The Daily Digest, 11Dec2020
The Daily Digest, 11Dec2020
Georgia COVID-19 Updates
The human immune system is amazing and incredibly complex. In fact, it’s one of the most intricate things I’ve ever had to learn. Effectively, you have your own personal army inside your body that relies on teams of specialized cells and communication networks between them. Just as tanks do a very different job than helicopters, your immune system has lots of weapons to bring to the fight. Every cell in your body has a name tag and cells in your immune system are constantly checking to make sure that only cells with the right name tag are there and removes anything with the wrong name tag. It can also learn about invaders it has seen before and prepare to recognize and defeat invaders the next time they’re encountered.
When a virus like COVID-19 comes into your body, it has an envelope surrounding with spikes coming out of it. These spike proteins serve as keys that are searching for a lock and the locks are found on the cells of your respiratory tract. In immunology we call these locks “receptors.” These locks have an important purpose in the body and they aren’t designed for viruses to enter, but viruses have evolved to take advantage of the locks that are available, even if they’re intended for other things.
One of the tools of the immune system that involves both weaponry and memory is the production of antibodies. Antibodies are Y-shaped proteins that your immune system generates in response to infection. There are two “invader” binding sites at the top tips of the Y. In the context of viruses, antibodies are what you want in order to protect you. But just like you need to have the right key for the right lock, you need to have the right antibody for the right virus. Since none of us had seen COVID-19 before when this pandemic began, nobody was producing the right antibodies. When the right antibody is present it can cover up the keys on the outside of the virus particle, getting in the way so that the key can’t enter the lock. If the key can’t enter the lock, then the virus never gets inside the cell and you never get sick. Antibodies can be made in response to natural infection or immunization.
So far, at least 15.8 million Americans have had the chance to make antibodies, or about 4.8% of the US population. That’s probably a low-end estimate, since we know that an estimated 40% of infected individuals never have symptoms and likely never seek a test. Disease underreporting is not uncommon in public health and that’s certainly true for COVID-19 too. But even if we assume that an additional 40% of what we have identified has been infected, then we’re still talking about only 6.7% of the US population. We’re still a long way off from herd immunity. The folks who have been infected already have presumably generated antibodies the old fashioned way. However, we don’t have data yet on how long that immunity lasts. In any case, that potential immunity that has already been achieved was not without cost. More than 290,000 Americans weren’t lucky enough to survive infection and countless others may have antibodies, but at the cost of cognitive dysfunction, permanent lung damage, strokes, etc. This is the advantage that a vaccine offers – the opportunity to gain immunity without suffering the ravages of this infection. We’ll talk about how the vaccine works next time. But when we expect that it will take 70% or more of our population to be immune in order to achieve herd immunity, then the vaccine is the way to accomplish that without hundreds of thousands of additional deaths. It is the path back to life that feels more normal.
On average, it takes about 7-10 days to start producing antibodies against an infection and you reach maximum production about 3 weeks after exposure (this is called the primary response). The next time you see the invader, your antibody response is both faster and bigger in order to protect you and this bigger and faster thing happens with each subsequent exposure (this is why booster shots work). This bigger and faster thing is called your secondary response. We don’t yet know how long natural immunity (through infection) lasts or how long immunity provided by the vaccine will last. It’s possible that boosters may be needed in the future.
Vaccines can make an enormous difference on suffering and death from a disease. The graph below shows how significant of a burden that pertussis (also known as Whooping Cough) used to be in the United States, by measuring cases reported each year. The first pertussis vaccine (called DTP, providing protection against a combination of diphtheria, tetanus and pertussis) was first introduced in the late 1940s. Prior to vaccination, the disease caused more than 250,000 cases in one year (around 1935). When DTP was introduced it took about 20 years but cases gradually declined to virtually nothing. It’s a reminder to us that the COVID-19 vaccines aren’t going to solve our problems overnight. But we can eventually get to a much better place, with more of us making it to a time when COVID-19 no longer impacts day to day live.
https://www.cdc.gov/mmwr/volumes/67/rr/rr6702a1.htm
There’s a lot more to immunology than just antibodies, and even producing antibodies requires the coordination of lots of different cells and processes. But antibodies are the superheroes of your body’s fight against COVID-19 so I wanted to explain a bit about how they work. Next time we’ll talk about what’s unique about the RNA vaccines that are leading the development pipeline for COVID-19.
Testing
Yesterday, I received the results of an open records request with the Georgia Department of Public Health (many thanks to their office of General Counsel) regarding the total number of tests reported to the state through their Electronic Laboratory Reporting system for PCR, antigen, antibody tests, etc, each week. As of December 5th, there have been 4,432,226 PCR tests, 403,670 antigen tests, 336,342 antibody tests, and 95,086 tests designated as “unknown.” Below, you can see a graph showing how the total number of tests reported varied over time.
Antigen tests first started being reported in Georgia during the week starting 28Jun and they have made up a bigger and bigger share of the total tests performed over time. In November, they made up 21% of all tests reported to DPH.
I don’t think we can nor should we try to calculate percent positivity for the antigen cases. Each antigen case represents just one person, regardless how many times they tested positive. But we don’t have a way to account for how many of those cases tested positive more than once. We also don’t know how many of those cases were identified through ELR or through more antiquated methods of communication. Finally, there are cases who may have tested positive by both PCR and antigen, in which case they are moved to the PCR column and removed from the antigen total. So, it’s a bit of a mess to try to estimate percent positivity, especially given the lack of context with the data. DPH is the organization best able to make that calculation with a full awareness of their data sources and limitations. But I think we can see how complicated that might be for them to actually do…which is probably why we haven’t seen that calculation so far. For now, I think the thing we take away from this latest record release is the growing relevance of the antigen test.
