GA COVID-19 Report July 3, 2020

I feel we cannot overuse this meme right
now.

Note on Format

Today’s report is my first time posting to Medium, rather than just self-hosting the report as a static page on bitbucket. This should allow for a more “blog-like” format, and make it easier to share and access the report (thanks to @ReesMorrison for the suggestion)! I’ve retooled the report to post to Medium automatically using the R package ‘mediumr’. Unfortunately this did require some refactoring of the original code-based used to generate reports, with the primary loss being that my interactive graphs that were created with ggplotly don’t seem to want to cooperate. As a result all the graphs here are static. If you want the interactive graphs, you can still get them at my daily upload on bitbucket, which can be found at https://asb12f.bitbucket.io/COVID19/7-3.html (for prior dates, just change the date at the end of the link).

Daily Summary & Notes

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

Data

Data Notes

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.

Cumulative Confirmed Cases

Cumulative Hospitalizations

Cumulative Deaths

Cumulative ICU Use

Change Patterns

Count Level Tracking

Z Score Fluctuations

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.

New Cases

For today’s cases, the 30-day mean is 1386.63 and the standard deviation is 771.29.

Hospitalizations

For today’s hospitalizations, the 30-day mean is 107.8 and the standard deviation is 60.68.

Deaths

For today’s deaths, the 30-day mean is 24.43 and the standard deviation is 18.53.

ICU Admissions

For today’s ICU Admissions, the 30-day mean is 19.07 and the standard deviation is 9.77.

Testing

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

Cumulative Testing

Positive Tests by Source

Total Testing Trends

COVID19 Molecular Testing Trends

COVID19 Antibody Testing Trends

Is Increased Testing Causing Increased Cases?

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.

Are We Flattening the Curve?

Reported cases are slowing — or rather they aren’t accelerating as much. We’ve shifted from an exponential growth rate to a more linear one — you can see that both in the overall cases graph and in in the “new cases per day” graph. In theory, this could be reflective of a potential flattening of the curve (as Dr. Carlos de Rio suggested back on 4/10.).

Is the Shelter in Place Working?

The shelter in place order went into effect on April 3rd, which means that any potential effects of the order will only begin to be apparent in the week after April 17th, and only then if that data is adequately capturing the current status of infection in the state.

Where is the Spike?

I’ve commented several times that I don’t think we’ll see a dramatic spike in cases as GA “re-opens”, not because contagiousness is a myth but because we failed to ever really close. Further, those Georgians who did take the efforts at mitigation seriously are generally continuing to do so. A much more probable pattern is a gradual increase in cases over time, but not the overnight “spike” that commentators keep talking about.

Is Herd Immunity A Viable Solution?

Here’s my understanding of all of this, based on what I’m seeing from various public health experts and background readings. It’s an area that can be complicated with well known diseases, and with the current Coronavirus we’re still figuring some of it out.

What About Using Common Sense?

I want to take a moment and talk about the “use common sense” talking point that’s been going around. It usually goes something like this “it’s all safe and fine, just use common sense and you won’t get sick”. Aside from the clear victim blaming elements, it fails to understand the way “common sense” works.

Should People be Protesting?

While I do have concerns that we will see protest-related spread, that’s still a week away before appearing in the data. We’ve seen protestors taking precautions against spread (wearing masks, limiting crowd time, emphasizing open areas, etc.) as well as police tactics that have likely exacerbated spread (tear gas, holding people in confined areas with poor airflow, removal of PPEs from protestors, etc.). It’s impossible to calculate the level of risk present. However, the public health and medical communities are unified around one point on the topic — systemic racism is a public health issue that has immense human, financial, and moral costs, and must be addressed. Further, public health experts are consistent in the message that if people take adequate precautions, the risk in speaking out against racism is outweighed by the benefit. The two issues — COVID19 and racism — are in necessarily intertwined; to quote the open letter from infectious disease experts at the University of Washington: “protests against systemic racism, which fosters the disproportionate burden of COVID-19 on Black communities and also perpetuates police violence, must be supported.” This is why you’re seeing so many medical professionals on the front lines of these protests, and why the WHO supports them.

Final Thoughts

As always, I should point out that I am NOT an epidemiologist, and I will always defer to the experts.

Documentation

Code and data available here.