COVID-19 Surveillance in the Biobank at the Colorado Center for Personalized Medicine: Observational Study

  1. Randi K Johnson
  2. Katie M Marker
  3. David Mayer
  4. Jonathan Shortt
  5. David Kao
  6. Kathleen C Barnes
  7. Jan T Lowery
  8. Christopher R Gignoux

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Abstract

Characterizing the experience and impact of the COVID-19 pandemic among various populations remains challenging due to the limitations inherent in common data sources, such as electronic health records (EHRs) or cross-sectional surveys.

Objective

This study aims to describe testing behaviors, symptoms, impact, vaccination status, and case ascertainment during the COVID-19 pandemic using integrated data sources.

Methods

In summer 2020 and 2021, we surveyed participants enrolled in the Biobank at the Colorado Center for Personalized Medicine (CCPM; N=180,599) about their experience with COVID-19. The prevalence of testing, symptoms, and impacts of COVID-19 on employment, family life, and physical and mental health were calculated overall and by demographic categories. Survey respondents who reported receiving a positive COVID-19 test result were considered a “confirmed case” of COVID-19. Using EHRs, we compared COVID-19 case ascertainment and characteristics in EHRs versus the survey. Positive cases were identified in EHRs using the International Statistical Classification of Diseases, 10th revision (ICD-10) diagnosis codes, health care encounter types, and encounter primary diagnoses.

Results

Of the 25,063 (13.9%) survey respondents, 10,661 (42.5%) had been tested for COVID-19, and of those, 1366 (12.8%) tested positive. Nearly half of those tested had symptoms or had been exposed to someone who was infected. Young adults (18-29 years) and Hispanics were more likely to have positive tests compared to older adults and persons of other racial/ethnic groups. Mental health (n=13,688, 54.6%) and family life (n=12,233, 48.8%) were most negatively affected by the pandemic and more so among younger groups and women; negative impacts on employment were more commonly reported among Black respondents. Of the 10,249 individuals who responded to vaccination questions from version 2 of the survey (summer 2021), 9770 (95.3%) had received the vaccine. After integration with EHR data up to the time of the survey completion, 1006 (4%) of the survey respondents had a discordant COVID-19 case status between EHRs and the survey. Using all longitudinal EHR and survey data, we identified 11,472 (6.4%) COVID-19-positive cases among Biobank participants. In comparison to COVID-19 cases identified through the survey, EHR-identified cases were younger and more likely to be Hispanic.

Conclusions

We found that the COVID-19 pandemic has had far-reaching and varying effects among our Biobank participants. Integrated data assets, such as the Biobank at the CCPM, are key resources for population health monitoring in response to public health emergencies, such as the COVID-19 pandemic.

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  1. Version published to 10.2196/37327
  2. ScreenIT

    SciScore for 10.1101/2022.02.15.22271018: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsConsent: Study Population: Enrollment in the CCPM Biobank is open to all UCHealth patients who are 18 years of age or older and able to provide consent for themselves through My Health Connection, the mobile EHR patient portal for UCHealth.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Experimental Models: Organisms/Strains
    SentencesResources
    Race and ethnic indicators were extracted as encoded in the EHR and categorized into 4 racial-ethnic groups to preserve >10 individuals in each group in all analyses, including: non-Hispanic White, non-Hispanic Black, any Hispanic, other.
    non-Hispanic White
    suggested: None
    Software and Algorithms
    SentencesResources
    To date, the Biobank has enrolled over 200,000 adult participants from among the 2.5 million UCHealth patients across Colorado.
    Biobank
    suggested: (HIV Biobank, RRID:SCR_004691)
    We created the survey in REDCap [7], a HIPAA-compliant database and research management platform, and created unique survey links for each Biobank participant.
    REDCap
    suggested: (REDCap, RRID:SCR_003445)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Lower participation among Hispanic individuals is consistent with observations in other outreach efforts [19806848] and is a limitation of the convenience survey design. Additionally, the Hispanic population in Colorado, as in many other states, had higher incidence of COVID-19 infections, hospitalizations, and death [4, 25-28], which may explain why they are more likely to be identified through the EHR. A key strength to this study is our ability to leverage an existing, living resource in the CCPM Biobank and survey engine to assess the health and wellbeing of our participants in ways that are not highlighted by the EHR. Further, because participants consent to re-contact, we have the opportunity to follow up with sub-populations within our cohort to collect additional information and monitor outcomes such as re-infection and vaccine uptake. Although our overall response to the survey was sizeable, we acknowledge that the composition of the underlying patient population at UCHealth who enrolled in the Biobank, and differential response to the survey may have introduced some bias and limited the generalizability of our results.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2022.02.15.22271018v1 on medRxiv
  4. Version published to 10.2196/preprints.37327