At the U.S. Department of Energy’s (DOE) Argonne National Laboratory, researchers from around the country continue to make progress in the global fight against COVID-19, helping to keep America healthy, secure, and prosperous.
At Argonne’s Advanced Photon Source (APS), a DOE Office of Science User Facility, many research groups are using APS beamlines to determine the exact structure of the proteins of the SARS CoV-2virus that causes COVID-19. The virus is composed of multiple copies of 28 unique proteins.
Researchers are not working with live virus, but with synthetic proteins that are nonhazardous.
As of April 6, 115 structures of these proteins had been submitted to the international Protein Data Bank (PDB), compiled by researchers around the world. In addition to work being done by a team led by Karla Satchell of Northwestern University and Andrzej Joachimiak of Argonne and the University of Chicago, many user groups have undertaken research at APS beamlines operated by five separate groups (IMCA-CAT, SBC-XSD, LS-CAT, GM/CA-XSD and NE-CAT).
All told, 23 groups of researchers have used or are scheduled to use APS beam time to analyze different aspects of the viral proteins, with the goal of providing insight towards developing an antiviral drug to treat the disease or an antibody vaccine that will help an individual’s immune system to fight the disease. As of April 1, 2020, the structures of six of the total 28 SARS CoV-2 proteins have been determined. In addition, several structures include bound potential antiviral drugs or antibodies, bringing the total number of structures determined at the APS to 13. Several more have been submitted to the PDB, but have not been released yet.
The APS is one of the best light sources in the world enabling science at scale, with high-brightness X-ray beams to illuminate the protein crystals at high resolution. A recent call for more research teams seeking beam time to investigate SARS-CoV-2 has yielded a number of new research groups wanting to use the APS beamlines, and more are expected in the coming weeks.
In addition to this effort, researchers in Argonne’s Decision and Infrastructure Sciences Division (DIS) have worked in support of the Federal Emergency Management Agency (FEMA) to update the Resilience Analysis and Planning Tool (RAPT), a census software tool that was originally developed at the laboratory. The updated tool gives emergency managers information about vulnerable populations in their community and is based on census tract population data.
For instance, RAPT lists populations over 65, individuals with disabilities, and those who lack health insurance in different areas. The tool also includes information on key infrastructure, such as nursing homes, pharmacies and hospitals (including the number of hospital beds). These facts are taken from the Homeland Infrastructure Foundation Level Data.
DIS is also helping the Department of Homeland Security Federal Protective Service (FPS) track and map areas affected by COVID-19 by using the Modified Infrastructure Survey Tool (MIST). Led by Argonne’s Laura Adochio, MIST allows FPS Headquarters and FPS Management to track and display each federal building affected by COVID-19. The tool also analyzes local hospitals and EMS facilities in relation to federal buildings and office locations.
Finally, the National Preparedness Analytics Center, located at Argonne, has developed a simple community web portal for Vermont residents to offer support to other residents, during the pandemic. Argonne economists, decision scientists and disaster recovery experts are providing models, analysis and recommendations. The team is led by Kyle Pfeiffer, Iain Hyde, Lesley Edgemon, John Dactelides and Matt Cowan.