Introduction
The following document contains details related to the data collection, cleaning, and analysis of metrics displayed on the Cook County Department of Public Health (CCDPH) COVID-19 surveillance dashboard.
For data grouped by week, CCDPH uses MMWR weeks(1), with the week ending date displayed. MMWR weeks are used by CDC to report the incidence of national notifiable diseases in the Morbidity and Mortality Weekly Report (MMWR). MMWR weeks run from Sunday through Saturday.
CCDPH’s jurisdiction covers Cook County, except areas that have their own state-certified local health department. These places include the cities of Chicago, Evanston, Oak Park, Skokie, and Stickney township. Whenever possible, we display metrics for CCDPH jurisdiction; however, when this level of geographic granularity is not possible, metrics may be presented at the county level or include other Cook County suburbs listed above.
How to Get Data
If you would like to work with the data displayed in this dashboard, you can submit an External Data Request using this form.
Reported COVID-19 Cases
All heathcare providers, laboratories, or other testing sites in Illinois are required to report COVID-19 cases, per Illinois Control of Communicable Diseases Code(2). Mandated reporters are required to report cases electronically using Illinois’ National Electronic Disease Surveillance System (I-NEDSS). Local health departments then investigate cases, complete missing information, determine case status (“uniform criteria to define a disease for public health surveillance”)(3), and implement disease control measures as needed. In this dashboard, we include all reported cases with a case status of either confirmed case, probable case, or potential re-infection case. “Potential re-infection” was added as a case status in Illinois on September 1, 2021; re-infections prior to this date were not counted. Cases are grouped by the earliest lab specimen collection date.
Test Positivity
COVID-19 test data for percent positivity calculations comes from a sentinel network of laboratories who voluntarily submit de-identified testing data for the purpose of public health surveillance. Antigen tests and nucleic acid amplification tests (NAATs) are included in percent positivity calculations; serology (antibody) tests are excluded. Percent positivty is calculated by dividing the number of positive tests over the number of tests performed. Tests are grouped using lab result date.
- As of December 2023, CCDPH’s sentinel network of laboratories includes COVID-19 testing data for suburban Cook County zip codes from LabCorp and Quest. These data are made available through the National Syndromic Surveillance Program and include historical data from June 2022 to the present.
Genomic (Variant) Surveillance
Since the beginning of the pandemic, the virus that causes COVID-19, SARS-CoV-2, has mutated many times. Occasionally, these changes affect the virus’s ability to spread disease, how severe it is, or its ability to defend itself against treatments or vaccines. Public health agencies, such as the World Health Organization (WHO), conduct genomic surveillance to monitor SARS-CoV-2’s evolution for these types of changes. The WHO Technical Advisory Group on SARS-CoV-2 Virus Evolution designates some SARS-CoV-2 variants as Variants Under Monitoring (VUM), Variants of Interest (VOI), and Variants of Concern (VOC)(4). These definitions have evolved over time(5). WHO also assigns some of these variants with easy-to-say labels, such as Alpha or Delta, to improve global communication.
VUMs, VOIs, and VOCs are identified on the WHO’s Tracking Variants website, as well as in their weekly epidemiological updates. CCDPH routinely reviews these forums to keep comprehensive lists of all monitored variants, past and present. Previous monitored variants with WHO assigned labels are listed below.
Currently, most circulating variants are descendants of the Omicron variant. Omicron sub-lineages designated for monitoring by the WHO, past and present, are listed below.
Dashboard display of genomic abundance shows the proportion of variants identified out of clinical specimens sequenced and reported to I-NEDSS. Results for residents of CCDPH’s jurisdiction are included. All listed variants above receive their own category for display. Other Omicron sub-lineages are aggregated to their nearest parent lineage from the table above. For example, BA.4.2 would be aggregated with BA.4, while BA.4.6 would not be aggregated with any parent. Variants with less than 5% abundance in all weeks analyzed are grouped under ‘Other’.
