that they start out with sticking a swab
up your nose, and the challenges that came from that point were the limited availability
for swabs, especially in the US.
It became common practice for the different companies to pick the cheapest vendor that
they could find, and most of the time those came down to two companies.
One is in China, one is in Europe, and when the crisis hit, those companies, they tried
their best to get it out to everywhere, but they just wasn't enough supply to go around,
and there wasn't enough options in the US in terms of US suppliers to get enough swabs.
So March, April, May were really, really tough when it came to being able to find supplies.
The same is true for the automation, and the liquid handlers, and the PCR instruments.
You know, it hit all these companies unaware, and none of these companies are very few of
these companies, even if they're based in the US, actually have manufacturing in the US.
So as you can imagine, when their governments came to them, they said, hey, you hold the
stuff for us first, which is understandable.
They have a response to their own people first.
But so that was one of the biggest first challenges, was just getting enough swabs, and I remember
having meetings after meeting after meeting, just on where the swabs came again from here,
can we use these instead, how about these, how about these, and they have to be able to
grab the sample, but also be the right type of material that won't cause interference
for a viral test.
And so that was the first challenge, and like I said, was getting all the consumables.
So after you draw the sample, you put it in the solution that stabilizes it, and then
you have to extract the nucleic acid out of it, which is a chemical process that you
can do, you can use automation to make it faster, but it's still quite involved.
And then once you have the purified RNA, because coronavirus is a positive trend, RNA virus,
since it's RNA, it's really unstable, you have to store it at minus 80.
And if you don't, it'll degrade within hours.
And so there's been a lot of problems with trying to get samples to where they need
to go fast enough.
Now that there's the vaccine that's on the horizon, the first one is a RNA one, and that's
why it needs to be stored at minus 70 degrees Celsius, is because it's RNA, and it's not
being processed into the material that is both non-talked to a human, but also stabilizes
the RNA.
So that was step one, and step two, then step three came with trying to get, say that
you've got the test, you picked a vendor, a vendor that's not going to know, I mean,
all the vendors pretty much all the big ones, they pretty much had a stranglehold on their
customers when it came to the supplies, because as we're getting everything you need to
have FDA emergency use authorization.
And so as a part of that, you can only use the consumables that were a part of that emergency
use authorization, which meant that a lot of the reagents you had to get from the vendor.
And so no, there was no deals on price, as you can imagine.
After that, once they actually could start them on the test, the thing that almost none
of these companies took a real good look at, oh shit, I'm not going that way, there's
a coyote sitting in the road.
There's a coyote sitting in the path right there, my friend, there's a coyote sitting in
the road right there, there's a coyote sitting in the road right there, okay, well I'll
let you go first.
So that's the first, oh, he's going to run away, is he running away, okay, he's gone.
Okay, good, all right.
Sorry about that.
Man, never know what you're going to find on this mountain.
So after they got past the problems with the reagents, they almost all had a wall with
their laboratory information systems.
It has been a grab of mine for a really long time about the reliance on all of these
companies on software vendors that are hostile to their users.
And emergency like this really puts that in focus.
You know, I am a free software person, but I understand it can't, not everybody is the
same way, which is up, you know, what can you do.
But where's that coyote, barely in the road?
If you hear me running, oh, there he is, all right, you know what, I'm going to turn
around.
So all these companies, they have this problem where they don't let their users have access
to the data.
And they also don't have developers or people in their implementation teams that actually
know the lab business.
So they either build solutions that don't actually work in practice, they've know they work,
you know, they're, they may be well engineered, they have bad user experiences, bad ways
to get the data in, almost impossible, a lot of times to get the data out, and they
don't make it really easy for systems to talk to it.
And if you want to integrate with anybody else, it costs you a fortune.
So that's been my experience for the last 10 years.
And that really does not work in a crisis.
So I spent the majority of my time in the last couple months being a data steward, figuring
out ways to get data out of these horrible systems.
All right, I'm not supposed to talk about my opinions out of the systems that make it
hard for you to get the data out.
