The Daily Digest, 06Nov2020

Georgia COVID-19 Updates

Good afternoon! Today we’ll discuss the latest data from Georgia Department of Public Health. First, yesterday I distracted myself from the drama unfolding with the presidential election by delving into the data for Colorado since I have family there and we have a complete set of White House Coronavirus Task Force reports for that state. If you don’t follow me on social media, here’s the thread via Twitter.

For those who want to join the subscribers only book club, we’ll start off by reading one of the books that I read in high school that made me want to become a microbiologist - The Hot Zone by Richard Preston. We’ll be meeting to discuss this book in January but I wanted to give plenty of heads up so that you can get a copy of the book, ask for it as a gift over the holidays, etc. For the month of November, we’ll be playing Solve the Outbreak and then discussing together via Zoom. This will be a limited size event and RSVP will be required. Subscribers, I hope to have the email with those details out this weekend, so keep an eye out for that. For those who haven’t yet subscribed, this is a great time to do so.

The School Aged Surveillance Data Report has not been released yet for today. If anything important shows up in those data when it is released (after I distribute this newsletter), then I will discuss it on social media and then link to that in the next newsletter on Sunday.


Testing

The biggest development for Georgia this week is that we now can see the number of cases identified through antigen testing. But we don’t yet know how many total antigen tests are being performed. But we know that it must be significant. Because of the 2802 newly identified cases reported today, 38% of them were identified through antigen testing.

Despite this, PCR remains the gold standard in testing. We can still consider test rate and percent positive rate, but these things may diminish in value as antigen testing gains in popularity. I mean, we might be doing really well on testing if we could see how many antigen tests were being performed. Until we have the total antigen test data, however, the PCR-based data are the best data we have for determining whether we are doing adequate testing.

Today there was a net increase of 19,573 new PCR tests reported and of those 7.8% were positive. Of the new PCR-identified cases reported today, 88% were reported through Electronic Laboratory Reporting (ELR). So this is a good sample for us and the 7.8% is likely an accurate estimate of our positive rate. In recent months, the percent positive rate has come a long way down from where we were during the summer surge and we have been at or near the goal of 5% for much of October. But things are starting to trend upward. I’ll discuss the weekly trends over time in my update on Sunday.


Cases

As I stated in the testing section, there was a net increase of 2802 cases reported today with 1738 identified through PCR and 1064 identified by antigen test. With today’s newly reported cases, the confirmed case total is 370,106 and our combined case total is 402,427 since the start of the pandemic. Of today’s newly reported cases, 36% came from nonrural counties (>50,000 residents) outside of the Atlanta metro. The next leading contributor to today’s cases was the Atlanta suburbs with 27% of the cases. Rural counties contributed 17.7% of cases and the Atlanta counties (Fulton & DeKalb) contributed 12.8%). You can check to see how I classify your county in the table provided in this post.

Below, I’ve provided the latest graph showing 7-day case rate per 100,000 people for each county type compared to the statewide average (black line). Ignore the big spike around 06Oct - that’s when the state of Georgia told us there were ~26,000 antigen test-identified cases and it’s an artifact of that data dump.

But what you can see is that things are increasing for the entire state. Nonrural counties have the highest case rate and Atlanta counties have the lowest. While the increase most recently is very sharp, it is too soon to know whether we’ve tipped over into exponential growth (a new surge). However, our current 7-day case rate is at a level that is only 28% less than our previous peak during the summer surge. For that reason, although many may have taken a break from disease exposure mitigation strategies, it really is time to buckle down and follow the guidance. I think we all remember how intense the summer surge felt at the time. If and when this latest increase becomes a surge, we might be in for a much higher peak than last time.


Hospitalizations

Today there were 100 new hospital admissions for COVID-19 disease and 17 admissions to the ICU. Both of these numbers are pretty similar to what we saw a week ago on Friday. The difference between a week ago and today, however, is that there are 138 more people currently hospitalized. In fact, there are 1511 patients currently hospitalized for COVID-19 and we haven’t been above 1500 since 15Sep, as we were coming down from the summer surge.

Similar to what I pointed out for cases, that we’ve started the next increase from a heightened position, the same is true for current hospitalizations. We bottomed out after the summer surge at a level that was twice as high as our level prior to the summer surge. It is my hope that if this increase becomes a surge that we will have a more prolonged effort to bring cases and hospitalizations down this next time. Otherwise we risk that each trip up the disease roller coaster is higher and higher.

Prior to the summer surge we saw this gradual increase that eventually tipped over into very large daily increases. We can limit hospitalizations by limiting cases. The actions we do or don’t take today to limit our exposures will impact hospitalizations two weeks from now and deaths three weeks from now. It’s therefore really important that we be especially careful now.

Twenty nine percent of adult ventilators are in use, similar to where we were prior to the summer surge. There are just two hospital regions using >90% of their ICU beds today, regions H (92.5%) and N (91.1%).


Deaths

There was a net increase of 30 newly reported confirmed deaths today, bringing the statewide total to 8156. The DPH does now report probable deaths, but the definition for those deaths is a bit more broad than I would prefer for combining those deaths with our total. As for the cases, here is the 7-day death rate per 100,000 graph across time and county types.

Statewide (black line), we are in a much better position than we were in at the height of the summer surge. We have seen some increases in the past couple days, but this may just be normal variation in the data that we’ve seen throughout the past. Nonrural counties continue to track along well with the statewide average while rural counties have a death rate that is 83% higher than the statewide average.

Lastly, to sign off today I want to congratulate Georgians on their historic turnout in the November election. I’m sure living in a newly minted battleground state is a surreal feeling. I certainly enjoyed hearing newscasters struggle to pronounce our county names correctly. But I also want to acknowledge that there will be people elated and people devastated over the election results. Please try to extend as much grace as possible. Coronavirus doesn’t discriminate political affiliation when it kills people. This virus and the damage it inflicts is very real. It is my hope that when the election news settles, we can turn our attention back to the crisis at hand - a growing surge of cases throughout the country and keeping that from materializing in Georgia. We have overcome enormous challenges in our history and I expect that we can do so again in the face of this challenge.


References

https://dph.georgia.gov/covid-19-daily-status-report

https://covid-gagio.hub.arcgis.com/

https://amberschmidtkephd.substack.com/p/pcr-percent-positive-rate-by-county


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My Ph.D. is in Medical Microbiology and Immunology. I've worked at places like Creighton University, the Centers for Disease Control & Prevention and Mercer University School of Medicine. All thoughts are my professional opinion and should not be considered medical advice.