COVID-19 Forecast for El Paso County — June 21

Plus, our resident microbiologist on COVID-19 antiviral pills.

Good morning, and happy Monday. On this pandemic date last year, a concert entitled “Live from Packard Hall- Summer Music Festival Artists Concert” was held on Facebook for the virtual Summer Music Festival. (This year, the festival is in-person and runs until June 25.)

Today, Phoebe Lostroh returns to give her weekly COVID-19 forecast for El Paso County and to explain the COVID-19 antiviral pills. 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, Phoebe Lostroh returned to give her weekly forecast. 

✉️In Your Inbox: 

• On Friday, June 6, CC Communications sent out an email about the updated summer visitor policy. Prospective students and two guests may come tour the school and students, staff, and faculty may have family members visit as long as they follow social distancing guidelines.

• On Thursday, June 17, Acting Co-Presidents Mike Edmonds and Robert G. Moore sent out an update about the Board of Trustees retreat. It included notice of outgoing members and incoming members of the board, as well as faculty members who have been promoted to full professor.

• On Friday, June 18, CC Communications sent out an email about commemorating Juneteenth, with an explanation of the importance of the date from Professor Manya Whitaker, associate professor of education.

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 June 18.

⚖️ How her predictions shaped up: June 19 is the last day of Morbidity and Mortality Weekly Report week 24 in the national public health calendar. It is the 67th week since the first case was detected in El Paso County. Since March 13, 860 El Paso County residents have died of COVID-19. Two weeks ago, Lostroh predicted between 469 and 717 new cases in El Paso County for the week ending June 10. There were actually 729 cases.

Predicted cumulative reported cases in El Paso County

🗝️ Key points: Reported cases are in black circles while the red, grey, and light blue symbols provide estimates based on curve-fitting for the most recent 21, 14, and seven days. The best-case estimate using the declining rate of new cases in the most recent two weeks is in medium blue. For the week ending July 1, Lostroh predicts 633-987 new cases in El Paso County.

Rolling seven-day cumulative incidence in El Paso County with predictions

🗝️ Key points: The actual calculated incidence is in black Xs, while the red, grey, and light blue symbols provide estimates based on curve-fitting for the most recent 21, 14, and seven days, respectively. The best-case estimate using the declining rate of new cases in the most recent two weeks is in medium blue. The green, yellow, and red-dotted lines show the CDC’s thresholds for risk categories. As of June 20, the incidence per 100,000 people in El Paso County was 67.

“The broad ‘fourth wave’ appears to be drawing to a close,” Lostroh said. “Factors contributing to declining incidence include residents with at least partial immunity and summer weather enabling many outdoor activities, including dining and athletics. It remains to be seen how these factors balance over the course of the summer but public health officials are already raising concerns about a fall resurgence for areas with low vaccination rates (such as El Paso County).”

Seven-day rolling percent positivity compared with daily percent positivity in El Paso County

🗝️ Key points: The seven-day rolling percent positivity for nasopharyngeal tests for viral nucleic acids is plotted in dark blue diamonds, while the daily percent positivity is plotted in open light blue diamonds. The green, yellow, and red-dotted lines show the thresholds for the CDC’s risk categories. As of June 20, the percent positivity in El Paso County was 3.5%.

New COVID-19 hospitalizations compared with the regional census of hospitalized COVID-19 patients

🗝️ Key points: Daily hospitalizations are plotted in blue using the left-hand axis, while the census of regional hospitalized COVID-19 patients is plotted in red on the right-hand axis. As of June 20, the seven-day average daily hospital admissions in El Paso County was at 4.7 admissions.

COVID-19 vaccinations in El Paso County

🗝️ Key points: The El Paso County vaccine dashboard tracks county vaccine distribution. The number of people who have been fully vaccinated in El Paso County is indicated with purple symbols. The highest number on the vertical axis is 300,000, which is about 41.5% of the county population. El Paso County has administered a total of 563,723 doses. Some of those doses were the first shot someone received, while others were the second shot to complete the vaccine series. As of June 20, 271,031 people have received both shots and thus have completed the immunization series.

