GA COVID-19 Report July 14, 2020

Today’s report uses the data from the 2:50PM Report from the GA Department of Public Health.

Today we saw 3394 new cases (our record for new cases is 4484), which brings us to 23493 in the past 7 days (19% of total cases so far). We also had 28 new deaths (our record for new deaths 100), which brings us to 155 in the past 7 days (5.1% of total deaths so far). We saw 207 new hospitalizations (our record is 442), bringing our 7-day count to 1459 (10.7% of total hospitalizations so far). Lastly, we had 19 new ICU admissions (54 is the record), bringing our 7-day count to 191 (7.2% of total ICU admissions cases so far).

For testing, we saw 23067 new COVID19 tests, bringing us to 151582 in the past 7 days (13.4% of total COVID19 tests so far). We also saw 178 new antibody tests, bringing us to 15093 in the past 7 days (8.1% of total antibody tests so far).

Yet another big day for new cases has arrived. If you haven’t noticed yet, things are getting quite a bit worse.

Something that happened a few weeks ago that I think is worth noting is a change in how DPH reports COVID19 testing by test-type. When they first started providing this data, they provided information on total tests, PCR tests (COVID19 tests), and serology tests (antibody tests). Recently, they’ve changed reporting to show total PCR tests, New PCR tests for today, and total serology tests. Setting aside the issue with not all labs reporting to the state (and thus not being included in these counts), this decision seems strange. After all, you’d think it would be important to characterize the total amount of testing being done, and to give people a sense of how much of each type of testing is being done per day.

Because I have daily data on totals, I’ve been able to calculate these daily testing statistics. What becomes apparent is that very little antibody testing is actually occurring. Given that one of the popular talking points for dismissing the increase in COVID19 cases in GA is that we’re mis-attributing antibody tests as positive cases, it would seem valuable to clearly convey in the table both that we aren’t doing widespread antibody tests, and that positive antibody tests don’t count as positive tests (instead of hiding this information in an info button you have to click on to read).

Regardless of the reasoning for these changes, it reduces the data available, and in my mind that’s the least beneficial thing we can do at this point. More information is always better than less, particularly when the health of the entire state (and country) are at stake.

There are two notable political issues related to COVID today that do need to be addressed. First, Trump’s decision to remove the CDC as the first recipient of COVID19 data cannot be seen as anything other than a radical new level of politicizing public health data. This sort of behavior is extremely dangerous. Second, we’re awaiting updates about whether Kemp will issue new orders. As Kemp has signaled conflict with mayors who have defied his order and enacted more restrictive policies, it will be interesting to see whether he will concede that there is a need to stop the statewide escalation of the virus, or if he will push forward with the current policies that have led to dramatic escalation of the virus this month. Let’s hope for the former.

Regardless of what Kemp does, you should stay home, wear a mask, and minimize your exposure.

You can access an interactive version of these graphs, including embedded data here.

Prior to 5/11, all data is taken from the noonish update from the GA Department of Public Health to present even time intervals between data points which is important for graph interpretation. On 5/11, reporting schedule shifts to being at 9AM, 1PM, and 7PM, so this report will capture to the 1PM reporting time. On June 2nd, reporting was reduced to once a day at 3PM. Data does reflect multiple inefficiencies and inaccuracies in the current reporting system, including showing tests before their results are returned, delays in reporting on weekends that create artificial spikes and valleys in change data. In general, interpretation should examine the general trends, and not focus exclusively on endpoint trajectories, which are highly influenceable by these data variations.

To help visualize the effects of State actions on the outbreak, I’ve added a few sets of lines to several of the graphs. The first — the vertical blue lines — show when the state of emergency went into effect (3/15; solid line) and when we might expect to see first effects from it (dotted line). The second — vertical red lines — is the Friday Shelter in Place was instituted (4/3; solid line) and the date we might expect to see first effects (dotted line). The third — vertical pink lines — show when the shelter in place was lifted (4/30; solid line) and the date we might expect to see first effects (dotted line).

Where point data is presented, a LOESS regression with 95% confidence intervals is shown to help the viewer interpret overall trends in the data. This is preferred over a line graph connecting all points, which tends to over-emphasize outliers in report.