Only a small proportion of laboratory specimens positive for SARS-CoV-2 are sequenced. Some of these specimens are selected through random sampling and others are sequenced as a part of public health investigations, or through provider ordering. Proportions represented in the dashboard may not be representative of all variants circulating in suburban Cook County. Results are grouped by specimen collection date and weeks with fewer than 15 specimens collected are excluded. Data for the previous 6 months are displayed.
Wastewater Surveillance
People infected with SARS-CoV-2 can shed virus in their stool, with or without symptoms. The virus can then be measured in wastewater, or sewage, as it makes its way to wastewater treatment plants. This method of surveillance is beneficial because it is not dependent on individuals seeking testing, or even knowing they are sick. However, because wastewater is a complex substance, made up of everything from human and animal feces to rain to industrial substances, measuring viral concentrations is a complicated process. Individual results are highly variable, but form a trend over time that can provide information on disease activity, especially when considered with other surveillance metrics(6).
Wastewater data for Cook County is made available through the Illinois Wastewaster Surveillance System(IWSS). Treatment plants who participate in IWSS volunteer to have samples collected from their facilities twice a week and tested to measure SARS-CoV-2 viral concentrations. In Cook County, all seven treatment plants operated by the Metropolitan Water Reclamation District of Greater Chicago participate in IWSS. One plant, the Stickney Reclamation Plant, has two sampling sites, at its north and south influents.
To monitor trends at the county level, CCDPH first normalizes SARS-CoV-2 concentrations by each plants’ average flow rate to get viral copies per liter. We then sum the viral copies per liter to get a county-wide value (displayed as points on the dashboard). Only days in which all eight sites have been sampled are included. We then use a generalized additive model to create a smoothed model of the data (displayed as a line on the dashboard). For the plant level table, we apply this same generalized additive model to plant level data and determine the trend by estimating the derivative of the smoothed line. When the upper limit of the derivative’s 95% confidence interval is less than zero, we consider the trend ‘decreasing’ (i.e., we are confident the rate of change is negative). When the lower limit of the derivative’s 95% confidence interval is greater than zero, we consider the trend ‘increasing’ (i.e., we are confident the rate of change is positive). Otherwise, the trend is ‘stable’ (i.e., we cannot confidently determine the rate of change). Prior to any analysis, we remove extreme outliers for raw SARS-CoV-2 concentrations (values more than 5 times higher than the upper limit of the sites’ interquartile range).
Hospital Admissions and Emergency Department Visits
CCDPH monitors two metrics for hospital visits associated with COVID-19. Data for both metrics comes from the National Syndromic Surveillance Program(NSSP). All acute care hospitals in Illinois are required to send a limited set of patient data for emergency department (ED) encounters and inpatient admissions to NSSP(7). To identify encounters associated with COVID-19, we use a CDC-designed query that identifies visits with any of the COVID-19 discharge diagnosis codes displayed below. Encounters for residents of suburban Cook County zip codes are included, regardless of which Illinois hospital the patient visited.
For emergency department encounters, CCDPH monitors the percent of all ED visits with a COVID-19 diagnosis. Visits are grouped by encounter date and are counted regardless of whether the person was admitted or discharged. Using the percent of visits associated with COVID-19, as opposed to counts, limits the impact of artificial increases or decreases in total visits due to data quality changes. However, data reflecting hospital admissions is subject to additional data quality monitoring by IDPH, enabling us to use counts for this metric. Admissions are grouped by initial encounter date and includes patients who are admitted from the ED, as well as direct inpatient admissions. Demographic age and race/ethnicity plots for admission data excludes patients with unknown age or unknown race and ethnicity, respectively. These demographics are typically missing for less than 1% of hospital admission records.
Mortality Estimates
CCDPH receives weekly de-identified death certificate data for all deaths that occur in Cook County (regardless of decedent residence). Fields include the immediate cause of death, contributing factors, and other significant conditions. If ‘COVID-19’, ‘novel coronavirus’, or ‘SARS-CoV-2’ appears in any of these fields, a death is considered associated with COVID-19. The percent of COVID-19 associated deaths, out of all deaths reported, is calculated.
