COVID-19 Research

BioHEAT is a short duration, limited scope effort to develop new methods for analyzing the stability and relative mutation rate of proteins. The program is creating a visual representation of evolutionarily stable regions and mutation hotspots within multiple SAR-CoV-2 proteins across coronavirus families and strains from the current pandemic, which may be used for better contact tracing.

Baylor researchers develop new modeling techniques to understand genetic stability of SARS-CoV-2, enabling faster discovery of therapeutics and vaccines
April 2020: Baylor College of Medicine, an IARPA performing team, is researching a novel Evolutionary Trace and Evolutionary Action software pipeline to analyze the stability and relative mutation rate of proteins. The team, in consultation with the National Biodefense Analysis and Countermeasures Center, used the pipeline to compare publicly available reference sequences and create a visual representation of evolutionarily stable regions and mutation hotspots within multiple SAR-CoV-2 proteins across coronavirus families and strains from the current pandemic. The analysis also validated previous studies that indicated mutations present appear to be natural in origin. This new computational pipeline enables tracking of mutations in the viral genome across time and space, potentially enabling improved contact tracing. Additionally, identification of stable regions may be used to develop medical countermeasures and high specificity detection platforms.

BioHEAT COVID-19 research: This seedling identifies functional hotspots in proteins and whether they arose through natural evolutionary processes or by unnatural engineering. Integrative analytics efficiently exploit evolutionary information, here in the Coronavirus superfamily (left). This produces a structural map of a natural functional hotspot in the Spike proteins (middle). A hotspot can serve as an antigenic site, a lead for peptide mimetic drugs, or, here, a target for docking repurposed drugs or discovery of new drug formulations. A comprehensive map of hotspots in all SARS-CoV-2 proteins is under development. (Figure used with permission)

The Intelligence Community Postdoctoral Research Fellowship Program was established in 2000 to support unclassified basic research in areas of interest to the IC. Funded primarily by the Office of the Director of National Intelligence, the program annually supports several postdoctoral fellows from U.S. accredited colleges, universities, and U.S. government laboratories across the country.

Intelligence Community Research on Audio Algorithms Pivots to Support Emergency Ventilator Efforts During COVID-19 Response
Dr. Ryan Corey is an IC Postdoctoral Fellow at the University of Illinois at Urbana-Champaign supported under an IARPA sponsored topic on research algorithms for distributed audio networks. Recently, Ryan made a major contribution to the development of a monitoring system for emergency ventilators. Many low-cost ventilators developed to address the COVID-19 pandemic lack the electronic monitoring and alarm features found in commercial ventilators. Dr. Corey and colleagues adapted a signal processing algorithm used to control loudness in hearing aids to efficiently process pressure signals measured in a ventilator to alert clinicians when specific errors occur. The Illinois RapidAlarm team designed the monitoring system to complement the Illinois RapidVent, a low-cost emergency ventilator that has been licensed by several manufacturers worldwide. The designs and source code for the Illinois RapidAlarm system are freely available online. The device can be constructed quickly at low cost using widely available parts, helping address medical supply shortages with safer, more useful emergency ventilators

Figure 1: Simulated alarm conditions initiating a response by the alorithm

Figure 2: Prototype of Illinois RapidAlarmsensor and alarm system attached