COVID-19 Forecast for El Paso County – July 6

Plus, our resident microbiologist on swine flu and testing upon entry

Good morning, and happy Monday. On this pre-pandemic date last year, Colorado Springs locals were browsing at the monthly “Cars and Coffee” show at the First and Main Town Center. (In our coronavirus world, shows are currently “on hold” for the year.)

Today, Phoebe Lostroh returns to give her weekly COVID-19 forecast for El Paso County. She also explains federal guidelines for testing and drops some knowledge about reports of a new swine flu with “pandemic potential.” Lostroh is a professor of molecular biology at Colorado College on scholarly leave who is serving as the program director in Genetic Mechanisms, Molecular and Cellular Biosciences at the National Science Foundation.

➡️ICYMI: On Friday, we recapped the new student and athletics Town Halls and looked at what other liberal arts colleges are planning for the fall. 

Phoebe’s Forecasts

NOTES: These forecasts represent her own opinion and not necessarily those of the National Science Foundation or Colorado College. She used the public El Paso County dashboard for all data.

✍🏻CORRECTION: An earlier edition of this issue misstated the number of deaths from COVID-19 in El Paso County. It has been updated to reflect the correct number.

⚖️ How her predictions last week shaped up: July 4 is the last day of Morbidity and Mortality Weekly Report week 27 in the national public health calendar. It is the 17th week since the first case was detected in El Paso County, and 113 El Paso County residents have died of COVID-19 since March 13. Last week, using the most recent trend, I forecasted 2,544 cumulative reported cases as of July 2 and in reality, there were 2,550 reported cases

We have likely entered a period of heightened danger in Colorado Springs. Based on public data, I recommend El Paso County return to stay-at-home conditions and stay there for the next two weeks. Signs we have entered a dangerous period include:

  1. The 14-day rolling incidence of reported COVID-19 cases in El Paso County was at its highest recorded level (63%) July 2. This level is well within the range the Colorado Department of Public Health and Environment regards as “high viral spread,” namely 50-100 cases per 100,000 people. 

  1. The percent positivity in testing has risen consistently since June 16 and has reached 9% as of Friday, which indicates a steep rise in cases is likely coming. 

  1. The exponential increase in reported cases has become almost as high as that for my “worst case scenario” predictions, which use data points from early in the local epidemic.

  1. Nearby states, including some in the Rocky Mountain West, are experiencing dramatic increases in cases.

  1. There is an outbreak among first-year students at the U.S. Air Force Academy.

Colorado granted El Paso County a “multi-sector variance,” so in addition to opening restaurants, businesses such as gyms and theaters can now resume operation at partial occupancy. Between June 26 and July 2, 263 new cases have been reported, and 124 new cases were reported in the seven days before the stay-at-home order. The number of active cases in the community is thus more than twice as high as it was before the stay-at-home order, and the exponential curve is nearly as steep. 

Predicted cumulative reported cases in El Paso County

🗝️ Key points: If these forecasts hold, we will exceed the reported cases in a 14-day-rolling window needed to remain under the “high viral spread” threshold during the week of July 18. This level ought to trigger the state to revoke the restaurant variance, but that decision could be modified by having a low percent positivity testing rate and high amounts of testing. 

How to use exponential curve-fitting to forecast the epidemic

🗝️ Key points: Although microbial behavior is predictable, human behavior is much less so. I have simplified my predictions by the following assumptions: People will keep behaving the way they have been most recently, unless something significant changes; and the virus will spread exponentially because most of the population is susceptible. 

Prediction for reported cases in El Paso County for the next 6 weeks

🗝️ Key points: As you can see, the exponential trend for the recent cases is very close to the worst-case scenario.

Prediction for 14-day rolling incidence in El Paso County for the next 4 weeks

🗝️ Key points: El Paso County was granted a restaurant variance and a multi-sector variance on May 24 and June 29, respectively. Those variances are contingent upon the 14-day-rolling incidence remaining below a threshold of 100 cases per 100,000 people. The threshold to revoke the restaurant and other variances is high, so by the time we reach it, even a stay-at-home order will take a long time to have an effect.

