COVID-19 Forecast for El Paso County — Jan. 4
Plus, our resident microbiologist on the governor’s latest announcements
Good morning, and happy Monday. On this pre-pandemic date in 2019, comedian Chuck Roy performed his stand-up routine for the Fine Arts Center at Colorado College. (This year, the FAC is putting on virtual programming for special events and the Bemis School of Art.)
Today, Phoebe Lostroh returns to give her weekly COVID-19 forecast for El Paso County and to explain Gov. Polis’ decision to loosen coronavirus restrictions the same week a more contagious variant of the virus was discovered in Colorado. 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.
😷Two CC students test positive during move-in: Yesterday, two students living on campus tested positive for the virus on the second day of move-in for spring semester. The college said in an email that the cases were related.
🚨News from the governor’s office: Colorado Gov. Jared Polis had a busy week, releasing three significant announcements about COVID-19 on social media over the course of a few days. We break them down for you here:
Dec. 29: Polis confirmed the B117 coronavirus variant from Europe, which early evidence suggested could be around 50% more contagious, was detected in Elbert County, Colo. The case was the first discovery of the B117 variant in the U.S., but the COVID-positive individual had no recent travel history, causing some people to speculate that B117 is already widespread across the country. Within days, the mutation was discovered in California and Florida as well.
Dec. 30: Polis announced changes to the state’s vaccine distribution plan, moving Coloradans 70 and older, teachers, and grocery store workers from Phase 2 to Phase 1B of vaccine priority. Some public health officials expressed frustration about not being aware of the change before it was posted on social media, and the lack of specific guidelines for counties from the governor’s office after they expanded Phase 1B from 100,000 people to roughly 1.3 million.
Dec. 30: Polis, citing the state’s sustained two-week decline in coronavirus cases and “only” 73% of ICU beds in use, said that all counties under Level Red restrictions can move to Level Orange guidelines effective Jan. 4 (today). The move allowed indoor dining, which was shut down completely under Level Red, to reopen at 25% capacity in counties statewide. Some public health officials expressed concern about decreasing restrictions.
On a completely unrelated note...
🍔Outbreak at In-N-Out: In late December, several media outlets across Colorado reported that the state’s two new In-N-Out restaurants, which both opened on Nov. 20 to massive crowds, had at least 122 employees test positive for COVID-19. Public health officials found 80 positive employee cases linked to the restaurant in Colorado Springs, and the Aurora location confirmed 42 cases among employees. According to The Denver Post, Colorado’s outbreak database does not list any customer cases tied to the In-N-Out restaurants.
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 Jan. 2, 2021.
⚖️ How her predictions last week shaped up: Jan. 2 is the last day of Morbidity and Mortality Weekly Report week 53 in the national public health calendar. It is the 43rd week since the first case was detected in El Paso County. Since March 13, 562 El Paso County residents have died of COVID-19. Last week, Lostroh predicted about 1,738-2,327 new cases during the week ending Dec. 31. There were actually 1,463 cases.
Cumulative reported cases in El Paso County with predictions
🗝️ Key points: Reported cases are in black circles while the other symbols provide estimates based on curve-fitting. The middle and low estimates are from exponential fits to the last 14 and seven days, respectively, while the best case is a linear fit based on data for the last 14 days. Horizontal boxes filled with a gradient from white to purple indicate the six weeks following an event that might reduce spread, such as the implementation of Level Orange or Red safety precautions, and boxes with a gradient from white to pink show the six weeks after an event that might increase spread, such as Christmas gatherings.
According to Lostroh, the data since Dec. 27 showing the most recent uptick in reported cases is insufficient to determine if that trend will continue. Depending on whether the decline in incidence continues, or if the virus resumes exponential spread, Lostroh predicts between 1,324 and 1,702 new cases in El Paso County for the week ending Jan. 7.
Rolling 14-day COVID-19 incidence per 100,000 people with predictions
🗝️ Key points: The actual calculated incidence is in black X’s, while the other symbols provide estimates based on curve-fitting as in the first graph. The dotted lines represent the incidence thresholds for red, orange, and yellow-level restrictions. Although there has been a sustained decline in incidence over the last two weeks, that drop became less steep over the last week. Now, Lostroh predicts incidence rates will not dip below the 350-case threshold for Level Red safety precautions until mid-January. As of Jan. 2, the 14-day incidence is 488 cases per 100,000 people.
Percent positivity for COVID-19 in El Paso County
🗝️ Key points: Average 14-day rolling percent positivity is plotted in dark blue while the daily values are in light blue. Since Dec. 27, percent positivity has hovered around 9% after a steep 20-day decline. As of Jan. 2, the percent positivity was still around 9%.
