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Link to the latest Data Dictionary: 2021-09-02 CDC-NACHC COVID19 Data Dictionary Year 2 v5


Anatomy of the data dictionary file

Sheets

  1. Change Log
    1. Will contain information on what data elements have been added, augmented, moved/removed, with space for comments/addenda
  2. Demographics-SDOH Variables
    1. Data elements pertaining to patient demographics and associated SDOH variables. 
  3. COVID-19 Diagnoses / Codes
    1. Data elements related to the encounters, exposure and diagnoses of COVID-19 and Post-acute Sequela of COVID-19 (PASC)
  4. COVID-19 Tests / Codes
    1. Data elements related to laboratory tests for COVID-19 (Antigen, Antibody, Molecular, Variants)
  5. Vaccinations / Codes
    1. Data elements related to influenza and COVID-19 vaccines / vaccination
  6. COVID-19 Co-morbidities
    1. Data elements grouping identified co-morbidities that affects COVID-19 morbidity and mortality
    2. ** Codes are not defined as all diagnosis codes related to COVID-19 project patient population are requested to be extracted.
  7. COVID-19 Outcomes
    1. Data elements related to encounters and outcomes
  8. COVID-19 Therapeutics / Codes
    1. Data elements related to the currently approved therapeutics for COVID-19
  9. Deprecated - NOT REQUESTED
    1. Data elements previously included, but is now removed due to difficulties in the presence or extraction of the data specified.

Columns

  1. Data class
    1. Data set allocation attributes and values related to health data (Diagnosis, Encounter, etc.)
  2. Variable
    1. Data element / concept
  3. Definition
    1. Formal or informal definition of the variable / data element, defined in standard terminology
  4. Data Type
    1. Attribute of the data element related to the intent of how the data will be extracted, transformed, loaded and analyzed
  5. Source
    1. Reference / Standard Terminology that defines the value sets (group of codes that define a concept) and codes. Assists in aggregation and data interoperability
  6. Value Sets / Codes
    1. Value Set OIDs that reference a set of codes, or a list of codes
  7. Response
    1. Expected response / type of data submitted
  8. Metadata
    1. Data attributes that are expected to come with the response (date, description, etc.)

Year 2 New Data Elements FAQ

  1. Post-Acute Sequelae of SARS-CoV-2
    1. There are multiple definition for PASC, depending on organization or regulatory body!
      1. CDC: "We use post-COVID conditions as an umbrella term for the wide range of health consequences that are present four or more weeks after infection with SARS-CoV-2. The time frame of four or more weeks provides a rough approximation of effects that occur beyond the acute period, but the timeframe might change as we learn more." : https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-care/post-covid-conditions.html
        1. For individuals with multisystem inflammatory syndrome (MIS) and COVID-19, assign code U07.1, COVID-19, as the principal/first-listed diagnosis and assign code M35.81, Multisystem inflammatory syndrome, as an additional diagnosis.
        2. If MIS develops as a result of a previous COVID19 infection, assign codes M35.81, Multisystem inflammatory syndrome, and B94.8, Sequelae of other specified infectious and parasitic diseases.
        3. If an individual with a history of COVID-19 develops MIS and the provider does not indicate the MIS is due to the previous COVID-19 infection, assign codes M35.81, Multisystem inflammatory syndrome, and Z86.16, Personal history of COVID-19.
        4. If an individual with a known or suspected exposure to COVID-19, and no current COVID19 infection or history of COVID-19, develops MIS, assign codes M35.81, Multisystem inflammatory syndrome, and Z20.822, Contact with and (suspected) exposure to COVID-19.
      2. BMJ: "There is no globally recognized definition for PASC. The general consensus is that any patient experiencing symptoms that extend beyond 3 weeks from first symptoms onset are considered to have “post-acute COVID-19,” and patients with symptoms extending beyond 12 weeks are considered to have “chronic COVID-19." https://www.bmj.com/content/370/bmj.m3026
      3. Nature:
        1. Long COVID has no single, strict definition
        2. long COVID represents symptoms that have been present for longer than two months, though there is no reason to believe that this choice of cutoff is specific to infection with the SARS-CoV-2 virus
        3. (Brodin P (January 2021). "Immune determinants of COVID-19 disease presentation and severity". Nature Medicine. 27 (1): 28–33. doi:10.1038/s41591-020-01202-8. PMID 33442016.)
      4. AHA/AHIMA: "“post COVID-19 syndrome clinically conveys causality and not a time reference" 
      5. National Institutes of Health: "Long COVID" can include fatigue, shortness of breath, "brain fog", sleep disorders, intermittent fevers, gastrointestinal symptoms, anxiety, and depression. Symptoms can persist for months and can range from mild to incapacitating, with new symptoms arising well after the time of infection. https://www.nih.gov/about-nih/who-we-are/nih-director/statements/nih-launches-new-initiative-study-long-covid
      6. British National Institute for Health and Care Excellence (NICE) https://www.nice.org.uk/guidance/ng188/chapter/Context

        1. acute COVID-19 for signs and symptoms during the first 4 weeks after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the first, and the other two are for new or ongoing symptoms 4 weeks or more after the start of acute COVID-19, both of which it includes under the term 'long COVID', and divides into:

          1. ongoing symptomatic COVID-19 for effects from 4 to 12 weeks after onset, and

          2. post-COVID-19 syndrome for effects that persist 12 or more weeks after onset.

        2. NICE describes the term long COVID, which it uses "in addition to the clinical case definitions", as "commonly used to describe signs and symptoms that continue or develop after acute COVID-19. It includes both ongoing symptomatic COVID-19 (from 4 to 12 weeks) and post-COVID-19 syndrome (12 weeks or more)".

        3. Defines post-COVID-19 syndrome as "Signs and symptoms that develop during or after an infection consistent with COVID‑19, continue for more than 12 weeks and are not explained by an alternative diagnosis. It usually presents with clusters of symptoms, often overlapping, which can fluctuate and change over time and can affect any system in the body.

        4. Post‑COVID‑19 syndrome may be considered before 12 weeks while the possibility of an alternative underlying disease is also being assessed"


Data extraction - Best Practices / Tips

  1. Leverage standard terminologies that your EHR data supports / uses
  2. As much as technically possible, use the value set OIDs and the codes within the value sets for your database queries
  3. As much as technically possible, always submit data with codes (local EHR codes, LabCorp/Quest lab codes, and other IF standard terminologies like ICD/SNOMED/RxNorm/LOINC} are not supported)

Preferred structure provided data.  

  1. As much as technically possible, data are preferred as normalized relational entities. 
    1. Example:
      1. Data (standard/local code or terminology with a description) provided should represent the following
        1. Patient/Demographics table
        2. Encounter table
        3. Rx table
        4. Dx table
        5. etc. 
    2. Tables should have foreign keys (e.g. an encounter table should have a patient id and an Rx table should have an encounter id, etc.). 
    3. The closer the data resemble the NACHC Standard Column Definitions or other standard relational data models (OMOP, PCOR, etc.) the better. 
    4. NACHC has tools available that can be leveraged to convert pivoted and other otherwise formatted data into a more relational/normalized model. 
      1. Tools can be used both in the context of this project and are also generally available for other applications.