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c_hawkthorne  ·  4 days ago  ·  link  ·    ·  parent  ·  post: Pubski: July 1, 2020

I got our entire county government called socialist because when your animal bites someone you need to confine it for ten days and take it to a vet to show it doesn't have rabies, and we don't pay for that.

c_hawkthorne  ·  42 days ago  ·  link  ·    ·  parent  ·  post: 383rd Weekly "Share Some Music You've Been Into Lately"

c_hawkthorne  ·  64 days ago  ·  link  ·    ·  parent  ·  post: I'm helping with disease investigation in this pandemic. AMA!

It's great your state defines that kind of stuff. I'm not sure which ones do and which ones don't. I think John Oliver's look into coroners and medial examiners is interesting. I haven't watched it in quite a while so I don't remember exactly how relevant it will be, but I remember being appalled at the lack of training some of these people need.

Actually, CDC adopted CSTE's definition between me posting that in Chat and now!. I don't know exactly which day, but they did accept it. In regards to other standards I couldn't begin to guess. But now that CDC has adopted hopefully that helps things out a bit. Now, of course that's new and who knows how long it will take for that to be adopted nationwide. As much as we like to think it'll happen overnight, that's a wildly optimistic viewpoint. That assumes every level is auditing the next level below, to the local head of disease investigation auditing their workers', and I can verify they're too busy to be doing that. Maybe the state is watching, but they won't be watching if labs and kits are EUA approved, that's my and my colleagues jobs. And the idea we have time for that is wild. We have to find time, but that means other things get pushed off. It's vital because that's the difference between an asymptomatic person being counted as Confirmed vs Not a Case. When I have a facility that tested everyone and have a pile of 40 tests all of which are from an unapproved lab and 3/4 of cases are asymptomatic, that's a ton of time whether or not I have to manually input those patients and labs and call them a case or if I just get to shred the report. All of my colleagues are running into the same issues.

We had a meeting on Friday at like 2:30 to review test kit and lab guidance and the determination was pretty much we're expected to do the legwork to find out if people are EUA approved or not, which includes calling labs and asking if they're approved and not on the FDA's site yet, if their kits are approved, or if they're all unapproved. And the lowly receptionists who answer the phones certainly don't know. So they bounce us up to a voicemail we may or may not hear back from. Now I get to play the game of "How many times do I have to call the lab?"

Oh, and Friday right after that meeting, I found a lab result in the system which said the lab and test kit are not EUA approved, but the assay medium in the test kit is. I bounced that up to my our head of disease investigation and am waiting on a response. I really hope I'm not expected to call a lab and find out they use a test kit then call the kit company and find out what specific part of the kit is approved then keep going to him and asking what is and isn't allowed. When I left Friday I still didn't have an answer. Yeah, it's gonna be a mess for a good long while.

c_hawkthorne  ·  66 days ago  ·  link  ·    ·  parent  ·  post: I'm helping with disease investigation in this pandemic. AMA!

I am so so grateful for everything the FDA is doing these days. It just makes my life harder that I can't accept any test that comes across my desk. But I know those poor bastards are working an insane amount to verify as many tests as they possibly can to alleviate the stresses on the current approved tests.

c_hawkthorne  ·  66 days ago  ·  link  ·    ·  parent  ·  post: I'm helping with disease investigation in this pandemic. AMA!

Fuckin' Florida...

So yes, I do believe death counts are being intentionally under-reported, and that shit Florida pulled is deplorable. However, when it comes to statistics in general, I think skewing statistics isn't that widespread, nor is it very intentional. Deaths yeah probably. Overall cases? Much less likely. I think it can moreso be attributed to the sheer amount of uncertainty and incompetence than intentional misleading.

Let's rip apart the case definition game, shall we?

I want to start off by saying it took me months to wrap my head around the concept of case definitions as a thing. I mean, if a doctor says this person has [disease], and they have symptoms, why does it matter if the tests aren't the required tests and the symptoms aren't the required symptoms? I remember in my first few days all that time ago first starting disease investigation, my boss at the time was talking about how that person clearly had a disease, but it had to be counted as not a case, and I was so confused. Then a few days later he was doing it the opposite way, classifying someone as a case when the doctor said it wasn't, solely due to symptoms and tests. That man was not and is not a medical doctor. But you don't have to be for disease investigation. We take data, we compare data, and we classify data. That's it. And for that data, we need a standard. Even if the standard isn't great, we need a standard so everyone is doing the same thing. That way, at least it can be adjusted later on assuming everyone is doing the same thing. I know the assholes at the state watch and audit what we enter to make sure cases of various conditions are classified correctly.

