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What’s your COVID-19 exposure risk in a gathering?

What’s your COVID-19 exposure risk in a gathering?

Thank you to reporter Kyle Pfannenstiel for highlighting some of U of I’s COVID-19 modeling efforts, as originally published in the Post Register.

University of Idaho mathematics professor and modeler Benjamin Ridenhour poses for a photo on UI’s Moscow campus.

If you’ll be at the dinner table with people you don’t live with this week, research from the University of Idaho can help you gauge how likely you are to bump into someone who has COVID-19.

In Bonneville County, for instance, 1 in 16 people are likely actively transmitting coronavirus, according to estimates Monday morning. In Madison County, that’s about 1 in 10.

Exposure risk is incredibly high, according to health officials, hospital administrators and experts who are pleading with people to practice safety precautions such as masking and distancing if they choose to gather with extended family and friends during Thanksgiving. Last week, the Idaho Falls Fire Chief said the region’s largest EMS system was on “razor’s edge.”

“We’re trying to express things in ways that might relate to people a bit more,” project director Benjamin Ridenhour, a U of I mathematics professor, said of his team’s map.

Determining risk is hard. One way is through rates of spread in an area — calculated by averaging the number of new cases, each week, and dividing that by a region’s population. That’s how most national virus trackers do it.

Or, as Eastern and Southeastern Idaho Public Health districts do, you could determine how many cases are suspected to be active.

Both those measurements don’t include people who have COVID-19 but don’t get tested.

Ridenhour said that “silent” COVID-19 population — asymptomatic people, and people with such minor symptoms they don’t get tested — account for much of the virus’ spread.

“There’s a range of symptoms from being asymptomatic to being life threateningly sick,” Ridenhour said. The Centers for Disease Control says about 40% of all people with the virus don’t ever show symptoms. Ridenhour said “only a small portion of those cases are you going to pick up in surveillance.” That’s because although testing has expanded significantly, “it doesn’t change the fact that you have this huge group of people … who are not going to get tested.”

The U of I exposure risk map is based off a national modeling effortfrom Georgia Tech University researchers. That map lets users plug in the size and location of a gathering to show the odds that someone will have COVID-19 there.

At a gathering of 15 people in Bonneville County, there’s a 52% chance that someone will have COVID-19, according to Georgia Tech estimates on Monday.

These risk displays only say the odds of someone having the virus. They don’t predict the likelihood of spread, nor do they account for whether masks or distancing will be practiced at an event — all things that can significantly reduce the risk of spreading the virus.

Research from the U of I pandemic modeling team comes through a supplemental grant from the National Institutes of Health. Originally, the new modeling team had a five-year grant from NIH for around $11 million. But as the pandemic began, NIH gave the team around $500,000 more to model COVID-19 in rural communities.

“The first focus was on urban communities because that’s where the first outbreaks were,” said principal investigator Holly Wichman, a U of I biology professor who directs the university’s recently started modeling center. New York and Seattle were some of the nation’s first hotspots. “I think people in rural communities felt pretty safe. They felt like … they were naturally isolated; they were naturally distancing. But over time, as the virus spreads into these communities, they’re in some ways less prepared to deal with it.”

“It’s harder to get access to testing; it’s harder to get access to hospitals. Now what we’re seeing is a huge explosion in cases in rural communities,” Wichman said. “If you look at the maps, it’s changed over time. And we knew it was coming. That’s why we proposed this modeling effort.”

The exposure risk map isn’t the only tool the U of I team is working on. Others include a forecast of Idaho’s COVID-19 virus progression, along with a survey on behaviors in rural communities that can help test what resources can help curb virus spread.

It Takes a Village (and a Research University)

This article was written by Alexiss Turner, Marketing and Communications Manager from the College of Engineering, for the recently published “Here We Have Idaho” magazine. IMCI and many of our faculty participants have been very involved in the COVID-19 pandemic response. We are proud to be part of the many research efforts campus-wide that continue to help ensure the health and safety of Idaho residents. Read the article in its entirety here.

U of I Works with Communities to Bring Innovation and Research Expertise in Response to COVID-19 Pandemic

As the global coronavirus (COVID-19) pandemic continues to impact Idaho, experts across the University of Idaho have united to bring innovative solutions to Gem State communities in need and help ensure the health and safety of Idaho residents…

A Cure Through Defense

A research team in the Department of Biological Sciences is working to develop a one-size fits-all drug that could protect human cells from many coronaviruses, including the one responsible for COVID-19.

“Humans have similar genetics,” Department of Biological Sciences Virologist and Assistant Professor Paul Rowley said. “From the point of view of a human protein, a targeted drug therapy could be a universal solution.”