“At this rate, we will reach 70% of the population vaccinated in late November, 2021,” Lostroh said. “We need to improve this rate in order to prevent yet another wave of infections, most likely in the fall when the weather cools and school begins.”

Q-and-A with Lostroh: Our resident microbiologist on the more transmissible Delta Variant.

This interview has been edited for length and clarity.

CCRP: The Delta variant is in Colorado and has proven to be more transmissible for unvaccinated people. What is different about the Delta variant compared to the Alpha variant and how does the variant impact vaccinated people?

Lostroh: So, it’s got changes in the spike protein and some other proteins. The changes in the spike protein are making it about 60% more transmissible than the Alpha variants, which we used to call B.1.1.7, and that one was 50% more transmissible than the original SARS-CoV-2 virus. So, we’re looking at much more transmission possibility than the ancestor that we all got used to last fall. Also, there’s multiple changes to the spike protein, some of which make the spike protein bind less well to antibodies that are being used commercially as drugs to treat COVID-19. So those drugs work less well against the Delta virus in some cases and not in others. It depends on the exact antibody in that formulation, and it’s the same thing with vaccination. So you need a lot more antibodies around the spike protein to get good protection, compared with what you could get away with for the Alpha variant. The most specific information I have read is that being fully vaccinated with one of the RNA vaccines provides 88% protection from serious illness; so from hospitalization or death. But, only one shot in the two shot series is much less, in the 30’s I think. It’s really important to get both courses of the shot if you’re getting the RNA vaccine. And, the Johnson and Johnson vaccine, I believe, is still approximately that efficacious against the Delta variant.

CC COVID-19 Reporting Project: The outdoor mask requirement has been lifted for the CC community recently. To what extent do you think this was a safe idea?

Lostroh: Well, I think that the Colorado College population is probably highly vaccinated compared with the general population of El Paso County, so it’s probably fine. It’s not as safe as not having that requirement, but I can see why the college would do it. If everyone has done as good of a job as they possibly can getting vaccinated, and with all of the other precautions, I think that it’s very safe to be outside where there’s basically infinite ventilation, unless you’re standing right next to somebody and, you know, literally breathing or coughing on them. I think the transmission is unlikely in a highly vaccinated population outdoors. I think that’s why the numbers in Colorado, and El Paso County in particular, are going down because most people are now able to gather outdoors instead of indoors. I think that the good weather is helping us a lot.

CCRP: An antiviral pill is being developed to treat COVID-19. What is an antiviral pill and when do you think these antiviral pills will be finalized?

Lostroh: So the most commonly used antiviral pills treat HIV, and antiviral pills have a medicine that is generally specific for that particular species of virus, it’s not the actual variant of the virus. For instance, you can’t take HIV medicine to treat influenza, or influenza medicine to treat COVID. We will have to find drugs that are little chemical molecules that bind to the enzymes that the virus encodes, and those are specific for the specific species. So, I think they are going to continue to make progress on having a pill to treat COVID-19 and that it will probably be some kind of medication that binds to the viral replicase protein and inhibits the replication of viral RNA, which is the same as a class of antivirals we have for HIV. So, the SARS Coronavirus-2 has a unique protease that is required for the virus to complete its life cycle, and so if we could make a similar type of drug that bound to that protease and prevented its function, then that would also help treat COVID-19. I’m hopeful that we are going to get there. I think that it will be within the year that we have the first truly effective specific antivirals against COVID-19. They’ve tested all these drugs that are already known to block kind of related viruses, like the HIV replicase, and the drugs are almost the right shape, but not quite the right shape for COVID-19. So, I guess I have faith in organic chemists, that they’re going to look at those structures and they’re going to screen through the banks of chemicals that they have available, and find good candidates, and move ahead. Once we have vaccination and a drug, the world will be a much safer place.

About the CC COVID-19 Reporting Project

The CC COVID-19 Reporting Project is created by Colorado College student journalists Cameron Howell, Will Taylor, and Ellie Gober 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.

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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