COVID-19 case definition from CSTE was released a few weeks ago. Actually, looking for an exact date, I found CDC finally adopted CSTE's definition for interim guidance. that page gives April 5th. So before April 5th, there wasn't necessarily a coherent definition for all people to follow. And that's okay. We lacked data. We needed to say - Here are the positive people, Here are the symptoms we see in positive people, Here are the common ones, how can we make it so we capture accurate-ish numbers for those who aren't tested?

Okay, so I like CDC's layout a lot better than the PDF above, so I'm going to use that for quick reference. It's the same definition, but just different pages.

So take Johnny. Johnny is some dude living in a nursing home. Poor Johnny lives in a unit with a few cases. Guidance from my department has been once there are a few cases, assume an epidemiological link, don't necessarily test everyone. There's a 30% false negative anyway and we'd hate for you to cohort a negative test who is truly positive with true negatives and then expose a completely clean population. So poor Johnny is chilling in his room, doing his thing. Unfortunately, he starts with diarrhea. Dealing with this a lot, I can say yeah, diarrhea is a common first symptom in the elderly. Then Johnny pops a fever and has a lot of fatigue, and a hint of confusion. Johnny goes suffers a heart attack and dies. Poor Johnny. Did he have COVID-19? Clinically, I sure hope he was put on precautions and treated as a positive. Will he be counted in the state's system? Let's look at that case definition. He never got tested and we assume epi link. So no test is being done, he can either be Probable or Not a Case. So now we have to look at the symptoms. Did he have two of the following: fever (measured or subjective), chills, rigors, myalgia, headache, sore throat, new olfactory and taste disorder(s)? Nope, just Fever on that list. At least one of the following symptoms: cough, shortness of breath, or difficulty breathing? Nope, he was breathing as well as he ever did. No low pulse O2, no shortness of breath beyond what he as an elderly person in a nursing home already had, and no coughing. Then did he have severe respiratory illness with at least one of the following Clinical or radiographic evidence of pneumonia, OR Acute respiratory distress syndrome (ARDS)? Nope, again his lungs were fine. This guy would be classified as not a case.

Now you have Rico. Rico is Johnny's roommate. Rico, like Johnny, went untested. Rico was entirely afebrile. No diarrhea, weakness, or confusion like his roommate. But he had a dry cough going for a week or so with a runny nose before recovering and living a few more years in quiet comfort. Using that same case definition, Rico is a probable case.

So the benefit is not that that keeps case counts low. It's that we have a clearly defined "not a case" vs "probable case" vs "confirmed case." There's no question as to whether or not Johnny should be counted as a case or not a case in the same way there's no question Rico is Probable. It's clear. It leads to even reporting which is better in the long-term for statistics. Yeah, might Johnny have been positive? Sure. And did Rico just get a cold and recover? It's certainly possible. Might the case definition be capturing too few people or the wrong people? Yeah. But when we go back ten, fifteen years down the road, we can adjust for these. I wouldn't be surprised if we had more case definitions by the end of this, and we will be able to analyze them and say when we changed the definition, probables went up x%, so we can raise the earlier case definition x% as well. With aggregate data, we can pull both these cases, see there's someone who is not a case with diarrhea, fever, and other (the system my state uses does not have symptom options for fatigue or confusion but I see those often), and a probable case with dry cough and runny nose. We can adjust these based on future definitions. So I don't think it's so much incentivizing inaccurate reporting as it is standardizing even if that standardization is far from perfect.

c_hawkthorne  ·  67 days ago  ·  link  ·    ·  parent  ·  post: Pubski: April 29, 2020

Yeah my regular job is regulatory. I just tell people they're wrong and they have to fix stuff, but I can't tell them how to fix it, that's up to them. Otherwise we might be playing too hard into their finances which becomes a hairy situation fast. We do conflict of interest paperwork annually and even the year after we leave as well. I don't envy the FDA these days. They're stuck between a rock and a hard place. I'm not saying it's wrong to not say how something has to be done, but they can be less vague about it. That lack of trust... the more I learn about everything the more I feel it.

c_hawkthorne  ·  67 days ago  ·  link  ·    ·  parent  ·  post: I'm helping with disease investigation in this pandemic. AMA!

Oh that's a fun one. A facility reported a non-EUA lab and I wanted to be sure so I asked them to send me the actual lab result. The FDA has a site for EUA lookups (below) that I'm not sure how often is updated. Often I hope... But if the lab paperwork itself said something about that EUA approval, I'd have called the lab and asked for the letter of approval as it was not and still is not on FDA's website. That "good standing" was the wording on the result. Looking on FDA's website for that exact wording I can't find it, but there's this page stating "Specifically, last month, as part of our broader strategy, the FDA issued a policy explaining that FDA does not intend to object when developers of serological tests market or use their tests without prior FDA review where: 1) the tests are validated by the developer to determine that they are accurate and reliable, 2) notification of the developer’s validation is provided to FDA, and 3) the tests are labeled appropriately, including that they are not to be used as a sole basis for diagnosis." - Whether or not the specific lab I experienced yesterday had wording stating it should not be the sole basis for diagnosis I do not remember. That is another fun game if the facility is using the positive result even in the person is asymptomatic. Fun times. I'm going to keep looking more for that test's wording on FDA's site. That would be fun.

