Methods and Metrics

Methods -thresholds for each indicator are described below. Source of COVID-19 case data is SC DHEC:

  • Indicators

*Cases Per Day Per 100k Population – This is the 7-Day average of the number of reported cases per day per 100k residents, as reported on the South Carolina DHEC site; it is the total number of confirmed cases combined with the total number of probable cases for Chester and Lancaster Counties. Available at: https://scdhec.gov/covid19/sc-testing-data-projections-covid-19

*Test Positivity  – This number is the 7-Day average of the percent of positive tests, determined using the Test/Test method. This number is reported by South Carolina DHEC with a two-day lag, available at https://scdhec.gov/covid19/south-carolina-county-level-data-covid-19

*ICU Beds in Use Per Week– This is the number of hospital beds in use for the past week for Charleston area hospitals, as reported by The Department of Health and Human Services. This data is updated weekly and corresponds to the previous week's data (Friday through the following Thursday). Available at: https://healthdata.gov/dataset/covid-19-reported-patient-impact-and-hospital-capacity-facility

*Effective Reproduction Number (Rt)– This is the estimate of infectious disease transmissibility. The R-Naught indicates the average number of people who are infected by each person who gets infected. If R-Naught is greater than 1 the epidemic will continue to be sustained. If R-Naught drops below 1 eventually the epidemic will cease to exist. The time-dependent reproduction number (R) is inferred from disease incidence time series and is calculated by inputting the number of new cases via an algorithm created by the authors: Thompson RN, Stockwin JE, van Gaalen RD, Polonsky JA, et al. Improved inference of time-varying reproduction numbers during infectious disease outbreaks. Epidemics (2019). Available at: https://shiny.dide.imperial.ac.uk/epiestim/

*Percentage of Population Vaccinated– This is the percentage of the aggregate number of people who have currently been vaccinated by county. This metric does not include individuals who may move across state lines in order to access vaccines. This data is reported by DHEC and is available at: https://scdhec.gov/covid19/covid-19-vaccination-dashboard

*Estimated Percentage of Population with Immunity– This is the percentage of the number of people who currently have either Natural (through infection with Covid-19) or Vaccine (they have received either one or both doses) Immunity in Lancaster county. This metric is an estimate and will be updated weekly. This data is reported by DHEC and is available at: https://scdhec.gov/covid19/covid-19-vaccination-dashboard

Estimated Immunity Calculations and assumptions:

(Note – we have updated some assumptions based on emerging data, and these are described for each parameter below as needed):

1) Population by county was culled from DHEC reports. Total population is used for the denominator for both the percentage of people with vaccination and for percentage of people with natural immunity.

2) COVID-19 diagnosed cases for the past 7-months by county is pulled from the New York Times publicly available database, which is derived from daily DHEC reports. (https://github.com/nytimes/covid-19-data/blob/master/us-counties.csv). We chose 7-months based on available high-quality data that now includes follow up to 7-months. Earlier we used 5-months as that was the longest reported in rigorous research studies. See https://doi.org/10.1101/2021.01.15.21249731 - “SARS-CoV-2 reinfection in a cohort of 43,000 antibody-positive individuals followed for up to 35 weeks”

3) A multiplier for the ratio of diagnosed to undiagnosed cases was derived from CDC estimates that for every 1 reported case there are 4.6 (Uncertainty Interval: 4.0-5.4) COVID–19 infections not reported. Thus, we assumed a multiplier of 4.6 with a range of 4.0-5.4 used for sensitivity analyses. (See: https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/burden.html).

4) Total number of people vaccinated for the COVID-19 virus by county with 1- and 2-doses of vaccine is derived from DHEC reports. To calculate the number who have had only 1-dose we subtracted the number who have “received at least 1-dose” from those fully vaccinated.

5) Immunity for those with only 1-dose (at 52.4%) is based on the Pfizer clinical trial data on efficacy after 1-dose to before dose 2. Sensitivity ranges are culled from these estimates (29.5%-68.4%). See Pfizer vaccine trial data: “Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine”, NEJM, Dec 31, 2020. Vol 383, No. 27. Earlier we used CDC estimates of effectiveness, but those data are limited to healthcare workers who have much higher exposure than the general population. https://www.cdc.gov/mmwr/volumes/70/wr/mm7013e3.htm?s_cid=mm7013e3_w).

6) Immunity for those with 2-doses (at 94.8%) is based on the Pfizer clinical trial data on efficacy 7-days after dose 2. Sensitivity ranges are culled from these estimates (89.8%-97.6%). See Pfizer vaccine trial data: “Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine”, NEJM, Dec 31, 2020. Vol 383, No. 27. Earlier we used CDC estimates of effectiveness, but those data are limited to healthcare workers who have much higher exposure than the general population. https://www.cdc.gov/mmwr/volumes/70/wr/mm7013e3.htm?s_cid=mm7013e3_w).

7) Those receiving the Janssen vaccine are counted as “fully vaccinated” and included in the count for those receiving the 2nd dose of the Pfizer or Moderna vaccine. The Janssen vaccine generates slightly lower immunity, but currently it represents a small proportion of all vaccinations and based on the way DHEC presents the data there is no way to disaggregate values by county. Pfizer vaccine trial data: “Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine”, NEJM, Dec 31, 2020. Vol 383, No. 27.

8) To avoid double counting those who received a vaccine and had a prior infection we assume that the number of people vaccinated who experienced a prior infection in the past 7-months is the same as that which occurs for the entire population aged 15 years and older. We then subtract these from the count of those with vaccine immunity.

