I second this 
As we discussed yesterday in the EHR WG call, the standard concept_ids in the Visit domain are notoriously limited in coverage & granularity. Currently, I suggest researchers use a combination of the care site, provider, dates and other attributes to define these long/chronic covid visits. If there was a standard visit concept_id for this, then the pre-processing can be done during the ETL. Isn’t that the OHDSI way? To quote the famous @Christian_Reich “put it on the ETL smucks” 
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100%!!! Emphatic yes!
And to be clear, we know that there’s a LOT of guess work being done at the site-level to figure out “who was seen in the Long COVID clinic” because it’s not easily captured. We can absolutely use the RECOVER sites to help figure out ETL implementation guides and best practice.
It will not be one size fits all but we can deduct how we get to a pre-processing stage. @mgkahn has been one of our first navigators of this tortuous journey. I am sure he will gladly share with the tribe the tribulations of pioneering this. 
Friends:
With respect to the Long Covid condition: This is not easy. We are stuck between the rapid speed of clinical research (and obviously the high urgency on this particular issue), and the slowness and contradictory nature of definitions evolving as we speak.
The solution is (you knew I would say it!) in the use case:
- If we want to create phenotypes of this condition - we don’t need anything. Long Covid becomes a cohort definition.
- If we believe the community has settled on a set of precisely defined conditions we should adopt something like @Mikita_Salavei’s mini-hierarchy.
- If we believe this is a moving target folks will not have a common clear understanding no matter what the various authorities @mik listed state, we should create one catch-all concept.
I would strongly suggest we go by 3. And you seem to have concluded likewise. This concept could be called sequalae, long, post, or any of these as synonyms. Whether or not there are differences in the patterns justifying the creation of different conditions will be the output of the research, not the input.
Regarding the Long Covid clinic: Visits are configurations of clinical care, where the main attributes are (i) does the patient come to the provider or the other way around, (ii) does the patient stay in bed over night and (iii) is the healthcare a focused activity or is there a permanent service available to intervene any time. All this is from the patient perspective, not the perspective of the provider.
In this case, you have to explain how a Covid clinic is any different than an outpatient visit. The nature of the disease is not sufficient to draw the line. Something else has to be substantially differently organized.
Is it?
I agree with @Christian_Reich
In the ICD10CM guidelines is stated
So, it might be a sequela or a long covid, there are several definitions.
So, what if we create an OMOP Extension concept, call it “Post COVID-19 condition” and map ICD10CM to it?
I would stick to the ICD name because it exactly describes this bucket code.
Then if we see in the data something like @Mikita_Salavei described, we can add that later as descendants of the “Post COVID-19 condition” concept.
Now I see the point around the Observation domain. Why don’t we call things by their names then?
We have a separate hierarchy of suspected conditions under the Observation domain here and suspected COVID sequela can become a part of it.
Pointing out to the similar discussion we had about COVID…
So it seems the only question is whether we already want to distinguish suspected and “confirmed” sequela of COVID by having 2 separate bucket codes.
Sure, but we want it to be crystal clear so users don’t mix it up with any of @Mikita_Salavei’s definitions. Especially considering the moment we’ll be adding these all to the vocabulary. This clarity will support future changes in the terminology and related ETL/mapping adjustments.
…as well as any condition that developed following a previous COVID-19 infection.
This one conflicts with one of @Mikita_Salavei 's definitions.
This is supposed to be a level 3 code, not the top guy. While ICD10CM, in fact, is just a history of COVID-19 and the most assumption we can do is mapping to “suspected COVID sequela” (if we believe it deserves a separate concept).
It is not. It’s clearly said that it’s something happenening to the patient
https://www.icd10data.com/ICD10CM/Codes/U00-U85/U00-U49/U09-/U09.9
and so what?
people have ICD10CM codes, we need to accomodate that.
Exactly! Something is happening not necessarily but presumably connected to previous COVID. While something is coded separately, this U09.9 code is somewhat in between:
-
the history of COVID (for the MIS case it’s clearly stated in the coding guidance).
-
suspected COVID sequela.
But what would be a landing target if this is basically an OR statement?
Pick the top-level general one?
Well, ICD10 code doesn’t include Ongoing symptomatic COVID-19, right?
So that’s the difference?
Again, there’s an EHR code and in most of the cases that’s the only available information.
And let’s say, someone have a history of COVID, then they got hit by a car got a brain trauma and got loss of smell (not post covid condition)
and someone else also have a history of COVID but wasn’t hit by a car, but lost smell as well (post covid condition).
Obviosly for the COVID research I need the second patient. and this “Post COVID-19 condition” code is what I have only. So we need that code as target you like it or not.
The difference is ICD10 is too old and doesn’t reflect the current agreements on terminology. It was probably designed as a bucket code, but now we have the flavors: 1.1, 1.1.1 and 1.2. All of them don’t fall into 1.1.2. That’s why it’s not an optimal one to be a bucket.
No worries! I completely agree we need. Here above I was talking even about 2 codes: one for suspected (to support the covid clinic encounter) and another one for a kind of confirmed COVID sequela.
I think we mostly agreed on the definition of U09.9. It’s time to agree on the assumption we do, and the way we map it.
Clarification: my note was talking about that code for the Long COVID Clinic visit that @stephanieshong created a map for (that’s what @DaveraG 's schema is).
Two thoughts were mixed into one here.
This is a visit_concept_id but in immature format.
I would not want the ETL pre-processing phase to be responsible for determining if this is “Suspected” sequalae of COVID. Seems dangerous tbh. Presence of a specialty visit <> presence of the condition. Different concepts.
