Increased Infectivity Drives COVID Evolution – Mutations That Allow the Virus To Escape Vaccines Become Dominant

DNA Chop Illustration

First announced by the World Health Organization on November 26, 2021, the SARS-CoV-2 omicron variant spread rapidly around the world, becoming the dominant variant in the U.S. and elsewhere. Now, researchers report in ACS Infectious Diseases and the Journal of Chemical Information and Modeling that omicron and other variants are evolving increased infectivity and antibody escape, according to an artificial intelligence (AI) model. Therefore, new vaccines and antibody therapies are desperately needed, the researchers say.

The team found that mutations to strengthen infectivity are the driving force for viral evolution, whereas in highly vaccinated populations, mutations that allow the virus to escape vaccines become dominant.

Understanding how SARS-CoV-2 evolves is essential to predicting vaccine breakthrough and designing mutation-proof vaccines and monoclonal antibody treatments. In a recent study in ACS Infectious Diseases, Guo-Wei Wei and colleagues analyzed almost 1.5 million SARS-CoV-2 genome sequences taken from people with COVID-19. They identified 683 unique mutations in the receptor binding domain (RBD), the region of the SARS-CoV-2 spike protein that attaches to the human ACE2 receptor on the surface of human cells.

Then, they used an AI model to predict how these mutations affect binding strength of the RBD to ACE2 and to 130 antibody structures, including several monoclonal antibodies used as therapies. The team found that mutations to strengthen infectivity are the driving force for viral evolution, whereas in highly vaccinated populations, mutations that allow the virus to escape vaccines become dominant. The researchers also predicted that certain combinations of mutations have a high likelihood of massive spread.

In another study in the Journal of Chemical Information and Modeling, Wei and colleagues took a deep dive into the omicron variant’s infectivity, vaccine breakthrough and antibody resistance. They used their AI model to analyze how the variant’s unusually high number of mutations on the spike protein affect RBD binding to ACE2 and antibodies. Their results indicated that omicron is over 10 times more infectious than the original coronavirus and 2.8 times more infectious than the delta variant. In addition, omicron is 14 times more likely than delta to escape current vaccines, and it is predicted to compromise the efficacy of several monoclonal antibody therapies. Many of these predictions have been verified by emerging experimental results, stressing the importance of developing a new generation of vaccines and monoclonal antibodies that won’t be easily affected by viral mutations, the researchers say.

References:

“Emerging Vaccine-Breakthrough SARS-CoV-2 Variants” by Rui Wang, Jiahui Chen, Yuta Hozumi, Changchuan Yin and Guo-Wei Wei, 8 February 2022, ACS Infectious Diseases.
DOI: 10.1021/acsinfecdis.1c00557

“Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance” by Jiahui Chen, Rui Wang, Nancy Benovich Gilby and Guo-Wei Wei, 6 January 2022, Journal of Chemical Information and Modeling.
DOI: 10.1021/acs.jcim.1c01451

The authors acknowledge funding from the National Institutes of Health, the National Science Foundation, NASA, the Michigan Economic Development Corporation, the Michigan State University Foundation, Bristol-Myers Squibb and Pfizer.

2 Comments on "Increased Infectivity Drives COVID Evolution – Mutations That Allow the Virus To Escape Vaccines Become Dominant"

  1. Howard Jeffrey Bender, Ph.D. | February 20, 2022 at 6:20 pm | Reply

    All the coronaviruses and all their variants have different protein spikes, with Delta and Omicron having spikes that are more efficient at getting around the vaccines. But the real problem is in the virus itself, not its protein shell, and why the most dangerous (MERS, SARS, and Covid-19) are so infectious. My independent research has found multiple one-in-a-million nucleotide sequence matches between all the coronaviruses and the human genome. Those sequences are the same as some of the loops of human tRNA. Using those loops and their amino acid code matches, viruses may be able to fool the nucleus membrane in cells to allow the virus to enter and associate with the human DNA, creating more opportunities for further infection. Our immune system may be compromised and may no longer be able to stop the virus and other diseases from attacking organs throughout the body. Vaccines that attack the virus protein shells while ignoring their contents are doomed to failure from the Darwin effect, but recognizing these loops suggests a possible approach to successful coronavirus vaccines. Only the infection process is considered in my work, not the innate virulence of the virus. For more info, check out this YouTube, Coronavirus – Using Your DNA Against You. https://www.youtube.com/watch?v=EeQcXlXwhUQ

  2. The artist’s rendition of the DNA molecule in this SciTech article is a left-handed helix. There are other obvious inaccuracies as well.

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