C+1

It is one day since the Texas Governor allowed businesses to reopen at 25% capacity. It is one day since the national stay-at-home recommendation was ended.

Families gather in athletic fields, in tight groups. People don’t move off the sidewalk when I pass. I have to swing way out into the grass, dodging dog feces landmines left by irresponsible pet owners. Traffic is heavier on the roads. Everything seems busier.

Every passing person is the battlefield and the bomb, all rolled into one. I keep my distance.

(PINK SOLID) Number of new cases averaged over previous 7 days. (PURPLE DASHED) Number of new cases on that day. (BLACK NUMBERS) Doubling rate of cases, determined by exponential fit to previous 7 days of data. Arrows indicate key policy decisions affecting Texas. Data is from the Texas Department of Health.

Collin County, TX sees it’s largest one-day increase in COVID-19 cases – 42 reported in one day. This beat the previous record, 37 new cases, reported 24 days ago. This isn’t even yet due to the impact of the loosening of social and policy restrictions on the growth and spread of the virus. This is either the work of increases testing detecting the infections that were already there, hiding in plain sight; or, this is the work of increasing infection from fatigue and complacency that accumulated in the past 15 days.

Or both.

I keep my distance from people when I am out running. Every one of them is the vector and the victim.

Yesterday, C-Day, was the day the U.S. effectively succumbed to a national policy of viral appeasement, turning a blind eye to the aggressor and ceding it the human territory it so desperately craves. With no national policy or strategy for testing, tracking, and quarantine, every American has been left behind on the battlefield, abandoned by the generals (who, by all reported, have hoarded ample testing for themselves [1]). We have been left in the trenches, in the rain, with only a standard-issue rifle, some trifling ammunition, a command to do our patriotic duty and die for the economy, and a lump of nameless fear in our throats.

Today is C+1.

[1] https://www.washingtonpost.com/politics/trump-white-house-events-coronavirus-testing/2020/05/01/21a9b5bc-8bbe-11ea-ac8a-fe9b8088e101_story.html

Racing toward 25%

Friday (tomorrow) is the day that Texas’s Governor allows all businesses to reopen, but only if they cap their in-house customers at 25% of capacity for their facility. So where is my county, Collin County, right now?

Anticipating this “momentous” day of continuing to re-open businesses in Texas, Collin County is stalled in its fight against the spread of SARS-CoV-2.

Data for Collin County, TX. (PINK SOLID) The number of new cases per day, averaged over the previous 7 days. (PURPLE DASHED) The number of new cases reported on a given day. (BLUE ARROWS) Key events in Texas regarding policy and COVID-19. (BLACK NUMBERS) The doubling rate of new cases, computed by fitting an exponential growth function to the prior 7 days of data.

Early on in the pandemic, Collin County achieved a 2-day doubling time for new cases. This is nothing to be proud of; the shorter the doubling rate, the faster the deadly disease spreads. Those early numbers and their rise is due to two effects: the spread of the virus, and the ramp-up of disease testing capability (when you look, you always find the cases that were already there in plain sight).

We peaked in new reported COVID-19 cases per day about 35 days after the first reported case in Collin County. It was around that time that the shelter-in-place orders put into effect between days 19-26 after first-reported-infection kicked in. We came down fast. Rather than doubling every 9 days (our rate when we hit the peak number of new cases per day) we fell to a low of about 10 new cases per day and a doubling rate of 35 days.

That was the best we did. Coincidence or not, about 15 days after the CDC recommended everyone wear a face covering (note that they recommended a covering, independent of its ability to stop infection), we bounced. New infections each day began to climb again, and our new-case doubling rate worsened to every 20 days. We’ve wobbled there now for days.

The Governor allowed all businesses to reopen for delivery or pickup about 6 days ago. Tomorrow, Texas businesses can accept people into their establishment so long as not more than 25% of capacity is utilized and social distancing is observed.

But in Collin County, TX, we are not seeing declining infection rates. We are hovering. And opening up more, now, will only lead to more spread of the virus.

