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Today we’re going to go over the two main types of testing, and why we can’t just jump to serology testing.

How does increased testing affect New Cases?

Let’s start with a point we made yesterday:

There are two primary reasons that we test in public health:

  1. To find out if a specific individual is sick. In the case of COVID-19 this would be to ask them — and anybody that they have been in contact with — to self-isolate to prevent further spread
  2. To find out how widespread a disease is in a community or geography (city, county, state, prison, hospital, nursing home, etc.)

There are two primary types of tests for COVID-19, at this point, essentially, one for each.

Test Types

This first time of testing makes up all of the confirmed cases that we know about in the US and is done exclusively (right now, as far as we know) by RT-PCR. This is the test where they put a swab far enough up your nose to tickle your brain, then use chemicals (reagents) to transfer the sample to a test tube or similar. After that, chemicals are added to convert virus’ RNA to DNA. Finally, the DNA is “amplified,” — increased — until there is enough of it to identify.

The RT-PCR test typically has a high degree of accuracy of identifying a sample where the virus really does exist, and successfully not identifying samples where the virus does not exist.

The RT-PCR test mostly tells you if you are sick right now. The RT-PCR testing is limited right now because the world doesn’t have enough of all of the supplies required — swabs, PPE, reagents, etc. — to test as many people as we’d like.

The RT-PCR test is also critical to contact tracing: finding everyone that has been exposed to someone currently infectious. If I expose you and the health department tests me positive and then calls you right away to let you know that you have been exposed you can stay home and stop the spread. Other tests — to date — don’t offer this kind of immediate payoff.

The type of test you may have heard about in the news — the antibody test or serology test — is a blood test that looks for antibodies, proteins that your immune system creates to fight off invading viruses and bacteria. The antibodies stick around after an infection, sometimes for a little while sometimes for the rest of your life.

The serology tests that we’ve seen so far are typically in the 95-98% accuracy range. To use an example from Dr. Osterholm, if the test is 95% accurate, and 5% of a population is infected, then testing 100,000 people will result in 5,000 who either were told that they were sick but weren’t, or were told that they were not sick and are/were

At this point we haven’t seen any serology tests accurate enough to use for a specific person. However, those levels of accuracy are good to enough for a population. For instance, if you wanted to know what percentage of Knoxvillians had been exposed to COVID-19 a serology test would work great, but it wouldn’t be very reliable on a per-person basis. [1]

The PCR tests are accurate but we don’t have enough supplies to test everyone. Also, they are snapshot of who is infected now. The serology tests, by contrast, can be done more widely (we have enough supplies) and tell us, broadly, who has been infected, ever. (Ever = up to this point, we don’t know how long COVID-19 antibodies will stick around as the virus itself has only been around for a few months).

There are other tests being thrown around, saliva based tests, antigen tests, but we haven’t seen any that are far enough along to report on, much less be useful in the real world. Eventually, you can expect to see a combination of PCR and serological tests being used to help inform the policy response and understand where we are at with COVID-19.

Bonus points: The best epidemiological models for COVID-19, to date, appear to be based on SEIR: Susceptible (people), Exposed (people), Infectious (people) and Recovered (people, which includes those who died). PCR can tell you about Infected, serological can tell you about Susceptible.

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Thanks to those that have shared kind words or liked these posts. We’re doing out best to put out data-driven analysis, each one of these takes about 2 hours. It’s helpful to know that they are being read.

If you want copies of the Excel sheet and PowerBI Reports we use to put these together email us, info@jmaddington.com. Right now, our PowerBI combines data from JHU, NYT, COVID Tracking Project, IMHE and the TN Department of Health. Most sets are updated daily.

[1] We are simplifying. This article goes over the accuracy in more detail and proper terminology. There are serological tests claiming higher accuracy but we haven’t seen any that have passed through peer review at those higher levels of accuracy.

Today will be a short post. We’ll hit the main numbers and then hit primary headlines for the day.

Before we get to get any of that, the National Academy of Sciences is holding their 157th Annual Meeting online this year. You can register for Saturday and Sunday sessions for free.

The 2:00-3:30 EDT session is on COVID-19 and includes Dr. Faucci (schedule permitting), Dr. Jeremy Farr and the Director-General of the Chinese CDC.

Register here.

If you’re reading our updates we literally can’t imagine why you wouldn’t want to hear from these guys.

Numbers

The US as a whole is just flat. The US positivity rate continues to drop, a sign that, maybe, national testing capacity is going to where it needs to be.

Click on any image to see it larger.

US New Cases by Day

US COVID-19 Cases and 7 Day Rolling Average, April 23rd, 2020 by JM Addington Technology Solutions
Source: Data from The COVID Tracking Project; Chart by JM Addington

US COVID-19 Positivity Rate by Day

US COVID-19 7-Day Average Positivity Rate, April 23rd, 2020 by JM Addington Technology Solutions
Source: Data from The COVID Tracking Project; Chart by JM Addington

Tennesse spikes in cases for a second day. Dr. Piercy indicated that this was expected and a result of testing a correctional facility. The positivity rate didn’t go up, which is a good thing. Also, Dr. Piercey stated that the weekend testing positivity rate was less than 2%. So, that’s not anywhere near a controlled study or randomized sample size, but the low rate is most likely a good indicator Tennessee as we move towards opening up.