The COVID-19 virus attaches to a human cell using spike proteins that have evolved to dock with the specific ACE2 receptor. Once attached, the spike protein begins transferring genetic material to the cell, tricking the cell to generate more virus.

Rowley is working with Jagdish Patel, a College of Science molecular modeling specialist and research assistant professor, and others to use computational modeling to virtually sift through millions of molecules and optimize existing drugs to identify potential inhibitors that could shield the ACE2 receptor, preventing the virus that causes COVID-19 from docking in the first place.

“By using a computational 3-D map of this human cell receptor, we can determine which virtual molecules, out of thousands, would bind strongly,” said Patel. “Using chemistry and physics-based algorithms, we can rank the binding and visualize the molecule on the computer to see how they bind. The strong binders — which bind as intended — will be purchased and sent to Dr. Rowley’s lab for empirical testing in the fall.”

Working collaboratively with researchers in the Institute for Modeling Collaboration and Innovation has helped the team earn funding needed to keep research developing through the summer and fall semesters.

U of I Researchers, Moscow to Build on COVID-19 Wastewater Testing and Analysis

This news release, published by central University Communications and Marketing, was written by Alexiss Turner in the College of Engineering. IMCI has research partners and participants in nearly all U of I colleges.

MOSCOW, Idaho — July 21, 2020 — Researchers at the University of Idaho have partnered with the City of Moscow to improve wastewater testing for the presence of SARS-CoV-2, the virus that causes COVID-19. The team hopes to develop an early warning system for spikes in local cases.

Testing wastewater for the presence of SARS-CoV-2 is being conducted in areas worldwide, and estimating cases within a community based on the concentration of viral RNA in wastewater samples is a science that is gaining ground.

“Our primary contribution would be toward a bit of an early warning test,” said Erik Coats, U of I civil and environmental engineering professor.

Test results with higher concentrations of the virus, especially in areas with low case numbers, could foretell of future spikes in diagnosed patients.

“We could help hospitals focus on clearing up beds, gathering more personal protective equipment and making sure people are well-rested in advance of a wave,” Coats said.

Coats is working with Research Scientist Cynthia Brinkman, Department of Biology Professor Eva Top and Research Support Scientist Thibault Stalder. Department of Mathematics Assistant Professor Benjamin Ridenhour will assist with sampling schemes, analysis and extrapolation of results.

Moscow participated in a subsidized testing program through Massachusetts-based startup Biobot Analytics. The city provided Biobot with 24-hour composite wastewater samples in May and July.

SARS-CoV-2 was not detected for the three tests in early May. Biobot estimated 190 cases of COVID-19 from a test later that month. Analysis of samples sent July 1 and July 13 indicated 1,400 and 1,800 cases respectively.

“It is important to note that the Biobot data provides estimates, not actual cases,” Moscow City Supervisor Gary Riedner said in a statement released from the city. “While we can’t rely on the accuracy of the case estimation, the thing that is certain is that we are seeing significantly increased concentrations of COVID-19 in our wastewater.”

U of I testing will start using the same sample submitted to Biobot on July 1. Samples from the City of Twin Falls also have been obtained for analysis, and Coats is reaching out to regional wastewater treatment plants that have also participated in testing.

By comparing test results from different sources, researchers can better confirm the accuracy of their method and learn more about how that could translate into estimated cases.

“We’re hoping to develop a baseline,” Moscow Water Reclamation Utility Manager Evan Timar said. “We’re trying to compare and contrast testing results from different sources to see where we’re at and relay that information. We’re still learning and using that information to be proactive about what’s going on and to do our part for the wellbeing of the community.”

The city will collect and provide samples to the U of I lab, where researchers will isolate the viral RNA within the sample, reverse transcribe it to DNA, and then quantify regions within this DNA that are specific to SARS-CoV-2. This process allows detection of the SARS-CoV-2 at low concentrations. The method is being validated and optimized.

“The importance is the increase we observed,” U of I Research Support Scientist Thibault Stalder said. “With more samples, we will see the trend. For now, the data mirrored with public health data will be a great complementary tool.”

Wastewater consists of suspended solids and water, and one of the biggest challenges is identifying where the virus is most present in the sample. Reports suggest all carriers of the disease, asymptomatic or not, shed the virus, although virus shedding may be more prominent upon a person’s early infection.

Research activities are funded through the Institute for Modeling Collaboration and Innovation, U of I’s Office of Research and Economic Development and through unrestricted funds to researchers. Support has included funds to purchase a new biosafety cabinet that was recently installed in Coats’s lab on the U of I campus. All testing will occur in one location approved by U of I’s Institutional Biosafety Committee for this work.