Notes

The plot is made using data from the Texas Department of Health. Collin County reported cases are updated daily by about noon, US Central Time. The actual figure is made using Python, specifically:

  • MatPlotLib: graphical representation of data
  • Pandas: data storage and analysis, including averaging over sequential days
  • SciPy: curve fitting an exponential growth function to ranges of data
  • Seaborn: high-quality time-series plotting

The Virus Strikes Back

(updated 4/26/2020 with demographic and testing data)

Maybe it’s because Texas, as a state, sent signals that it was “okay” to behave like we used to. Maybe it’s because the President lied to the nation over, and over, and over again about the reality of COVID-19. Maybe it’s because people have become complacent. Maybe it’s because testing is improving in our county. Maybe it’s because that kid who helped Jodi with her groceries today, who decried shutting down What-a-Burger just to save human lives, has been going out for fast food with his friend more than he let on.

Any way you split it, Collin County, TX is losing ground to the SARS-CoV-2 virus. We are home to a population of 1 million people. As of April 13, the county had only performed 3464 tests of people for SARS-CoV-2. As of today, we have 639 known cases of COVID-19. The number of cases reported each day is climbing again, doubling about every 22 days; that’s a decrease in the doubling rate from our recent best, which was 35 days (over one month). Our worst doubling rate was before shelter-in-place restrictions were put in place, with a case doubling rate of every 2 days.

Texas public health data says that new cases of COVID-19 are on the rise, doubling at a rate not seen in about a week, reversing recent positive trends. Something has changed, and not for the common good. Rolling average of new cases per day, over 7 days. is in pink; new cases each day is in dashed purple. Key events in Texas health policy are indicated with arrows. It’s honestly too soon to know how the re-opening of the state is actually affecting the case load, but the coincidences are stunning.

Update: if scientists were part of our county’s process of planning for the economic reopening, they would be able to inject data from other places that have relaxed social distancing and re-opened. We have much to learn from cities and regions that have already tried this experiment… and it hasn’t gone well.

(Tom Inglesby is the director of the Johns Hopkins University Center for Health Security. He is a medical doctor who completed his internal medicine and infectious diseases training at Johns Hopkins University School of Medicine, where he also served as Assistant Chief of Service in 1996-97. Dr. Inglesby received his MD from Columbia University College of Physicians and Surgeons and his BA from Georgetown University.)

Coda

The judge who oversees Collin County proclaimed on April 24 that his executive order from March 20, declaring various closures, shall expire on April 30. This he proclaimed even as the progress the county had made in controlling the virus’s spread was reversing. Here is what will end on April 30 as a result of this new order ending the March 20th order:

Effective as of 11:59 PM on Friday, March 20, 2020, and continuing for as long as the Declaration of Local Disaster for Public Health Emergency remains in force;

  • All Collin County government offices shall be closed for unscheduled in-person services.
  • All Collin County government offices shall remain open for scheduled in-person appointments, as well as by phone, by mail, and online. Citizens requiring in-person services may schedule an appointment by contacting the appropriate department.
  • The Collin County Commissioners Court shall continue to meet as scheduled. Commissioners Court meetings will not be open to on-site visitors, but all meetings will continue to be broadcast live on the county website, and provision will be made for the public to participate electronically in every meeting.

The spice must flow

As I wrote several days ago, Zoom has become highly unstable on my desktop computer. I’ve tried everything, including switching from the KDE desktop environment to the XFWM one; switching off compositing; using all different versions of the NVIDIA drivers; swapping other NVIDIA cards into the system; different kinds of LINUX kernels. Nothing helps. So I’ve employed my work laptop as the backup system. Actually, now it has become my primary teaching system, because I cannot afford stupid graphics system/software crashes in the middle of class. The Yeti and the good camera attach to a USB-C hub on the work laptop; the Snowball and the worse camera are now relegated to the desktop machine.

The spice must flow.