And get and have them get to where they need to go.
And one of the biggest things that they need, where they need to go is to the Department
of Health.
I want to say Department of Health, it sounds like it's one thing, but in the US it's
not.
Every state has its own Department of Health, and every county has its own Department
of Health, and different states that give the counties more and more or less responsibility
for the reporting of infectious disease outbreaks.
And for this emergency, every case or expected case is a part of the things that you need
to report.
Under no more circumstances, you only have to report the positive cases, so like for the
flu or for a midi or something, you only have to report the positive, you don't report
every time you write a test.
But right now, the emergency authorization and then the crisis they ask for every single
test to be reported.
That's why you know.
That's why we know things like the incidence rate and the percent of positive patients
per amount of tests that are being done is because of the people that are sending in the
results to the Department of Health.
So in some states, so one thing is true is that they're all different.
Reporting to all the different states are all different.
Some counties ask you to also report to them.
Some counties say report to us and we'll report it to state, and all the different states
gather the data up, and then they report it to the CDC.
The biggest problem is there is no standard format for delivering this information.
And there might be some among you saying, but what about HL7?
Yes, there actually is an HL7 standard around setting in this type of data.
But if you remember work with HL7, you know that it's not really a strict standard.
It's kind of like a, it's like guidelines and people can put the data in different formats
and add things that are optimal for some people to require for others.
And they might want to lump code here and another company, another place might want to
snub a code or ICD code.
And so, you know, when you want to be a company, so I worked with a bunch of regional companies
that stayed in California.
Those were pretty easy to set up.
Even though I still have to do a lot of work to get the data from their systems or from
a seller or have to get the data, I would engineer a solution that would be able to take
the data and get it into a format that the state of California wants, and then send it
to the state of California, usually automatically, sometimes not.
And so a lot of states that said, okay, we know that not every company that's just starting
out has HL7 because a lot of these vendors, they don't do it out the box and you're not
required as a laboratory to have any certain type of electronic system.
So some people just have itselfiles with their manager whole life.
It's just how they are doing it.
So they have acceptable, you know, CSV file formats for some states, other states, most
states have that, but the states that have that also have an HL7 option.
And so, you know, a company that wants to go national, they have to have the requirements
for every state.
And then now the results are accordingly.
If they want to go through a new state, they need to know what the requirements are for
the state first.
And that has been a real big challenge to try to keep up with some of my clients and
how fast they want to move, because they want to try to bring, you know, results to their
patients, but we have to get all the regulatory ducks in the room and our data ducks in the
room first.
And so, you know, that's what I've been doing for the last nine months is helping laboratories
get started.
The ones that are already started, helping them scale and all of them trying to get their
data in a format for the different states so that they can report the results to the
different departments of health.
Just one comment on that is that it is an absolute fact that we are under reporting the
COVID test, because it is completely up to the goodwill of all these different laboratories
to report.
And I have to imagine there are some that are small enough that either aren't or aren't
doing it very quickly or aren't getting the data to the laboratories and to the departments
of health in a format that is suitable and they are getting either postponed or getting
uploaded because the internal analysts at the Department of Health have the plaintiff
first.
So, if you see the numbers, if you look at the Johns Hopkins numbers like I do, and you
see that they change and they go down and they go up for the same date, that's why it's
because there's a lot of under reporting and late reporting that's happening.
And a lot of it is one, life just doing the best of the can was what they have and what
they have in terms of data infrastructure is not very good.
Alright, well that's been enough, it's been a very interesting episode, I got to almost
have to fight with a coyote in the middle of it, but I hope this was useful.
So for all of the other Hacker Public Radio listeners, I encourage you to send up your
own episode whenever you can, I know it's been tough with all the things that are going
on right now, but you know, this is one outlet that is great for all of us, it's a way
to escape a little bit and think about other things, it's also a way to just have community
when we're kind of not really having too much community as much right now with all the
locked-ups.
Alright, well that's it, stay hacking.
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