Activity Level
Following CDC methodology(8), weekly risk levels for COVID-19 are primarily determined by the COVID-19 admission rate (number of hospital admissions with COVID-19 diagnosis per 100,000 residents) for suburban Cook County. The number of hospital admissions is determined as described above in ‘Hospital Admissions and Emergency Department Visits’. When the hospital admission rate is less than 10 admissions per 100,000, COVID-19 risk is considered to be low. When the admission level is between 10 and 20, risk is considered to be medium. When the admission rate exceeds 20 admissions per 100,000, risk is considered to be high. However, CCDPH may choose to override this risk level as needed, after careful review of all available surveillance metrics and discussion with subject matter experts.
Corresponding CDC recommendations for individuals and communities (8) are displayed in the Key Points section of the dashboard.
COVID-19 Vaccination Data
During the COVID-19 Public Health Emergency and initial vaccination roll-out, vaccines against COVID-19 were purchased by the U.S. Government and provided to the public for free via pharmacies, providers, and health departments, among others. In return for receiving supplies from the federal government, organizations administering COVID-19 vaccines were required to report these administrations to local immunization registries. In Illinois, this immunization registry is I-CARE, or the Illinois Comprehensive Automated Immunization Registry Exchange, operated by the Illinois Department of Public Health (IDPH). Reporting immunizations to I-CARE is otherwise voluntary in Illinois, so this requirement was crucial to CCDPH’s ability to estimate vaccination coverage during the initial phases of roll-out.
With the ending of the Public Health Emergency declaration on May 11, 2023, COVID-19 vaccines will commercialize(9); when the federal government’s current supply of vaccines is exhausted, procurement and payment will move to traditional pathways and vaccinations will no longer be reportable to I-CARE. As a result, data from this source is likely to be less accurate. Commercialization began in early fall of 2023(9). CCDPH will continue to update vaccination coverage estimates using I-CARE data on a monthly basis here, and eventually transition to using periodic survey data to estimate coverage.
References
1.
Centers for Disease Control and Prevention. MMWR weeks [Internet]. [cited 2023 May 16]. Available from: https://ndc.services.cdc.gov/wp-content/uploads/MMWR_Week_overview.pdf
2.
Control of communicable disease code [Internet]. Illinois Administrative Code Apr 22, 2022. Available from: ftp://www.ilga.gov/jcar/admincode/077/07700690sections.html
3.
Centers for Disease Control and Prevention. Coronavirus disease 2019 (COVID-19) 2023 case definition [Internet]. 2023 [cited 2023 May 16]. Available from: https://ndc.services.cdc.gov/case-definitions/coronavirus-disease-2019-covid-19/
4.
World Health Organization. Updated working definitions and primary actions for SARS-CoV-2 variants [Internet]. 2023. Available from: https://www.who.int/publications/m/item/updated-working-definitions-and-primary-actions-for--sars-cov-2-variants
5.
World Health Organization. Historical working definitions and primary actions for SARS-CoV-2 variants [Internet]. 2023. Available from: https://www.who.int/publications/m/item/historical-working-definitions-and-primary-actions-for-sars-cov-2-variants
6.
Centers for Disease Control and Prevention. National wastewater surveillance system [Internet]. 2023. Available from: https://www.cdc.gov/nwss/wastewater-surveillance.html
7.
Illinois Department of Public Health. Syndromic surveillance [Internet]. [cited 2023 May 16]. Available from: https://dph.illinois.gov/data-statistics/syndromic-surveillance.html
8.
Centers for Disease Control and Prevention. COVID-19 by county [Internet]. 2023. Available from: https://www.cdc.gov/coronavirus/2019-ncov/your-health/covid-by-county.html
9.
Health & Human Services USD of. Commercialization of COVID-19 medical countermeasures [Internet]. [cited 2023 May 16]. Available from: https://aspr.hhs.gov/COVID-19/Pages/FAQ-Commercialization.aspx