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

(Patrick Ryan) #1

AMA is preparing to release new codes for COVID-19 vaccines in anticipation of their potential FDA approval.

As an example, they have posted codes for the Pfizer and Moderna vaccines.

So my questions: (pinging @Christian_Reich @clairblacketer and @hripcsa for their guidance but would welcome other input)

  1. How will we ensure these new COVID codes make it into the OMOP Vocabulary? Does anyone know how the AMA deliberations manifest into the input data tables that we regularly download and integrate into our vocab?
  2. How should we coordinate across the OHDSI community to ensure we all align to the Vocabulary version when we begin to support vaccine surveillance efforts? (e.g. do we agree on 1 vocab version that we’ll all adopt at the same time? and then stay on a constant cadence (e.g. quarterly/semi-annually/annually) thereafter?)
  3. In the CDM, how do we model the exposure (e.g. the vaccine code) and the administration (e.g. the vaccine administration code for first or second dose)? Will we capture each vaccine code+administration code combos as distinct DRUG_EXPOSURE records? Presumably we will also capture NDC codes as DRUG_EXPOSURE records. This modeling decision will impact how we think about designing cohort definitions to extract ‘new vaccine users’ and distinguish first exposure from second exposure.

Given the public health impact and OHDSI’s potentially important role in supporting our regulators in their safety surveillance effort, I think this topic is worth OHDSI coming together to author clear data standards guidelines that we can embrace and apply across our community. I’m happy to work with others on this as more information comes to light.

(Christian Reich) #2


We will add them with the normal refresh mechanism of CPT4/HCPCS. If that gets a hiccup for some reason we’ll make sure manually it’s in there. I’ll expect RxNorm and CVX to add them on short notice as well, and then we cross-link. Will send a note to RxNorm. Everything should be a Drug concept at the end of the day.

Will reply here when it’s done. From then on, all releases will have these concepts. If they are overwritten for some reason we will report. We will also keep the Corona Virus page up to date.

Unfortunately, that has been proven unsuccessful. Reason is there are so many parallel and unrelated vocabulary updates that we cannot seem to be able to get on a routine release schedule. It’s been a rolling release, and I don’t see how that will ever be different. In fact, with the addition of more and more vocabularies the situation will not get worse.

Generally, vaccines are drugs, and hence they are in DRUG_EXPOSURE. The actual procedure of administration is trivial (shot in the arm or other muscle), which means it needn’t get recorded. If the source data contain both NDC and HCPCS/CPT4 codes then you will have two records at the same day. That could be suppressed at the ETL level, or you use the DRUG_ERA table, or you use the cohort definition mechanism not to double count.

Whether it is the first or second dose we will only indirectly have. If that causes issues we need to talk about how to handle. Right now, the OMOP CDM generally drops these implicit timing information in codes.

Yes please. :slight_smile:

(Vojtech Huser) #3

The key problem will be separation of manufacturers.

For Influenza - Not sure if current billing codes allow distinguishing Fluarix (GSK) from Fluzone(Sanofi) in CPT world.
See https://www.cdc.gov/flu/professionals/acip/2020-2021/acip-table.htm

For vaccines using same “principle” (like the Moderna and Pfizer are)- having still separate codes by manufacturer will be key. Does any one know of AMA plans to have it specific (like in the world of drugs) or have it bundled (like in the world of devices).

(Melanie Philofsky) #4

Generic coding at the source might be a potential issue. Most Epic immunization data are coded in the CVX vocabulary. CVX codes don’t identify the manufacturer and usually don’t distinguish between formulations. Fortunately, EHR data usually contain “billing” codes. These are CPT/HCPCS codes and it looks like the AMA will distinguish the two manufacturers.

In Epic, immunization data live in tables separate from the traditional “drug” tables. @krfeeney and others heavily involved in the covid research projects might want to suggest sites add source vaccine data to their OMOP pipeline now in anticipation of the drugs being approved for use.