What does that "validated by the developer" look like? Who the hell knows. I couldn't begin to guess where to find that information, I don't have time at work to look, and I will not spend my days off doing that. Maybe that's available on a website somewhere for the general public to audit, but that would surprise me, because trade secrets or some bullshit.

As to who is using the labs, a lot of people are no doubt. It's something we need to watch for as results are sent in. The extra fun part only the lab or the test kit need to be EUA certified, not both. So in the case of this facility, neither are, but I had a coworker who had test kits that were approved, even while the lab wasn't. We were told to count and upload those. Now most of the time we don't get both the lab and the test kit manufacturer. But when we get a result from one who is not, we try to ask the facility to fax the paperwork to us so we can look into it. That's how my coworker and I ran into that fun lab vs testkit vs EUA game.

Per our health dept physicians, false negatives run 25-30%. Should those have gotten EUA approval? When should that EUA approval be removed because we have better standards? When facility of 300 tests every person, they have 200+ and 100-, they cohort those positives and negatives to try to keep the other 100 healthy and conserve PPE, but 25 or 30 of those negatives are really positive and now it can easily spread through the extra population, what should be done? This is why at some point we say just assume everyone has it. It's why cohorting is recommended for a time, but at some point there's just no point. CDC guidance on cohorting in correctional facilities.

Does the lab you're using have EUA approval? Check FDA's site here.

c_hawkthorne  ·  67 days ago  ·  link  ·    ·  parent  ·  post: Pubski: April 29, 2020

For context: kb posted a WaPo article a few days ago in Chat regarding death counts. I mentioned something about how in my state's reporting system, in order to say that COVID-19 contributes to death, we need a death certificate. Now I feel the need to point out we still list death in the investigation, but there's a specific question as to whether the condition contributed to death. We can't answer that question without the death certificate. That went into talks about how underreporting deaths is just shooting oneself in the foot due to a lack of true counts which will affect federal funding, which then devolved into a slight rant about disease investigation and how much of a shitshow it can be. Chatski doesn't allow paragraphs, but I paragraphed below to make all your lives easier.

c_hawkthorne[429121142]: @am_Unition [42935723]: Oh it gets even more fun. Welcome to the wonderful world of Disease Investigation. Alright, so every reportable disease has a case definition. For the most part, they're on the CDC's website. It's buried deep, but the state system links to it and I'm sure other state systems do as well. That website is here: https://wwwn.cdc.gov/nndss/conditions/

Okay, so now that you've looked through that, you'll see COVID-19 isn't even on there! Fortunately, we have our friends over at The Council for State and Territorial Epidemiologists (CSTE) to thank, because they've released a defintion that we are using. We being my area, others within the state and other states, who knows. Again, I can only speak for what we are doing. So CSTE's definition is available in this ten page PDF document: https://www.med.ohio.gov/Portals/0/CSTE%20COVID-19%20Case%20Definition_1.pdf It boils down to -- Confirmed is PCR test through an EUA lab. Probable is other types of tests, including antibody, again from an approved lab, but that person also has to be exhibiting specific symptoms or have an epidemiologic link. Then Probable can also be the same set of specific symptoms and an epi link. The last probable is death certificate (remember that one? Ha).

So now we get to what is actually happening, especially with respect to asymptomatic people. We see a massive facility. 150 people. They decide to test everyone. Whoops, they don't do their research and use a lab under EUA review, but not with EUA approval yet. FDA has even said if you're a lab in good standing, whatever that means, and if you validate your test in some magic way, again super vague, that you're fine and don't need anything more. But this specific lab is not EUA approved. As such, right away no case from the facility can be "confirmed" per the definition. Now due to the way we're dealing with healthcare facilities, you live or work in one, you have epi link. So that's not a concern. The problem is symptoms at this point. Every case with a positive result from a test under EUA review who is asymptomatic or not showing the correct symptoms gets counted as "Not a case". We don't even waste time putting it in the system. If that test gets EUA approval, we will not go back and change anything, because we aren't putting them in the system and we're told not to put them in the system at a later date. Now one of my facilities decided to test the entire population. 60-75% of the reports I've recieved so far don't meed clinical defintion, and as such aren't even a case. This way, state gets to say look, we have cases, but we're keeping case counts in facilities low. There's a massive ordeal around long term care facilites and COVID. Being able to keep case counts low but not too low is a good thing. It feels like that's what they're trying to do.