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Illinois Team Tracks COVID ‘Spike’ Protein for 2020 iGEM Competition

The COVID-19 pandemic created unprecedented challenges for a worldwide competition that brings high school and college students together to tackle big questions in synthetic biology.

But it also provided a unique research opportunity for the University of Illinois team competing in this year’s International Genetically Engineered Machine (iGEM) Competition.

The six undergraduates are pooling their talents — remotely — to contribute to the fight against SARS-CoV-2, the coronavirus that causes COVID-19. They’re creating a web tool to build visual models of a key part of the virus as it mutates — specifically the infamous “spike” protein that allows it to attack human cells so easily. The hope is to give researchers crucial information about the virus as they design new drugs and vaccines.

“Our database will be real time, and it will allow researchers to upload their newly collected coronavirus sequences and get those newly mutated protein models for their research,” said Yan Luo, a sophomore in bioengineering on the Illinois team.

Mentored by graduate students and postdocs, iGEM teams meet in the spring to brainstorm ideas for innovative synthetic biology research and develop them over the summer. The projects culminate at the annual Giant Jamboree, iGEM’s international competition, to be held virtually this year in November. The event attracts teams from nearly every continent who can earn bronze, silver, or gold medals by achieving certain standards. Overall winners are chosen from the gold-medal teams.

They decided on a purely computational project, which would be far easier to manage remotely. Given the pandemic, the students wanted to do something COVID-related, Rao said.

“We all just wanted to start fresh and have our own idea,” said Mary Cook, a junior in bioengineering.

Besides Luo and Cook, the team includes Sachin Jajoo, a senior in molecular and cellular biology; Angela Yoon, a junior in integrative biology; Suva Narayan, a junior in bioengineering; and Royal Shrestha, a sophomore in biochemistry. They are mentored by CABBI researchers Matthew Waugh, a chemistry postdoc, and ChBE graduate students William Woodruff and Carl Schultz. CABBI Research Coordinator Anna Fedders and IGB Outreach Activities Coordinator Daniel Ryerson provide administrative support.

The students started work in March, after the coronavirus shutdown. They each came up with an idea for a computational project with synthetic biology applications that would fill a research need. Shrestha suggested a 3D database as an interactive way to show viral structures and help scientists learn more about SARS-CoV-2.

The team presented the idea to their mentors, who helped focus it into a useful deliverable. The students also consulted with professors across campus involved in COVID-related research, including Erik Procko in biochemistry, Mohammed El-Kebir in computer science, and two faculty members in ChBE — Huimin Zhao and Diwakar Shukla.

Those conversations narrowed the project to spike proteins specifically, Cook said. The team also decided to try, to design an antibody with the information they collected, rather than just a database.

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Publication Date: 08/19/2020
Photo credits: Gerd Altmann on Pixabay
Editor: Julie Wurth