TN New Cases

TN COVID-19 Cases and 7 Day Rolling Average, April 23rd, 2020 by JM Addington Technology Solutions
Source: Data from The COVID Tracking Project; Chart by JM Addington

TN Positivity Rate (about 7%)

TN COVID-19 Positivity Rate, April 21st, 2020 by JM Addington Technology Solutions`
Source: Data from The COVID Tracking Project; Chart by JM Addington

By the way, if you want to see the same graphs for your state click here, we pull nearly all of our own visuals from this report. Typically updated at the same time the evening’s post goes up.

Here are GA new cases.

Also, you can do it on your phone but it is much easier to navigate on a bigger screen.

The Knoxville area continues to see a slow growth in cases. New cases in several of the surrounding counties.

Knox County total cases by day

Source: Knox County Department of Health

Nine county are cases by day.

April 23rd, 2020 COVID-19 cases for Anderson County, Blount County, Grainger County, Jefferson County, Knox County, Loudon County, Roane County, Scott County, Sevier County and Union County
Source: Data from the New York Times; Chart by JM Addington

National/International News

The biggest piece of news today is that a New York serological study (antibodies) estimates that nearly 14% of residents have had COVID-19. Real epidemiologists on Twitter believe that this is in line with their expectations.

The CDC director publically said that 19-20 states may be ready to re-open by May 1st. He didn’t name Tenessee specifically.

“There are a number of states – 19, 20 states – that really have had limited impact from it. So I think we will see some states that are, the governors feel that they’re ready, we’re poised to assist them with that reopening,

Dr. Robert Redfield

The House passed the stimulus package the Senate has already passed which includes over $320bn for the Paycheck Protection Program. We assume that it is headed for reconciliation before hitting the president’s desk.

Get your paperwork in order today and be working with a bank that wants to help you.

We spent part of the day helping another small business get their application done. We’d be glad to help you too, however we can.

Bloomberg is reporting that meat is headed for a shortage. Pork output is down 25% and beef down 10%. We wrote about this yesterday and Monday.

Pork could be a long shortage because farmers will have to decide soon if they need to kill their current piglets, or try to raise them when there aren’t plants to slaughter and package them in the future. Farmers are more likely to keep cows, but that doesn’t address the shortages in bee production, or the increasing amount of beef purchases as pork output slides.

“What people don’t realize is in the coming months, that’s going to be one the biggest issues out there is getting the meats and provisions, for not only restaurants, I hate to say it, but grocery stores as well,” said Peter Cancro, chief executive officer of Jersey Mike’s Franchise Systems Inc

Bloomberg

Poultry can ramp up the fastest, however, the plants all share a common problem of simply being set up for physical efficiency: physical distance was never the goal when designing the slaughterhouses, so COVID-19 can spread easily in these settings.

Meat prices are already low and feeding animals that can’t sell along with competition from meat imports will continue to hammer farmers who are already hurting. Finally, if North Carolina has the same problems with its pork plants then the meat issues supply chain disruption will get worse.

Two of the top ten pork slaughterhouses are in NC.

NC New COVID-19 Cases by Day

NC COVID-19 Cases and 7 Day Rolling Average, April 23rd, 2020 by JM Addington Technology Solutions
Source: Data from The COVID Tracking Project; Chart by JM Addington

Knox County News

Out of today’s health briefing this exchange was the most interesting:

Dr. Buchanan on opening up: “I think there are a couple of things going on that make us feel comfortable with taking this step. One is that we never had a big peak. We had a slow increase in the number of cases and that’s pretty much stayed the same. We haven’t had any big shift in that.”

“So we believe that it’s safe to re-open, we’ll continue to see that slow increase, hopefully not have a peak. If we do we’ll have to take measures to adjust the re-open.”

Also, to be honest, closing down businesses was never a long-term solution to keeping the COVID-19 numbers down. Its really important for us to do contact tracing, getting folks who are at risk out of the population so we can stop that transmission. When you look at other countries where they’ve had to do these things related to HIV or Ebola, getting those people that might make other people sick out of the general population is really how you stop that chain of transmission. That’s what my team and our community is working to do.”

Dr. Osterholm’s weekly podcast came out yesterday and made a similar case (broadly, not specific to Tennessee).

“We have to understand: we’re going to open up. We cannot exist in a closed down mode for how many many months before we get a vaccine that could, in a sense, rescue us from this virus.”

Dr. Osterholm, Osterholm Update: COVID-19 Episode 5: Living with the Virus April 22, 2020

“We’re only maybe in the second inning of this ballgame.” He views this as a gradient where we open some, close some, open some, close some.

“We may not get it right the first time. We may not get it right the second time. But I fear we’re going to have multiple opportunties to get it right.

Dr. Osterholm

Likewise, he points out that there isn’t (or shouldn’t be) Team Open and Team Stay Closed. We’re all doing our best to get through this together, and we will.

Osterholm Update: COVID-19 is available on Apple PodcastsSpotify and Google Play.

“It’s us against the virus.”

Dr. Osterholm

“At the same time we have to face the reality of what this virus can do and how it does it. It is not going to go away… therefore, what we have to figure out is how we let it exist with us so that we try to suppress it so that we hope to get to a vaccine at some point, but at the same time release people into the public.”

Dr. Osterholm

Get In Touch

Need help thinking this through? Access to more data? Help getting your technology in order to handle what’s here and what’s coming? Contact us today.

Other

Thanks to those that have shared kind words or liked these posts. We’re doing out best to put out data-driven analysis, each one of these takes about 2 hours. It’s helpful to know that they are being read.

If you want copies of the Excel sheet and PowerBI Reports we use to put these together email us, info@jmaddington.com. Right now, our PowerBI combines data from JHU, NYT, COVID Tracking Project, IMHE and the TN Department of Health. Most sets are updated daily.