In the effort to respond to the COVID-19 pandemic, few tools have been as crucial as genomic sequencing. Determining the exact nature of the virus at the genetic level allows scientists to identify which known variant a virus sample pertains to and whether any new virus mutations are present.
New funding from the Centers for Disease Control and Prevention (CDC) has set the stage for the University of Minnesota Genomics Center (UMGC) to sequence 6,000 samples of SARS-CoV-2—the virus that causes COVID-19—over the course of the next year. Under the nearly $750,000 contract, UMGC will collaborate with the Minnesota Department of Health (MDH) to aid in national and global viral surveillance efforts.
“Sequencing and genomic surveillance have been, and will continue to be, really important throughout the pandemic,” said Daryl Gohl, PhD, principal investigator on the CDC contract and group leader with UMGC’s Innovation Lab. “Understanding when the virus is evolving and how it is changing lets you determine how outbreaks are happening and if additional public health interventions are needed.”
Public health experts can use information obtained through sequencing to trace where virus outbreaks originate, monitor for new variants, and spot changes in the virus as it attempts to evade the immune system. This information can inform public health responses, spurring investigation into clusters of outbreaks or other measures designed to curb the spread of the virus.
UMGC will collaborate with MDH to identify which samples to sequence, and then provide the resulting data and analysis from those samples. The data released will only contain genomic information from the virus itself, not from the human who provided the sample. To further maintain patient privacy, the minimal metadata included alongside the genomic data will not contain information that can be used to identify an individual.
Ready to Respond
The new collaboration will amplify existing sequencing activities, which include over 3,000 viral genomes sequenced by UMGC for MDH in recent weeks. While most of the CDC-funded sequencing will remain in-state, a portion of the samples may come from surrounding states in the Upper Midwest. The structure of the CDC contract spreads out the available sequencing resources over the next 12 months and allows for UMGC and MDH to respond to unexpected virus surges by concentrating more sequencing at those times.
“If there is suddenly a new outbreak to respond to, then we’ll be ready for it,” said Kenny Beckman, PhD, UMGC director. “There are already experts suggesting that SARS-CoV-2 could become an endemic virus that changes and evolves over the long term, much like influenza. To have genomic surveillance in place makes sense as a way to become more proactive against these potentially deadly threats.”
Experts may either use sequencing in a targeted manner to monitor specific outbreaks or in an untargeted manner, where a random sample of COVID tests are sequenced to provide a broader picture of which strains are most prevalent and find new mutations early on. Scientists in the United Kingdom, for example, used untargeted sequencing to discover the B.1.1.7 COVID-19 variant in December, which is thought to be more infectious than previous variants and is now the most common source of new infections in the United States, according to CDC data.
Sequencing also plays a role in the context of research into COVID-19. As a larger portion of the population becomes vaccinated, studies designed to monitor “vaccine breakthrough” infections can track how many vaccinated individuals still develop an infection.
“This new resource not only will keep the momentum of the COVID-19 variant surveillance within Minnesota, but also boost the entire US central region states’ SARS-CoV-2 whole genome sequencing effort,” said Sean Wang, DVM, PhD, sequencing and bioinformatics supervisor at MDH, who will lead the state’s role in the project along with Ruth Lynfield, MD, state epidemiologist. “More importantly, the research component will help University of Minnesota researchers further understand COVID-19 host-pathogen interactions through sequencing.”
The sequencing will also contribute to the national and global picture of the virus’s spread, as all of the data UMGC generates will be added to public health repositories that other scientists around the world can study to provide a more holistic understanding of the virus.
COVID Surveillance on Other Fronts
As another way to watch for new strains of SARS-CoV-2, UMGC has collaborated with the Metropolitan Council to monitor the wastewater flushed down toilets in the Twin Cities. UMGC has used quantitative PCR, digital PCR, and, most recently, next-generation sequencing to interrogate samples from the primary sewage treatment plant in St. Paul, in order to spot early warning signs of new COVID outbreaks.
In addition to sequencing, UMGC has performed hundreds of thousands of COVID-19 tests over the course of the pandemic in collaboration with the UMN Medical School. As employers and schools look to return to in-person working and learning, the center is equipped to provide testing support to these and other organizations that need large-scale, low-cost testing.