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University of Missouri Research Team Identifies 46 Mutations Specific to the SARS-CoV-2 Omicron Variant That Could lead to Improved Clinical Laboratory Tests, Treatments, and Vaccines

Many of the mutations were found at sites on the spike protein where antibodies bind, which may explain why the Omicron variant is more infectious than previous variants

Scientists at the University of Missouri (UM) now have a better understanding of why the SARS-CoV-2 Omicron variant is more infectious than previous variants and that knowledge may lead to improved antivirals and clinical laboratory tests for COVID-19.

As the Omicron variant of the coronavirus spread across the globe, scientists noted it appeared to be more contagious than previous variants and seemed resistant to the existing vaccines. As time went by it also appeared to increase risk for reinfection.

The UM researchers wanted to know why. They began by examining the Omicron variant’s mutation distribution, its evolutionary relationship to previous COVID-19 variants, and the structural impact of its mutations on antibody binding. They then analyzed protein sequences of Omicron variant samples collected from around the world.

“We know that viruses evolve over time and acquire mutations, so when we first heard of the new Omicron variant, we wanted to identify the mutations specific to this variant,” said Kamlendra Singh, PhD, Associate Research Professor, Department of Veterinary Pathobiology at UM’s College of Veterinary Medicine (CVM), in a UM press release.

The UM scientists published their findings in the Journal of Autoimmunity, titled, “Omicron SARS-CoV-2 Variant: Unique Features and Their Impact on Pre-existing Antibodies.”

Kamlendra Singh, PhD
Kamlendra Singh, PhD (above), an associate research professor in the Department of Veterinary Pathobiology at UM’s College of Veterinary Medicine, led the team that identified 46 mutations of the SARS-CoV-2 Omicron variant. “I went to India last April and I got infected by the Delta variant. So, it then became personal to me,” he told NBC affiliate KOMU. The UM team hopes their findings lead to improvements in existing COVID-19 antivirals and clinical laboratory tests. (Photo copyright: University of Missouri.)

In their paper, the UM team wrote, “Here we present the analyses of mutation distribution, the evolutionary relationship of Omicron with previous variants, and probable structural impact of mutations on antibody binding. … The structural analyses showed that several mutations are localized to the region of the S protein [coronavirus spike protein] that is the major target of antibodies, suggesting that the mutations in the Omicron variant may affect the binding affinities of antibodies to the S protein.”

Other findings of the UM team’s research include:

  • Phylogenetically, the Omicron variant is closely related to the SARS-CoV-2 gamma variant.
  • There are a total of 46 highly prevalent mutations throughout the Omicron variant.
  • Twenty-three of the 46 mutations belong to the S protein (more than any previous variant).
  • Twenty-three of 46 is a markedly higher number of S protein mutations than reported for any SARS-CoV-2 variant.
  • A significant number of Omicron mutations are at the antibody binding surface of the S protein.

“Mutation is change in the genome that results in a different type of protein,” Singh told NBC affiliate KOMU. “Once you have different kinds of protein after the virus and the virus attacks the cell, our antibodies do not recognize that, because it has already been mutated.”

Omicron Mutations Interfere with Antibody Binding

Of the 46 Omicron variant mutations discovered by the UM researchers, some were found in areas of the coronavirus’ spike protein where antibodies normally bind to prevent infection or reinfection.

“The purpose of antibodies is to recognize the virus and stop the binding, which prevents infection,” Singh explained. “However, we found many of the mutations in the Omicron variant are located right where the antibodies are supposed to bind, so we are showing how the virus continues to evolve in a way that it can potentially escape or evade the existing antibodies, and therefore continue to infect so many people.”

These findings explain how the Omicron variant bypasses pre-existing antibodies in a person’s blood to cause initial infection as well as reinfection.

The UM team hopes their research will help other scientists better understand how the SARS-CoV-2 coronavirus has evolved and lead to future clinical laboratory antiviral treatments.

“The first step toward solving a problem is getting a better understanding of the specific problem in the first place,” Singh said. “It feels good to be contributing to research that is helping out with the pandemic situation, which has obviously been affecting people all over the world.”

Singh and his team have developed a supplement called CoroQuil-Zn designed to reduce a patient’s viral load after being infected with the SARS-CoV-2 coronavirus. The drug is currently being used in parts of India and is awaiting approval from the US Food and Drug Administration (FDA).

New discoveries about SARS-CoV-2 and its variants continue to further understanding of the coronavirus. Research such as that performed at the University of Missouri may lead to new clinical laboratory tests, more effective treatments, and improved vaccines that could save thousands of lives worldwide. 

JP Schlingman

Related Information:

MU Study Identifies Mutations Specific to Omicron Variant

Omicron SARS-CoV-2 Variant: Unique Features and Their Impact on Pre-existing Antibodies

SARS-CoV-2 Variants and Mutations

MU Researcher Identifies Mutations of the Omicron Variant

A Study to Assess the Safety and Efficacy of CoroQuil-Zn 750 in Comparison to the Standard of Care for the Treatment of Mild to Moderate COVID-19

Scientists Estimate 73% of US Population May Be Immune to SARS-CoV-2 Omicron Variant