COVID-19 Forecast for El Paso County — Sept. 28
Plus, our resident microbiologist on health equity during the pandemic
Good morning, and happy Monday. On this pre-pandemic date last year, runners were lining up at the starting line of the Colorado Springs marathon. (This year’s event was virtual.)
Today, Phoebe Lostroh returns to give her weekly COVID-19 forecast for El Paso County and to explain news about interferon response in COVID-19 patients. 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 Wednesday, we talked to Colorado College co-presidents Mike Edmonds and Robert Moore about what it’s been like since they took over on July 1 and their plans for the rest of the academic year. We also spoke to CC vice president for information technology Brian Young about some of CC’s new COVID-19 testing strategies.
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. Lostroh prepared these forecasts on Sept. 26.
⚖️ How her predictions last week shaped up: Sept. 26 is the last day of Morbidity and Mortality Weekly Report week 39 in the national public health calendar. It is the 29th week since the first case was detected in El Paso County. Since March 13, 174 El Paso County residents have died of COVID-19. Last week, Lostroh predicted between 6,993 and 7,090 cumulative cases reported as of Sept. 24, and in actuality, there were 6,874.
It usually takes three or four weeks for changes in behavior to affect the number of reported COVID-19 cases. Labor Day weekend, which included a cold snap immediately afterward, was less than three weeks ago, so the holiday is unlikely to have any impact on reported cases. Four weeks ago, the Democratic Governor Jared Polis changed the last call for serving alcohol at bars from 10 p.m. to 11 p.m., and some K-12 schools began to meet in person. Those changes coincide with last week’s substantial reversal in the previous declining trend in El Paso County’s reported cases, Lostroh says.
Lostroh’s Method: Lostroh fits curves to the most recent seven, 14, or 21 days of total reported case data or to recent “worst case” or “best case” stretches, and then she calculates how those curves would project into the weeks ahead. She chooses the 7-day, 14-day, or 21-day data set based on whether the trend in reported cases seems to be in the midst of changing (seven days) or sustained over two or three weeks. She uses the 21-day data set when the trend is longer than three weeks. (This method is most accurate when human behavior is stable.)
Any exponential curve fit assumes that the reproduction number for COVID-19 is greater than one, while a linear fit assumes that the reproduction number is one. The reproduction number is defined as the new cases that arise from a single infected person. In the table below, she based the “worst case” projection on an exponential curve-fit to the 21 days of the total reported cases just prior to the statewide mask mandate. She fits the “exponential recent” and “linear recent” curves to the most recent 14 days of data, which is appropriate because the rate of newly-reported cases abruptly stopped declining two weeks ago. She didn’t report a best-case scenario this week because the trend in reported cases is increasing; the “best case” is synonymous with the linear curve fit.
Predicted cumulative reported cases in El Paso County
🗝️ Key points: Between Sept. 26 and Oct. 1, El Paso County will probably see a total number of cases somewhere between the linear curve fit and the exponential curve-fit because the 14-day rolling percent positivity for nose swab tests has been below 5% for the month and below 3% for the most recent two weeks. Lostroh predicts between 7,153 and 7,166 total reported cases as of Oct 1.
After next week, Lostroh expects cases to increase more rapidly for four reasons:
The Labor Day holiday. If people gathered on Labor Day while letting some physical distancing measures lapse, Lostroh expects reported cases to increase at a faster rate starting next week.
Later last call for alcohol at local bars. El Paso County is currently in “Safer Level 1,” meaning that starting Sept. 21, bars in El Paso County could serve alcohol until midnight. El Paso County won’t know whether relaxing the restriction to midnight will have an effect for another three or four weeks.
Expanded in-person instruction for K-12.
Infections among students at the University of Colorado at Boulder. Because the entire Front Range is connected, a high number of cases in Boulder will most likely affect other cities along the Front Range, starting with Fort Collins and Denver first, but ultimately reaching Colorado Springs.
K-12 school guidance for El Paso County
🗝️ Key points: The Harvard University Global Health Institute suggested the thresholds Lostroh uses in this forecast. El Paso County has been in the yellow zone for almost six weeks. Lostroh expects El Paso County to stay in the yellow zone for two more weeks, meaning that grades K-8 are safe to meet in person if pandemic-resilient buildings, classrooms, and practices are in place. If El Paso County crosses into the orange zone, only grades K-5 should meet in person.
Q-and-A with Lostroh: Our resident microbiologist on interferon
This interview has been edited for length and clarity.
CC COVID-19 Reporting Project: Colorado College recently obtained rapid and wastewater tests. How might CC’s access to those tests fit into larger discussions about health equity?
Lostroh: What you would really like in this kind of global pandemic situation is … some kind of governing body that makes a logical decision that the communities that are most likely to be hurt by an infection are X, Y, and Z, and so every technology then is rolled out to those communities first. And so it’s great that we [CC] have them. It’s absolutely great and maybe it will help keep everybody and the surrounding community safe, but in terms of urgent need for communities in Colorado Springs at risk of getting COVID and getting serious complications from COVID, we aren’t it. We’re just not. ... It’s clearly some kind of inside channel that CC is proud of, some kind of parental connection that has led to us acquiring those tests, and so it just makes me feel a little bit funny because the college has a lot of resources compared to other parts of our community. ... And I want everybody on campus to be as safe as possible, but is this really the best use of this very scarce and very important resource? I don’t know. I’d rather that all those nurses who are doing all the swabbing had access to those tests, or that the restaurant workers had access to those tests, or that the meat pack workers, or that the people picking the peaches had access to those tests. I think it’s probably more important in those settings, or even nursing homes here in town, if not the schools or the jails. I don’t think that’s probably an option. I think the option was either you take this generosity or you don’t. I think that that is a perfect illustration of what structural advantage and privilege is like in our country. None of us are actively choosing to be racist or classist, but the outcome of CC having these rapid tests, and the communities surrounding us that are more in need not having them — it’s structural racism and classism that’s going to hurt people’s health.
CCRP: Why is a recent development about interferon response important?
Lostroh: There was a big finding about interferon this week. Interferon is a signaling protein that the immune system that all of our cells use to tell other cells they’re in trouble and going to die from a virus. So if a cell in the middle gets infected, it emits interferon and the cells nearby change their physiology and enter something called the antiviral state. If that middle cell dies from the virus infection, the little viruses come out, and when the new baby virus has tried to get into the neighboring cell, they get in but can’t complete their infection. So this protein called interferon interferes with replication of the virus when it gets into the new cell. So it was discovered because it interferes with influenza infection. There’s been a genome-wide study of thousands of people who got very serious COVID disease, and it’s turning out that many of them have mutations that alter and actually make worse their interferon response. It’s called attenuate their interferon response, so they are not able to mount this interferon-mediated innate immune response like other people are. It seems to explain a lot, not all, of the reason why someone gets a serious case compared with a mild case, but we are starting then to get a handle on how important the interferon response is for this virus.
About the CC COVID-19 Reporting Project
The CC COVID-19 Reporting Project is created by Colorado College student journalists Miriam Brown, Arielle Gordon, and Isabel Hicks, in partnership with The Catalyst, Colorado College’s student newspaper. 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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