UNMC scientists use new technology to discover SARS-CoV-2 mutations in Nebraska

UNMC scientists use new technology to discover SARS-CoV-2 mutations in Nebraska

Scientists at the Nebraska Public Health Laboratory have found mutations to the novel coronavirus using new technology that allows the state to track COVID-19 across Nebraska more precisely. 

The technology enables scientists to conduct a new kind of whole gene sequencing that helps officials confirm whether cases of COVID-19 reinfection come from the same clone of the virus or represent a mutated form of SARS- CoV-2, according to a press release issued by UNMC Thursday. 

Using this tech, contact tracers will now be better able to determine whether people within certain populations, like nursing home residents or meatpacking workers, have been infected with the same variants of the SARS- CoV-2 virus. 

Nebraska Public Health Laboratory scientists—all of whom are faculty at UNMC—worked with a medtech start-up to validate the automated-sequencing technology and obtain Emergency Use Authorization from the FDA in September 2020.

California-based Clear Labs helped UNMC validate the technology using a new instrument called the GridION nanopore sequencer. An important feature of the GridION sequencer is its capacity to automate, as automation increases the number of samples that can be processed daily.

Previous technology limited sequencing to a small part of the RNA or genome of the virus. But the new tech allows UNMC investigators to see a more complete picture of the pandemic’s effect on Nebraska, including the details to indicate whether a sample represents the original version of the virus or a new mutation. Several positive COVID-19 specimens from across Nebraska are now being analyzed.   

So far, variants found by Nebraska Public Health Laboratory scientists using the new tech include two mutations thought to reduce the virus’s ability to cause infection and severe symptoms, said Baha Abdalhamid, MD, PhD. Abdalhamid is an assistant professor of pathology and microbiology at UNMC. 

Research continues on the severity and transmissibility of the most common and widespread variants of the SARS- CoV-2 virus, known as the UK, Brazil and South African variants. The new whole gene sequencing technology will help officials forecast whether a given variant might increase the number of cases among high-risk populations or delay herd immunity. Officials will then be able to make more effective public health recommendations.

This might not be great news to the ears of pandemic-weary Nebraskans, according to Peter Iwen, PhD, director of the Nebraska Public Health Laboratory.

“If we have a more highly transmittable virus, we’re going to have to tighten up again to prevent the spread,” Iwen said. “That’s not what people want to hear.” 

But, Iwen said, it’s important to know what mutations are occurring and how this affects the spread of the virus in Nebraska. He and Abdalhamid said they are optimistic that current and upcoming vaccines will effectively inoculate patients against new SARS-CoV-2 variants. 

Recent news reports, however, have indicated that both existing and trial vaccines are showing lower efficacy in studies conducted in South Africa, where officials last year identified one of the major variants now circulating.

According to UNMC and Nebraska Public Health Laboratory researchers, this finding demonstrates the importance of whole gene sequencing, as understanding changes in the virus could lead to a mutation-specific treatment or vaccine in the future.  


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