9) We estimated the 7-month efficacy of natural immunity at 95.2% (CI-interval used in sensitivity analysis: 94.1%-96.0%) based on a literature review, and largely based this on a high-quality study that followed 43,000 antibody positive patients for 35-weeks to assess reinfection. See https://doi.org/10.1101/2021.01.15.21249731 - “SARS-CoV-2 reinfection in a cohort of 43,000 antibody-positive individuals followed for up to 35 weeks” We earlier used data from a study in Denmark that followed patients for 5-months, which had a more limited timeframe. See: “Assessment of protection against reinfection with SARS-CoV-2 among 4 million PCR-tested individuals in Denmark in 2020: a population-level observational study" by Holm Hansen et al. Lancet 2021; 397: 1204–12. https://doi.org/10.1016/S0140-6736(21)00575-4).

10) Sensitivity analyses were conducted via stochastic modeling with Palisade @Risk V8.1 software. Confidence ranges presented represent the minimum and maximum values derived across 10,000 iterations of the stochastic model.

Estimation of Distribution of Weekly Cases by Immunity Status

1. The distribution of cases is based primarily on a high quality study conducted by the University of Oxford using data from the United Kingdom (See: https://doi.org/10.1101/2021.04.22.21255913 - “Impact of vaccination on SARS-CoV-2 cases in the community: a population-based study using the UK’s COVID-19 Infection Survey”). In this study the investigators followed 1,610,562 people. Among this group 24,871 people had a prior COVID-19 infection and had not been vaccinated. They report the infection rate by immunity status, including for 7 categories over a 5-month time interval:
a. Not vaccinated, not previously positive, >21days before vaccination
b. Not vaccinated, not previously positive, 1-21 days before vaccination
c. Vaccinated 0-7 days
d. Vaccinated 8-20 days
e. Vaccinated >=21days after first dose
f. Fully vaccinated
g. Not vaccinated, previously positive

2. Using the categories above of participants, we combined the infection percentages into 4 groups:
a. Not vaccinated (84.9%)
b. Partial vaccination (9%)
c. Fully Vaccinated (0.6%)
d. Not vaccinated, previously positive (0.7)

3. We utilized values on percentage of the population and number in each setting that map to the categories in item 2 above.

4. We culled data from DHEC on the total incident infections in each setting over the past week.

5. Finally, we distributed the number of incident infections by the categories of immunity multiplying the total number of cases by the percentage distribution by category of immunity observed in the University of Oxford study.

  • Growth in Number of Reported COVID-19 Infections: Weekly change of reported infections for the Lancaster region (Percentage change in 7-day average of new infections over the past week).

*This metric is updated daily M-F, while the remaining metrics are updated weekly.

GREEN – The percent change in the 7-day average in growth of confirmed cases over the past week is 1% or less (or negative).

YELLOW – The percent change in the 7-day average in growth of confirmed cases over the past week is 2-5%.

RED – The percent change in the 7-day average in growth of confirmed cases over the past week is 6% or greater.

 

  • Trajectory of documented cases (Increasing or Decreasing): Downward trajectory of documented cases within a 14-day period.  

GREEN -There is a negative slope of the trend line (downward trajectory) of the daily 7-day average of number of cases for each of the past two-weeks.

YELLOW -There is a negative slope of the trend line (downward trajectory) of the daily 7-day average of number of cases for one of the past two weeks (one week positive, one week negative).

RED – There is a positive slope of the trend line (upward trajectory) of the daily 7-day average of number of cases for each of the past two-weeks.

 

  • Number of Reported COVID-19 cases in last week: Number of reported cases per week is manageable with regard to medical care and capacity for effective contract tracing.

GREEN -Number of reported cases per week less than 1 per 1,000 population.

(Population = 130,256: equivalent to 13 or fewer cases a week)

YELLOW - Number of reported cases per week is 1-5 per 1,000 population.

(Population = 130,256: equivalent to 13 - 65 cases a week)

RED - Number of reported cases per week greater than 5 per 1,000 population.

(Population = 130,256: equivalent to GT 65 cases a week)

 

  • Diagnostic Testing Availability: Diagnostic testing availability for all people with COVID-19 symptoms.

GREEN – 100% of those meeting criteria and seeking testing receive testing

YELLOW – 80%-99% of those meeting criteria and seeking testing receive testing

RED – Less than 80% of those meeting criteria and seeking testing receive testing

 

  • Return of Diagnostic Test Results: Return of diagnostic test results is done in a timely manner and that allows for rapid contact tracing.

GREEN – Results returned within average of 2 days from sample collection

YELLOW – Results returned within average of 3-4 days from sample collection

RED – Results returned within average of 5 or more days from sample collection

 

  • Hospital Capacity to treat Critical Patients: Area hospitals have ability to treat critical patients requiring hospitalization without resorting to crisis standards.

GREEN – Area hospitals have greater than 15% of total staffed ICU beds available

YELLOW – Area hospitals have between 5% - 15% of total staffed ICU beds available

RED – Area hospitals have less than 5% of total staffed ICU beds available

 

  • Super spreader events and congregant facility outbreaks: Number of super spreader events or cluster outbreaks of significant magnitude (GT 10 cases in discrete social group or setting) in past 30 days.

GREEN – None reported in past 30 days

YELLOW – 1-2 reported in past 30 days

RED – 3+ reported in past 30 days

 

*Metrics shown reflect the day events occurred, not the day they were reported. There is typically a one-day lag in the release of data from DHEC on newly diagnosed cases. There is typically a two-day lag in the release of data from DHEC on percent positive of COVID-19 Tests.