Preparing for COVID vaccine codes in the vocabulary and modeling in the OMOP CDM

[Vojtech_Huser (Vojtech (Vojta) Huser)]

Karthik, can you elaborate on the CPT codes you mention. This page (https://www.ama-assn.org/find-covid-19-vaccine-codes) shows codes 0001A and 0011A. But are those modifiers (those only have two characters) in addition to CPT codes 91300 to 91303.

[Dymshyts (Dmytry Dymshyts)]

@cukarthik

COVID vaccines are being coded as CVX, CPT, and RxNorm

are already in OMOP vocabulary

[cukarthik (Karthik)]

Oh, great to hear! The last version I downloaded didn’t have it or had missing relationships. Now the only piece is the CVX to RxNorm mappings, so we can use one vocabulary for drug analyses.

[MPhilofsky (Melanie Philofsky)]

@Alexdavv or @Dymshyts

I found another custom source value which lacks a code, "JOHNSON & JOHNSON, SARS-COV2 (COVID-19) VACCINE ". What’s the appropriate concept_id for it?

[Alexdavv (Alexander Davydov)]

Here you are:
https://athena.ohdsi.org/search-terms/terms/739906

[MPhilofsky (Melanie Philofsky)]

Thanks, @Alexdavv!

[JayGee (Jay Greenfield)]

I am ETLing COVID-19 vaccinations collected using a section of the 5July2021 WHO COVID-19 Core CRF into the OMOP CDM. How do you suggest I proceed?

Keep in mind that in future versions of the CRF we expect that the lists of vaccines administered will grow.

[MPhilofsky (Melanie Philofsky)]

Our source data has new source values for COVID-19 vaccines. What are the most accurate mappings for the following:

MODERNA, 100 MCG, SARS-COV2 (COVID-19) VACCINE
MODERNA, 50 MCG, SARS-COV2 (COVID-19) VACCINE BOOSTER
PFIZER, PED 5-11, SARS-COV2 (COVID-19) VACCINE

[Alexdavv (Alexander Davydov)]

@JayGee

I am ETLing COVID-19 vaccinations collected using a section of the 5July2021 WHO COVID-19 Core CRF into the OMOP CDM. How do you suggest I proceed?

Keep in mind that in future versions of the CRF we expect that the lists of vaccines administered will grow.

Are we missing some of the vaccines even in the CVX?

The most painful thing is RxNorm doesn’t make a difference on the ingredient level and we have to map to the drug components / clinical drugs. It works unless the low-dose formulation is on the market, but it’s already there and we have to address it somehow.

So let’s get back to the issue:

@Alexdavv

It’s valid while the only formulation exists. Let them introduce a lower dosage or something else, we are screwed up. For sure, official mappings will be fixed, but it’s an additional work and a big pain to constantly review the custom mappings done here and there.

But the problem is that we don’t have any better option - CVX is very specific too (or very general).

@MPhilofsky

MODERNA, 100 MCG, SARS-COV2 (COVID-19) VACCINE

Supposed to be a classic Moderna, so SARS-CoV-2 (COVID-19) vaccine, mRNA-1273 0.2 MG/ML Injectable Suspension

@MPhilofsky

MODERNA, 50 MCG, SARS-COV2 (COVID-19) VACCINE BOOSTER

Low-dose booster, but the mapping is the same - SARS-CoV-2 (COVID-19) vaccine, mRNA-1273 0.2 MG/ML Injectable Suspension
The thing is we’re losing the distinction between the two.

@MPhilofsky

PFIZER, PED 5-11, SARS-COV2 (COVID-19) VACCINE

Currently we map it uphill to SARS-CoV-2 (COVID-19) vaccine, mRNA spike protein losing the distinction even between Pfizer and Moderna.

We are aware of the issue and currently working on the solutions at the OMOP vocabulary end.

[MPhilofsky (Melanie Philofsky)]

Thank you, @Alexdavv !

Please let me know when the solution has been found and implemented.