“Last week it appeared that we might go beneath 5% during the first week in January, potentially making normal contact tracing possible, but that trend has stopped for the moment,” Lostroh said, referring to an earlier announcement from El Paso County Public Health that they were struggling to conduct contract tracing with a rising positivity rate.
Q-and-A with Lostroh: Our resident microbiologist on the B117 variant
This interview has been edited for length and clarity.
CC COVID-19 Reporting Project: The town of Simla, Colo. in Elbert County was the first location in which a case of the B117 coronavirus variant was found in the United States. How was this case found, and what does it mean for the state?
Lostroh: One question I have about that is how in the world does someone in Simla get sampled and have their virus sequenced? The U.S. is infamously under-sampling and under-sequencing the virus so that, unlike basically every other country that has a similar impact on the global economy as we do, we’re sequencing very few virus isolates. It also suggests that the person got it in the community, because they had not travelled recently. So that variant is in the United States, probably in many, many places. If it’s in Elbert County, in a guy in his 20s who has not travelled outside of the county, let alone Colorado for a month, it’s widespread. That’s obviously very concerning. I hope that the scandal of this will lead us to have more coordinated sampling of patients across the entire country and sequencing of their viruses. I actually was flabbergasted to learn that we don’t have a coordinated system for doing that. I assumed that, just like we do for influenza, there was a coordinated national plan where people in every state were in charge of making sure that a certain number of people were sampled and that their virus was sequenced, and that those sequences were uploaded to the database. And apparently, that’s not the case, so that’s a problem. Now, as far as that actual variant goes, it has at least one mutation that affects the function of the part of a virus called the spike that binds to host cells. In laboratory tests, viruses that have similar mutations to that are more infectious in tissue culture. But as far as I know, the observation of how much more transmissible it is than the original, those are all based on epidemiology kinds of measurements or population measurements and not necessarily lab tests.
CCRP: On Dec. 30, Gov. Jared Polis announced that Coloradans 70 and older, teachers, grocery store employees and other essential workers would be moved to Phase 1B of vaccine distribution. How will this affect the way individual counties use their supplies of vaccine shots?
Lostroh: I think that this is going to be difficult. I have a friend who got the shot. She’s over 75. She qualified and for whatever reason, the shot was available. I mean, I thought all those shots had to go to people in long term care facilities, and doctors and nurses and what have you first, and clearly all of them have not yet been vaccinated. But she got contacted by UCHealth, saying, ‘okay, we have a vaccine available for you if you can come in.’ Her theory is that she happens to be somebody who reads her email, and who’s in good touch with UCHealth, so they were able to find her and therefore give her the vaccine. But clearly, there is insufficient coordination. I feel terrible for these public health officials flooded with calls from people asking when they can get the vaccine. I mean, they can’t win right now. If it’s not somebody calling up to say, ‘I’m going to kill you because you’ve kept the restaurants closed,’ it’s somebody calling up to say, ‘Can I please have the vaccine tomorrow? I have heart palpitations.’ I mean, it is really a hard time to be a public health official in the United States right now.
CCRP: Late Wednesday evening, Gov. Polis posted an announcement to social media moving counties at Level Red safety precautions to Level Orange, effective Jan. 4. How do you think this new order might impact the jobs of county public health officials?
Lostroh: So apparently, it came out on Facebook and Twitter. There are some public health offices in the state of Colorado that learned about it through social media. There hasn’t been any certification program to improve the indoor safety of places where people could eat or drink. So for instance, to certify the ventilation is adequate, or to certify that humidity is adequate, which is really important in Colorado — that program hasn’t happened yet statewide. This is clearly an overriding concern from the hospitality industry to open the economy rather than a careful look at the numbers and the risk of what might happen. Many counties at Level Red restrictions are still significantly in the red in terms of incidence, number one. Number two, not able to do adequate contact tracing. Number three, still having percent positivity higher than 5%, which means that cases are being missed. So in combination with missing cases, and not being able to fully complete contract tracing, to me, that means that the situation could reverse itself rather quickly. That’s worse when the amount of cases over the last 14 days is already elevated. So this decision is confusing to me and feels like Polis is listening to different advisors now than maybe he was earlier in the epidemic.
About the CC COVID-19 Reporting Project
The CC COVID-19 Reporting Project is created by Colorado College student journalists Isabel Hicks, Esteban Candelaria, Lorea Zabaleta, and Cameron Howell 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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