Throughout the COVID-19 pandemic, scientists have tried to understand and track SARS-CoV-2 without a proper parts list.

Much of the research emphasis has been on proteins — such as the “spike” proteins that cover the COVID-19 virus and attach themselves to human cells. Scientists continue to study how these proteins function and interact.

But Yale biochemist Anna Marie Pyle says there is also much to be gained by understanding the RNA of the virus and the structures within it. The “shapes” formed by the RNA in a viral genome influence its efficiency at copying itself, making proteins, and packing into the viral particle, which is a key factor in pathogenicity.

Pyle and her team have spent 10 months cataloguing and exploring the intricate biological makeup of the viral RNA genome after it infects a human cell. The result is a detailed map of the SARS-CoV-2 genome with an unprecedented level of detail that contains more than 100 identifiable structures within the genomic RNAs of the virus.

The genome RNA folds up like origami... certain aspects of the virus, such as how fast it copies itself, will be controlled by these shapes.

“It has a well-organized genomic architecture,” said Pyle, a Sterling Professor of Molecular, Cellular and Developmental Biology and professor of chemistry at Yale. “The genome RNA folds up like origami, into distinct shapes that impact how well the virus functions. This is important because certain aspects of the virus, such as how fast it copies itself, will be controlled by these shapes.”

The researchers developed a technique to probe the role of individual RNA structures by designing modified, synthetic nucleic acids that interact with specific regions in the virus, and watching the nucleic acids’ effects on viral growth.

Pyle’s lab had been conducting genome mapping for other RNA molecules before shifting its focus to SARS-CoV-2. What the researchers found, they said, was surprising: an RNA genome in which more than half of its 30,000 nucleotides are packed into loops, knots, stems, and other stable structures. This is in stark contrast to the majority of viruses, that have large, unorganized areas.

In a series of new studies published in the journals Molecular Cell and Journal of Virology, and posted on the pre-print website bioRxiv, Pyle and her colleagues present their findings.

In addition to mapping the virus’ genome and identifying structures within it, part of the team led by Dr. Craig Wilen, assistant professor in laboratory medicine and immunobiology, shows how SARS-CoV-2 RNAs change within a human cell over time.

Pyle said the team’s work will aid in identifying better ways to detect the virus using diagnostic kits and new therapeutic strategies for fighting SARS-CoV-2, as well as providing the scientific community with crucial information to fight new coronaviruses that may emerge in the years ahead.

“When a new virus comes along and is wreaking havoc, it’s often something we haven’t seen before,” Pyle said. “It’s helpful to have an established parts list for understanding how it is likely to behave and what it is likely to do. This research gives us a look under the hood of coronaviruses for the first time.”

Pyle called special attention to a quartet of Yale graduate students whose work helped propel the research: Han Wan in molecular, cellular & development biology, Nicholas Huston in molecular biophysics & biochemistry, Rafael Tavares in chemistry, and Madison Strine in immunobiology and laboratory medicine.

“This is the first time we’ve looked at the full, structural genome of the virus in living cells,” Wan noted. “I’m proud to have contributed to something that will be so useful.”

Huston, who lost a grandfather to COVID-19 during the pandemic, echoed the personal commitment and sentiment that infused the research. “We’ve been able to reveal how much information you can get, just by looking at the structures in this virus,” he said. “This virus killed someone I loved. Now I’m helping to kill the virus.”

Additional Yale co-authors of one or more of the new studies include Gandhar Mahadeshwar, Neal Ravindra, Mia Alfajaro, Victor Gasque, Victoria Habet, Jin Wei, Renata Filler, Klara Szigeti-Buck, Bao Wang, Guilin Wang, Ruth R. Montgomery, Stephanie Eisenbarth, Adam Williams, Akiko Iwasaki, Tamas Horvath, Ellen Foxman, Richard W. Pierce, and David van Dijk.