Amid a surge in COVID-19 cases and the detection of new variants of the virus on campus, the Innovative Genomics Institute, or IGI, at UC Berkeley aims to sequence viral genomes to improve student safety.
Led by IGI senior genomics scientist Stacia Wyman and assistant professor in the department of bioengineering Liana Lareau, researchers at the IGI receive and sequence samples testing positive for COVID-19. The purpose of sequencing efforts is to help determine the best response to novel strains of the virus and cases on campus, according to IGI spokesperson Andy Murdock.
“This allows us to know the prevalence and which variants are on campus so that the (University Health Services) and University administration can make the best decisions to keep everyone safe based on the most current information,” Murdock said in an email.
Campus postdoctoral researcher Haridha Shivram added that a better understanding of the different variants of the virus could lead to the development of a more effective vaccine. While the institute has sequenced between 800 and 900 genomes so far, Shivram said, researchers still hope to increase the scale of sequencing to identify which variants are spreading rapidly.
The IGI testing facility — established in the span of weeks in March 2020 in response to the early stages of the pandemic — has played an essential role in campus surveillance testing, Lareau added. According to a Berkeley News release, IGI researchers identified two cases of B.1.1.7 variant first discovered in the United Kingdom as well as multiple instances of a variant called CAL.20C first recorded in California.
“It was totally a homegrown effort, it was all volunteers at first and that’s been what’s enabled Berkeley to do all of this really important surveillance testing for students to make sure that people who are on campus or near campus are able to stay as safe as possible, so that’s been really a game changer for Berkeley,” Lareau said.
Researchers at the institute hope to decrease the period of time between receiving a testing sample and sequencing then uploading the entire genome to their database, according to campus graduate student Phil Frankino. The institute currently processes about 100 samples weekly, Frankino added, but he said he hopes to see the volume increase to 1,000 samples each week with the necessary personnel.
With recent policy changes at the state level, Murdock emphasized the need to proactively identify cases to help notify individuals who should isolate themselves.
“The longer this goes on, the more people tire of taking the precautions necessary to keep everyone safe,” Murdock said in an email. “With the vaccines coming, we have reason for hope, but we just have to stay safe and hold on a little longer. We’re almost there, but we can’t let our guard down now.”