Nasal Swab Testing for SARS-CoV-2 and Percent Positivity in El Paso County, 7-day rolling averages

🗝️ Key points: Percent positivity is one of the metrics the state uses in order for businesses to remain open. Rolling percent positivity has been rising steadily since June 16, faster than any increase in testing. The county dramatically increased the number of total tests after June 10, so that increase in tests drove down the percent positivity. The 7-day-rolling percent positivity is 2.5 times as high now as it was on June 16, whereas the total number of tests administered is only 1.5 times higher. Thus, although the percent positivity is not itself much higher than 5% as a rolling 7-day calculation, the trend upward is concerning.  

Tests results on the day they were reported and the percentage of them that were positive

🗝️ Key points: The actual percent positivity for June 26 to July 3 isn’t calculated as a rolling average but instead calculated for each day. Note: sometimes people get more than one test.

Q-and-A with Lostroh: Our resident microbiologist on entry-level testing and three-day quarantines

This interview has been edited for length and clarity.

CC COVID-19 Reporting Project: As a microbiologist, what’s your reaction to the CDC guidance and Colorado College’s plans not to test everyone when they return to campus?

Lostroh: The Centers for Disease Control and Prevention agrees that it’s not a good idea to test everyone. That’s based on a research study done by some people out of Johns Hopkins University, which was a meta-analysis where they analyzed data that other people published in a variety of other publications. Those data showed that 100% of the time, five days before somebody developed symptoms, they got a negative test, even though they weren’t actually negative. A contact of mine at MIT said a lot of those data that they reviewed were from older nasopharyngeal (NP) tests that are different from the ones we’re running now. Therefore, the idea that you can’t test asymptomatic cases with NP swabs is very likely wrong. And so they don’t believe this study. They think it’s incorrect or misleading because of pooling data with older tests with that from newer tests.

CCRP: Now that we have some more information about CC’s plans for the fall, what do you think about them? 

Lostroh: When somebody is burglarized we get a safety announcement from Campus Safety, and to me, positive COVID-19 cases are also campus safety issues. I noticed that in the town hall I attended, they didn’t clarify whether positive tests among employees and students would be reported to the entire campus. I think we need to have some guidelines for if somebody tests positive in a building. Will everybody get tested? Are they only going to test the people who get contact traced? And I really feel like that should be transparently available to the entire campus as a safety measure. 

I’m worried about bringing people to campus from all over the country. Why are we bringing people from high prevalence areas to this low prevalence area? The three-day quarantine for people coming from “hot spots” confuses me, and I don’t see where that comes from in the scientific literature at all. Maybe quarantine for three days and then get a test because if you were asymptomatic for those three days the test might be more likely to be positive on the third day, but I don’t understand the basis of that decision. 

CCRP: Should we be concerned about recent reports of a Swine Flu with “pandemic potential?”

Lostroh: I have all good news about the swine flu. There is an incredible international network of microbiologists who agree to try to watch out for influenza pandemic potential. The swine virus that has been discovered is a possible future human influenza. Right now it’s not in human beings. They discover possible swine and avian influenza that have this potential every year because of this incredible international collaboration, but only rarely have those viruses actually gotten into human populations. So, the swine flu story, as alarming as the story sounds, actually has some really good stuff underneath it, about international collaboration and how the groundwork of having good science in place before a pandemic happens has actually now helped us with this pandemic. If that groundwork wasn’t in place, we wouldn’t know anything about how the coronavirus is evolving on a global scale.

About the CC COVID-19 Reporting Project

The CC COVID-19 Reporting Project is a student-faculty collaboration by Colorado College student journalists Miriam Brown and Arielle Gordon, Journalism Institute Director Steven Hayward, Visiting Assistant Professor of Journalism Corey Hutchins, and Assistant Professor of English Najnin Islam. Work by Phoebe Lostroh, Associate Professor of Molecular Biology at CC and National Science Foundation Program Director in Genetic Mechanisms, Molecular and Cellular Biosciences, will appear from time to time, as will infographics by Colorado College students Rana Abdu, Aleesa Chua, Sara Dixon, Jia Mei, and Lindsey Smith.

The project seeks to provide frequent updates about CC and other higher education institutions during the pandemic by providing original reporting, analysis, interviews with campus leaders, and context about what state and national headlines mean for the CC community. 

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