Omicron variant UF Health scan supports transmission issues

A University of Florida health researcher successfully analyzed the many mutations in the omicron variant of the SARS-CoV-2 virus, a crucial step in better understanding the variant’s potential threat and ways to combat it.

Immunologist David A. Ostrov was commissioned by a global consortium of scientists to analyze and map the locations of omicron mutations. Its analysis for the Global Virus Network found that omicron had many more mutations than the delta variant at four key sites of the virus. At least one of these sites – which can affect the transmissibility of the omicron – has more than three times as many mutations as the delta variant, Ostrov found.

Mapping omicron mutations is helping scientists around the world better understand its potential for immune system escape, transmissibility, and death.

The first reports from around the world have linked omicron to mild disease, but experts say more data is needed. Other scientists have said that the omicron is about five times more transmissible than the delta – a point that was confirmed by Ostrov’s analysis.

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“The mutations strongly suggest very high transmissibility. And there are a number of mutations that are completely unknown in terms of function, ”said Ostrov, associate professor in the department of pathology, immunology and laboratory medicine at UF College of Medicine.

Mutations in unexpected places

Ostrov said it’s not just the number of mutations that is of concern, but more importantly their locations. The virus appears to be mutating in unexpected places, which Ostrov says suggests it is trying to escape a protein known as the co-receptor. Sometimes co-receptors can prevent viruses from infecting a cell.

A cluster of seven “interchain” mutations also speeds up a process that leads to infection, Ostrov said. Mutations allow the virus to attach to a host cell and “slide” the viral membrane inside.

In another key piece of omicron, Ostrov found 14 mutations compared to just two in the delta variant. These mutations, located in an area known as the receptor binding domain, allow the virus to attach to receptors and enter cells, resulting in infection.

Omicron is currently classified as a variant of concern by the Centers for Disease Control and Prevention, which means that there is evidence of increased transmissibility or other factors such as decreased effectiveness of the vaccine or antibodies. . If it shows an ability to evade diagnostic tests, decrease the effectiveness of the vaccine, or cause more serious disease, omicron would be elevated to a variant with significant consequences.

“As a variant of concern, it appears that omicron also has the potential to be a variant with significant consequences,” Ostrov said.

While the analysis of omicron mutations is concerning, Ostrov said it was also a starting point for developing strategies to contain and neutralize the variant. Discussions are underway to start a human clinical trial in South Africa, where omicron was first detected. He would study the effectiveness of two common compounds that inhibit the SARS-CoV-2 virus. At the end of last month, Ostrov and his colleagues published results showing that a combination of an over-the-counter antihistamine and a protein found in cow’s milk reduces virus replication by 99% in human cells. and monkey.

“A clinical trial takes time, but we already know that a combination of safe and approved drugs can inhibit coronavirus replication,” he said.

The omicron analysis comes shortly after Ostrov and a colleague from UF discovered a previously unrecognized pattern of mutations in the coronavirus. This pattern of mutations apparently has strong effects on the transmissibility of SARS-CoV-2. Mutations in these models need to be carefully considered and used as the basis for artificial intelligence prediction of emerging variants, Ostrov said. The results could be used to develop new antiviral drugs and vaccines against variants that may emerge, according to Ostrov and Dr. Glenn W. Knox, associate professor of surgery at UF College of Medicine-Jacksonville.

Antiviral drugs show promise against omicron variant

More generally, Ostrov said that antiviral drug combinations hold great promise against the coronavirus – in the same way that antivirals have been deployed against HIV and hepatitis C.

“We have to use all the tools in the toolkit to inhibit the replication of this virus,” Ostrov said. “We should vaccinate. We should give booster shots. We should update the vaccines with the sequences of the viruses currently in circulation. And we should be looking at combinations of antiviral drugs. “

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