Why R0 Is Problematic for Predicting COVID-19 Spread

Dr. Benjamin Ridenhour, Assistant Professor in the Department of Mathematics and Statistical Science and IMCI modeler, recently made significant contributions to an article in The Scientist, a magazine for life science professionals:

In the meantime, epidemiologists are reckoning with the uncertainty around SARS-CoV-2’s biological parameters by assuming a range of values rather than fixed numbers, says University of Idaho epidemiologist Benjamin Ridenhour, who is helping state officials predict the spread of the virus. He’s placing confidence intervals around every biological parameter in his model. His R0 could be anywhere from around 1.3 to 4, he says. “That way, obviously the chances that anything you model is exactly correct are zero, but hopefully you can capture it in that range somewhere.”

Read the entire article, written by Katarina Zimmer, here.

University of Idaho Works to Develop Cure for COVID-19

University of Idaho Works to Develop Cure for COVID-19

This press release was written by Leigh Cooper in University of Idaho Communications and Marketing. View the original press release here. See the article published in the Idaho Press here. Dr. Marty Ytreberg is the Associate Director of IMCI.

MOSCOW, Idaho — April 20, 2020 —The University of Idaho is working to identify a cure for coronaviruses, including COVID-19.

The Department of Biological Sciences team expects to finish preliminary tests within a year. Researchers will also develop a pipeline for identifying drugs that block viruses from infecting human cells.

The project is funded with $100,000 from a National Science Foundation EPSCoR grant issued to U of I Department of Physics Professor Marty Ytreberg. The EPSCoR funds were provided to determine how amino acid changes modify the way proteins interact with other molecules.

“Funding agencies are giving leeway to researchers with existing grants to shuttle resources toward the COVID pandemic,” Ytreberg said. “We decided this was a good investment, because it has the potential to lead to a therapeutic and fits within the theme of the grant.”

The team includes molecular modeling specialist Jagdish Patel, a research assistant professor; virologist Paul Rowley, an assistant professor; and evolutionary biologist JT Van Leuven, a research assistant professor. The research is being conducted within the Institute for Modeling Collaboration and Innovation, U of I’s multidisciplinary, collaborative research program that houses biomedical research modeling experts.

“The University of Idaho’s research engine has pivoted quickly in the battle against COVID-19,” President Scott Green said. “I’m proud of this team for taking the initiative to help develop a cure for this virus. Their work is rising to the challenge we all face during this difficult time and will help save countless lives in the process.”

The team hopes to create a drug that shields human cells rather than attacks viruses. The severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus is shaped like a ball with spikes on the surface as shown in widely-used photos. The spike proteins have evolved to dock with a specific protein — called the ACE2 receptor — on the surface of human cells. The attachment of the spike protein to ACE2 begins the infection process by which the virus transfers genetic material to the cell. This genetic material tricks the cell into generating more virus.

Patel and his team want their drug to shield the ACE2 receptor from interacting with the SARS-CoV-2 spike protein.

Drugs targeting human cells, as opposed to viruses, are likely to be effective for a longer period of time, Patel said. Viruses can rapidly evolve at their binding sites to render antiviral drugs ineffective.

The team will improve the known molecules and screen a large library of molecules on computers that might act as inhibitors for SARS-CoV-2. They will test potential inhibitor molecules against a SARS-CoV-2 pseudovirus, a harmless virus with SARS-CoV-2 spike proteins. Promising molecules would then be sent out for testing against the real SARS-CoV-2 virus and subsequently for clinical studies.

“The ACE2 receptor is being used by other coronaviruses as well,” Patel said. “If we find a drug that blocks SARS-CoV-2, the drug should have multiple purposes, protecting us from other coronaviruses like those that cause mild to severe respiratory infection, SARS and NL-63.”

Jagdish Patel, a University of Idaho research assistant professor, is a molecular modeling specialist and among U of I team members working to identify a cure for COVID-19.

Through the process of studying and testing potential inhibitors to combat COVID-19, the team will have developed and refined a multidisciplinary pipeline for antiviral drug development during future outbreaks.

“With the pipeline in place, we will also be able to respond much more quickly to any other disease outbreaks,” Patel said. “We’re designing the pipeline to be flexible so we can adjust to the different challenges each virus poses.”

Within their new pipeline, the researchers will identify antiviral drugs for human receptors other than ACE2, inhibitors that target the virus instead of human cell receptors and inhibitors for other animal viruses.

The awards are made through NSF EPSCoR as part of its Research Infrastructure Improvement (RII) Track-2 investment strategy. RII Track-2 is intended to build national research strength by initiating research collaborations across institutions in two or more EPSCoR jurisdictions. EPSCoR is a program designed to fulfill NSF’s mandate to promote scientific progress nationwide.

This project, “Using biophysical protein models to map genetic variation to phenotypes,” was funded under National Science Foundation grant No. OIA-1736253. The total amount of federal funds for the project is $6 million, which amounts to 100 percent of the total cost of the project.