Because percentage growth becomes misleading over time, I’ve added a floating 4-week Z-score visualization for each measure to help put into perspective the magnitude of daily variation in numbers.

For those who don’t spend a lot of time in the world of statistics, a Z score is a measure that describes the relationship of an observation (in this case, a particular day’s number) to the average across the entire group. It is calculated by taking the difference between the observation and the mean, and dividing by standard deviation.

Z = (Observed Score — Mean) / Standard Deviation

For example, if the mean score for a group is 50, and the standard deviation is 10, then a score of 60 woud have a Z score of (60–50) / 10 = 1, and a score of 20 would have a Z score of (20/50) / 10 = -3.

This can be useful in identifying patterns in data reporting, and help put daily fluctuations in perspective. Because the data is more localized, it doesn’t fall victim to the diminishing returns effect. These visualizations are limited to the data from the last 30 days, which further helps illustrate trends and fluctuations.

For today’s cases, the 30-day mean is 2209.4 and the standard deviation is 1004.4.

For today’s hospitalizations, the 30-day mean is 147.9 and the standard deviation is 83.68.

For today’s deaths, the 30-day mean is 20.1 and the standard deviation is 14.37.

For today’s ICU Admissions, the 30-day mean is 20.93 and the standard deviation is 10.89.

These graphs contain several markers that reflect the changing nature of the testing data that has been provided over time.

As of 4/28 specific counts of the number of tests administered by the government and commercial providers stopped being reported. Additionally, on this date we began to track data on the number of positive tests conducted by the CDC.

On 5/27, specific counts of serology tests (antibody tests) became available, which had previously been aggregated into the total test count. This date has been marked with a vertical gold line on the graphs. This distinction is important, as positive antibody tests do not result in new cases in the overall count, and thus both suppress the positive test rate and artificially inflate estimates of test prevalence. The daily data for daily COVID19 tests and serology tests is tracked starting on this date.

For today’s new tests, the 30-day mean is 19531.8 and the standard deviation is 6496.58.

For today’s new tests, the 30-day mean is 17185.6 and the standard deviation is 6423.94.

For today’s new tests, the 30-day mean is 2346.2 and the standard deviation is 2399.21.

A popular talking point recently is that the increase in cases that are being detected is not reflective of increased spread, but rather a result of increased testing. There is a certain logic to this — the more tests that are run the more potential cases we can identify. However, this can lead us to significant logical errors, and these in turn can lead to dangerous behaviors. While our data does not allow a perfect causal analysis, we can examine what associations between testing and cases exist in our data.

If we run a simple correlation between total number of tests and total number of cases, we get an initially persuasive graph. Note that this graph includes both antibody and molecular tests.

This gives a correlation of 0.98! This is inviting, but it mostly just shows that both of these numbers are increasing. This is potentially misleading because it looks at cumulative data. In fact, if we run a correlation between the total number of tests administered and a simple series of ascending numbers (1, 2, 3, etc.) we get a correlation of 0.97. Because our hypothesis (increased testing causes increases in reported cases) is more about fluctuations in these two variables than cumulative growth, we need a different analysis.

If we look at the daily increase in cases against the daily increase in tests, we get a different picture:

This gives us a correlation of 0.6480831. But this number is also misleading, because there are significant time lags in reporting of tests and new cases within the data.

To better assess the relationship, let’s look at 10-day moving averages for both new tests and new cases, and see what correlation exists between them. This will help balance out the issues of delayed results.

This gives us a correlation of 0.7. By the observational nature of our data, we can’t infer causation, and we can’t remove eliminate extraneous factors, but we can observe that the association between these two variables is limited, and that the increases in cases cannot be attributed purely or even primarily to the quantity of testing occurring.

Is Herd Immunity A Viable Solution to COVID-19?

Is Using Common Sense A Viable Solution to COVID-19?

Should People be Protesting During COVID19?

As always, I am not trained in epidemiology, and defer to recognized experts in the field on all issues. These analyses and commentary are solely designed to help lay persons approach the publicly available data and larger public health conversations.

Stay Home.

Wash Your Hands.

Wear a Mask.

Code and data available here. Analysis conducted using R.



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