COVID-19 Forecast for El Paso County — Sept. 3

Plus, our resident microbiologist on how COVID-19 rapid tests work

Good morning, and happy Thursday. On this pre-pandemic date in 2018, Colorado Springs residents were enjoying the final day of the annual Labor Day Liftoff hot air balloon event at Memorial Park. (A pandemic-friendly 2020 event is scheduled for this weekend, but residents should view the balloons from their homes, not the park.)

Today, Phoebe Lostroh returns to give her weekly COVID-19 forecast for El Paso County. We at The CC COVID-19 Reporting Project were ready to publish these forecasts on Monday, then on Wednesday, but — well, you know what happened. (Send coffee.) Lostroh also explains recent news about COVID-19 reinfections, and she talks about the possible benefits of new coronavirus rapid tests. 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: Yesterday, we explained Colorado College’s new fall plans, which include asking most students to leave campus by the end of Block 1, and offering most classes remotely for the remainder of the semester. (CC administrators are hosting a virtual information session about the changed plans today at 12:45 p.m. MT. If you can’t make it, don’t worry. We’ll be there, and we’ll have a recap next week.) 

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 Aug. 28. 

⚖️ How her predictions last week shaped up: Aug. 29 was the last day of Morbidity and Mortality Weekly Report week 35 in the national public health calendar. It is the 25th week since the first case was detected in El Paso County. Since March 13, 154 El Paso County residents have died of COVID-19. Last week, Lostroh forecasted that the rate of new cases might continue to fall. She expected between 5,872 and 6,076 cumulative cases reported as of Aug. 27, and there were actually 5,959.   

Predicted cumulative reported cases in El Paso County

🗝️ Key points: The worst-case scenario is based on an exponential curve-fit to the two weeks prior to the statewide mask mandate. The exponential and linear scenarios are based on fitting an exponential curve or a straight line, respectively, to the most recent 21 data points. (Both curves have an equally good fit to the data.) To make the best-case scenario, Lostroh averaged the total reduction in newly-reported cases over the past three weeks and subtracted that number from the new caseload every day, using the average number of cases in the last seven days as the highest number of new cases.

Cumulative reported COVID-19 cases in El Paso County

🗝️ Key points: El Paso County is likely to fall somewhere between the best-case and linear scenarios next week because the mask mandate remains in effect, and test positivity has been less than 5% for the last 11 days. If the loosening restrictions on bars and/or holding face-to-face instruction in schools cause an increase in spread, El Paso County will probably start to detect that impact in about two weeks.

14-day rolling average of daily new cases per 100,000 people in El Paso County

🗝️ Key points: The Harvard University Global Health Institute suggested the thresholds Lostroh uses in this forecast. El Paso County was in the orange zone from July 21 to Aug. 7 but has been in the safer yellow zone for about two weeks. Lostroh expects El Paso County to stay in the yellow zone for two more weeks, meaning it’s safe for grades K-8 to meet in person if pandemic-resilient buildings, classrooms, and practices are in place.

Total nose-swab tests reported and percent positivity

🗝️ Key points: The total tests reported in 14 days is plotted in pink using the left-hand axis while the percent positivity in those 14 days is plotted on the right-hand axis in blue. El Paso County has been beneath the concerning 5% positivity threshold for 11 days.

Q-and-A with Lostroh: Our resident microbiologist on COVID-19 reinfection 

This interview has been edited for length and clarity.

CC COVID-19 Reporting Project: Someone in Nevada, and someone in Hong Kong were each recently reinfected with COVID-19. What should we know about the possibility of reinfection? 

Lostroh: So the previous case documented in Hong Kong, they knew that it was a reinfection because they had isolated the virus from the person the first time and sequenced its genome. When the person got sick again, they isolated the virus and sequenced its genome. And they could tell the genetic sequence is different enough that there’s no way it could have come from just being in his body for ... 48-60 continuous days, but that person got less sick in terms of symptoms the second time. The case in Nevada, the level of evidence showing that reinfection really did happen is equally strong, and it’s well-accepted that this is a case of reinfection. But unfortunately, the person got more ill, worse symptoms, and was much sicker the second time around. And now this is only one person. So we don’t know, is the person in Hong Kong the representative case? Is the person in Nevada that representative case? We don’t know. 

Lostroh: Now, there are some viruses such as yellow fever virus and Dengue fever virus that cause something called antibody dependent enhancement. And this is where if someone has a reaction to an initial infection, and then they get exposed to a slightly genetically different virus later, the fact that they had an immune response to the first one actually makes the disease worse. We know what happens with yellow fever and with Dengue fever, it hasn’t been observed in people with something like SARS, or MERS, or the coronaviruses that cause the common cold. It was observed in some animal trials with ferrets using SARS-CoV-1 spike vaccine to look at level of protection. So that was kind of in the literature, and we were all ‘yeah, that wouldn’t happen with SARS-2.’ Now, they didn’t study the patient’s immune system in Nevada. So we don’t know if that is in fact what happened. It may not have been antibody dependent enhancement. There may be something else going on. But it’s just concerning ... because we were hoping that immunity would protect you from getting it a second time at all. It’s concerning because the person got a worse infection the second time, and it’s concerning because it’s often hard to make an efficacious vaccine for infections that don’t themselves provoke longer-term immunity. So with an infection like the measles, if you naturally get the measles, you’re immune for most of the rest of your life; you get smallpox, you’re immune for most of the rest of your life. Those vaccines work very well in part because they provoke long-term immunity, and that seems to correlate with lifelong natural immunity. In other cases where immunity isn’t lifelong, what we see is that it’s just generally more difficult to make a long-lasting efficacious vaccine, so booster shots could be required.

CC COVID-19 Reporting Project: Where might the new COVID-19 rapid tests fit into existing testing procedures? 

Lostroh: There are nucleic acid-based tests where you’re doing a quick test for the genome of the virus, and what makes it different from the tests that we use now is that it’s much less sensitive. You have to have more virus in your sample in order for it to be detected by the procedure. And then there are tests that actually look for the intact parts of the virus that are not nucleic acids, that look for the protein components. Those are called antigen testing, which is not the same as antibody testing — that’s testing someone’s blood for the presence of antibodies. Antigens are what immunologists call the parts of microbes that provoke an immune response. So both antigen testing and these quick PCR tests can be done on saliva. This is very advantageous because it means that an individual can collect their own sample, and it doesn’t require a trained healthcare provider to collect the sample. So that means that much less PPE is consumed, and much less personnel time is consumed. People have argued that they didn’t want such a quick test because it is not as sensitive to lower levels of virus. But now the thinking about that is changing because of course the amount of virus you have in your body is related to how much of it you are exhaling into the world. If we can detect it when it’s at high enough levels for these tests, maybe we are detecting the most infectious people even when they don’t have symptoms. The current thinking is that if we could have a fast test, where the turnaround time was very fast, and people could use it more than once a week, we would still be able to detect cases before people develop symptoms, and therefore ask people to isolate themselves … before they can spread it to too many other people, especially if everyone continues to maintain their physical distancing and enhanced hygiene and mask-wearing practices. So I have high hopes for this.

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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