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UNC research program studies COVID-19 variants


Patricio Cano uses laboratory equipment to assist in the CORVASEQ project at the UNC Lineberger Cancer Center on Monday, Jan. 31, 2022.

While a COVID PCR test indicates whether or not there is genetic viral material in an individual sample, the technique does not reveal the specific variant of coronavirus that made a person sick. 

Once a test is determined positive, the test sample is sent to a lab for sequencing to determine the specific variant of COVID-19, such as delta, alpha, omicron— or an entirely new variant.

At UNC, the Coronavirus Variant Sequencing Surveillance Program serves as a viral sequencing program funded by the NC Policy Collaboratory in partnership with the NC Department of Health and Human Services Division of Public Health. 

The goal of the project is to improve surveillance of COVID-19 virus sequencing, said Audrey Pettifor, a professor in the Gillings School of Global Public Health who also serves as a principal investigator in the project. 

“The goal is to improve SARS-CoV-2 sequencing surveillance for the state of North Carolina by supporting partners to report results to a centralized reporting system (GISAID) and DHHS,” Pettifor said.

The project also hopes to improve communication between groups doing sequencing and help to improve more systemic methods of genomic sequencing, Pettifor said.

While there is a nationwide effort to sequence coronavirus variants, there are different partners. The CORVASEQ team consists of multiple universities and healthcare institutions in order to capture samples from over 65 hospitals across the state and from all 100 counties, she added.  

“This is a statewide initiative that really helps us look at the way we look at different things. When we started noticing 80 percent of our strains were of the omicron variant, we stopped using two of our monoclonal antibodies for treatment,” said Amir Barzin, the director and lead physician of the Carolina Together Testing Program who also serves as a principal investigator on the project. 

The network is evolving every day due to its complexity, Barzin said. The team sometimes has to change lab techniques and adapt some primers so they are more effective.

When a PCR test amplifies a piece of DNA, the sample is considered positive. 

Dirk Dittmer, professor in the Department of Microbiology and Immunology and principal investor, said about 300 PCR tests are needed to sequence the entire virus genome.

“In the UNC community, most of the infections are Omicron. Giving someone five thousand dollars worth of antibodies that don’t work—we don’t have to do that anymore,” Dittmer said. 

Dittmer said there have been about 15,000 COVID-19 sequences generated over the last year which have helped understand and predict future viral strains. 

“That’s the immediate benefit for the community," he said. "For the world, it helps us understand the pandemic and helps us build better vaccines,” he said.

Once established, the CORVASEQ will serve as an early warning system to detect new variants that may emerge, Dittmer said.

Dittmer described the network as an “honor system” where public and private institutions upload viral sequences for laboratories around the world to use. As a result, the CORVASEQ team is able to do the same for North Carolina, he said. 

“The prediction is that every six to eight months, a new variant will come up," he said. "Even after the current (omicron) wave ends, we will continue to sequence and see what comes up. What omicron has shown us is that the virus is always evolving, but the selection course on the virus is transmission — those viruses will be selected for and enriched.”

With CORVASEQ, Barzin said UNC is leading the way and could potentially sequence other respiratory illnesses in the future and quickly respond to future pandemics in developing mitigation strategies and vaccines.

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