U09.9 is confirmed COVID sequalae.
and you suggest to map to the
right?
Didn’t you say these patients are suspected to have a long COVID?
And then @Christian_Reich said it’s not another Visit concept because the clinical care attributes from the patient’s perspective are pretty the same as for conventional outpatient visits.
It’s also not another Provider specialty.
Long COVID clinic is supposed to be a care_site, right. We still support the place_of_service field that is supposed to be a high-level characteristic of the setting. Is it also from the patient perspective? Maybe it wouldn’t be so painful if we add another type of clinic to the Visit Domain, @Christian_Reich? We already have plenty here.
But even when Christian give up… I don’t think it’s wrong to map long COVID clinic visits to the suspected COVID sequela and capture such patients this way.
No, just another assumption the doctor made on the available knowledge at the moment.
I think it mostly depends on what we do with the long COVID clinic visits and the conventions we create.
- If it requires mapping to the suspected COVID sequela, then U09.9 can go to the bucket with everything that is clearly defined in the @Mikita_Salavei’s list.
- If not, I’d separate U09.9 (suspected COVID sequela) and everything is clearly defined (COVID sequela).
Except we already support other flavors of outpatient visits.
These are clinics stood up for the sole purpose of treating Long COVID. If a center is organized, maybe it can be a CARE_SITE. But widespread adoption of CARE_SITE with any level of rigor is low.
No. These are clinicians logging that people have come to a specialty clinic stood up for this purpose.
It’s the epitome of a visit concept. It’s a tag about where a clinical encounter physically occurred. Not different than if someone’s data says that Outpatient visit occurred at a Federally Qualified Health System. Same idea. Outpatient visit subsumes this type of encounter.
Whether or not a clinician AT that visit concept logs a subsequent sequalae of COVID-19 code is a different story. I would not conflate the two. A Long COVID clinic visit is not a clinical diagnosis. It’s the presence of a visit to a clinic for this purpose.
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Friends:
I love these debates. But I think we can conclude:
- Suspected diagnoses are diagnoses. You can qualify its rigor in the condition_status_concept_id.
- There is no common ground for the definition the condition that occurs after overcoming a Covid-19 infection. In fact, it is the output of our (Kristin’s in this case) research, not the input.
So, let’s create one catch all bucket “Long/Post/Sequalae of Covid-19” concept. When the time comes that the scientific community has figured this out we split it up. Or leave it. Or maybe drop it, when we find out there is no such a thing. I doubt the latter, though.
Regarding the Covid clinic: Sure, we can have a descendant of an outpatient Visit. But what is the use case? Why would it matter? Reminds me of the “Booster vaccination”. That term will be obsolete next spring, when we will have booster-booster shots, and so on.
It could work. Except we decided differently, dropped or never had “suspected” Condition type and said to use another hierarchy for that.
And let me remind, we already did a rollback of the same decision we’re falling into again:
Yes!!
we already have 2 votes for this decision: mine and Christian’s
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Ok. How will this “bucket” concept we are creating relate to the SNOMED-CT Long COVID-19 concept Post-acute COVID-19 (disorder)?. Note that this SNOMED-CT concept is not currently included in ATHENA.
Also note that this is just one of three Long COVID-19 concepts that SNOMED-CT added in the January 2021 International release. The other two are Acute disease caused by Severe acute respiratory syndrome coronavirus 2 (disorder) and Chronic post-COVID-19 syndrome (disorder).
My use case is that we are looking for a Long COVID-19 concept (the condition_occurrence_id) for the radiological occurrences (an R-CDM extension) through which we are capturing lung and brain stem image data. In this research we are undertaking an international science project to help determine what Long COVID-19 is with more specificity.
In this use case the radiology occurrence takes place within a visit occurrence that might be inpatient, outpatient or specialty clinic. Our methodology for capturing radiological occurrences is catch-as-catch-can.
You are right, @Alexdavv. We did create the “Disease suspected” concept. The problem is that we are operating in somewhat of a fog: When we say “suspected” - is that lack of certainty about whether or not there is a disease, or whether or not the well established symptoms are related to Covid? We can put out all sorts of well contrived definitions - but what if the community cannot utilize it?
Good point. The reason is that we have this cadence of SNOMED refreshes, where we have to keep the international, UK and US version in sync. That concept just missed the boat at the last refresh cycle.
The first one is the acute version of Covid-19, as a child of the existing generic COVID-19. It essentially makes that generic Covid a category, consisting of the acute and the various chronic ones. Not sure I like that drift of the meaning, and not unhappy we don’t have it yet.
The Post-acute one, which has the synonym “Long COVID-19”, is defined as “Symptoms attributed to SARS-CoV-2 infection that persist for more than four weeks following onset and with a negative infectious virus status.” The Chronic post-COVID-19 syndrome is not called “Long Covid”, and defined as “Symptoms related to COVID-19 that persist more than 12 weeks following onset.” Not sure this makes a lot of sense. The difference essentially is in the duration of persistence, and by taking the definition strictly the >4 week Post-acute Covid contains the >12 week Chronic post-Covid. It’s a mess. We are going to bring it up with SNOMED next week.
Here you go! Wonderful. This will actually answer some questions.
Bottom line: We should still just create our own generic concept defined as a disease that is after and due to an acute Covid-19 infection. And then we let science run its course.
N3C is asking sites to label their visits with this level of specificity. They want to use it as an anchor in machine learning to do a data-driven approach to consider what features may or may not be playing a part in who shows up in a Long COVID clinic.