Today there were 35,358 new PCR test results reported by DPH and 11.9% were positive. We’ve already surpassed last week’s total test output, and I’ll be back on Sunday to summarize testing along with everything else in the Week in Review.
Cases
We set a new record for cases reported in a single day yesterday, with a net increase of 7623. Today was calmer but still a really big day - there was a net increase of 6191 newly reported cases with 4729 identified by PCR and 1462 identified by antigen test. This brings the updated statewide total to 531,593. Our state case rate per 100,000 is now 41.8% higher than at the peak of the summer surge if PCR and antigen cases are included.
Our case growth is the predicted outcome of Thanksgiving gatherings. However, the people who got sick at Thanksgiving probably didn’t feel sick right away and continued to go out in the community, exposing others. So this isn’t a situation of one big burst of infection that is subsequently over. It is going to mushroom out. Remember that each person is going to go on to infect about 2 people, with some spreading more or less. The more interactions an infected person has while they’re contagious, the more people might be infected in the end. The end result is that while yesterday was noteworthy for the record-setting case number, I expect that record will be short-lived. I expect we will be breaking records several times over the next week or two, and possibly beyond. The Governor has indicated that he expects this problem to be solved by members of the public who take it upon themselves to do the right thing. So we will continue to have these big case days until more people start doing the right thing or the Governor changes his mind. I commented to a reporter yesterday that it is as though Georgia is on fire right now, but too many people are just standing around watching it burn. At what point is the fire intense enough that people start trying to put it out?
Meanwhile, we get the School Aged Surveillance Data reports from the state on Fridays. The graph below is the first of two I plan to show you (the other is in hospitalizations). These are the number of cases (PCR + Antigen) among K-12-aged children over time. Note that these are not necessarily associated with a K-12 setting, just the right age groups for K-12. The number of cases among school-aged kids has skyrocketed, dwarfing the peak we saw in the summer. The case growth is being observed for all three age ranges (elementary, middle school and high school). Given the family nature of Thanksgiving gatherings, it’s possible these kids got sick through those celebrations. But I’m sure other community exposures play a role too.
Using the criteria of the Harvard Global Health Institute tool, there are 122 Georgia counties now in the red zone (or 77% of the state’s counties) if PCR and antigen cases are considered. The images below show the Harvard map if only PCR cases are considered (this is what GA provides to external organizations) and the map on the right shows the map when antigen cases are included. The live image of the PCR + antigen map can be accessed by clicking on the map below. There you can click or hover over your county of interest to see the actual number.
Big takeaways here are that the northern half of the state (including the entire Atlanta metro) are in a tough spot. But it’s not just limited to that region. We have red counties impacting multiple regions of the state.
Hospitalizations
Today 304 Georgians were admitted to the hospital for COVID-19. We haven’t seen a number this high since 12Aug. Forty-two COVID-19 patients were admitted to the ICU. There are 2834 patients currently in the hospital for COVID-19. We are only 11% less than the number of patients hospitalized at the height of the summer surge.
Meanwhile, 85.6% of the ICUs across the state are occupied and seven hospital regions (of 14) are using >90% of their ICU beds: B (95%), C (91%), E (97%), G (93%), H (93%), L (93%), and N (95%). Thirty one percent of adult ventilators are in use across the state - this is not a scary number, it’s pretty typical of where we were prior to the summer surge).
This next graph comes from the School Aged Surveillance Data report, showing us how ER visits for COVID-19 are trending for school-aged populations. The COVID-19 ER visits have risen dramatically across all age groups, with the sharpest increases observed for those elementary (5-10) and high school aged (14-17). It’s one thing to see cases increase among children. Many will brush that off knowing that kids are resilient and so far spared most of the worst effects of COVID-19. But it’s another thing entirely to see that more serious cases of COVID-19, requiring an ER visit, are increasing among these populations.
Deaths
Today was a noteworthy day for deaths, in that if you combine confirmed and probable deaths due to COVID-19 then we surpassed 10,000 (10,031 to be exact). I tend not to include the probable deaths in my analyses because the definition is really broad and I think these individuals may be best accounted for in excess deaths. It could include those who were tested by antigen test or those whose death certificates indicate COVID-19 but with no accompanying laboratory evidence - their disease and demise were consistent with COVID-19. This is an ongoing effort, as DPH goes back and finds death records, even from way back at the beginning of the pandemic.
If we only consider confirmed deaths, then there were 52 newly reported today. Nearly half of them came from nonrural counties outside of the Atlanta metro. The statewide death rate is ticking upward this week, but it’s too soon to know if this is part of a larger trend. What we do see is that nonrural and rural counties have death rates that are higher than the state average. That’s how the other death surges played out also, but again, it’s too soon to know if this week is the start of a surge.
So I know that most of my readers are already the sort who are trying to put out this fire. Thank you so much for all that you are doing. Your communities and neighbors need you to keep doing it.
References
https://www.cdc.gov/mmwr/volumes/67/rr/rr6702a1.htm
https://dph.georgia.gov/covid-19-daily-status-report
https://covid-gagio.hub.arcgis.com/
https://epidemiologyschoolreport.s3.amazonaws.com/SchoolAgeSurveillance1130.html
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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.