Omicron has mutations detected in previous variants, which explains the vaccine’s effectiveness, scientists say

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Omicron only emerged as a variant of concern in November 2021, but all but one of the mutations it contains had been previously described.

Researchers from the Federal University of São Paulo (UNIFESP) in Brazil, supported by FAPESP, attribute this factor to the effectiveness of existing vaccines against the variant, reflected in the relatively low number of severe cases and deaths despite the transmissibility enhanced by Omicron.

The hypothesis is raised in an article by scientists published in the Journal of Medical Virology (JMV) as a letter to the editor in January 2022.

“In light of the data available so far, we believe that existing vaccines are indeed effective against all variants of the virus, all things considered. They can also be effective against any other variant that emerges in the future,” said Ricardo Durães-Carvalho, the paper’s final author. Durães-Carvalho is a researcher affiliated with the faculty of medicine of the university (EPM-UNIFESP) and a fellow of FAPESP.

In October 2021, before the World Health Organization (WHO) recognized the emergence of Omicron, another study conducted by Durães-Carvalho described several mutations shared by a number of variants. An article on the subject is published on the pre-publication platform medRxiv (not yet certified by peer review).

The group analyzed more than 200,000 genomes of SARS-CoV-2 and other human coronaviruses. They found identical mutations in different strains, which could serve as targets for future vaccines.

“Omicron corroborates our study. Of 35 mutations in the variant spike protein [used by SARS-CoV-2 to bind to a specific receptor when infecting human cells], only one was unknown. Twenty-five were in RBD [receptor-binding domain] 15 and RBM [receptor-binding motif] 10, regions of the virus that bind to human cells and are therefore potential targets for neutralizing antibodies,” Durães-Carvalho said.

“This may explain why vaccination has so far been effective even though none of the vaccines on the market have been designed specifically for Omicron. They do not prevent transmission, but they do prevent severe cases and deaths, such as you can see that by comparing this new wave with previous waves that happened before there were vaccines or when a smaller proportion of the population had been fully immunized,” said Robert Andreata-Santos, first author of the Letter to the Editor in JMV Andreata-Santos is a postdoctoral researcher at EPM-UNIFESP with a grant from FAPESP.

The researchers point out that the paper is based on currently available data on Omicron and on the genomes of other variants sequenced so far. As the pandemic progresses and more data is collected, it may be possible to confirm their assumptions.

Shared Mutations

In the study published on the preprint platform in October, Durães-Carvalho and various co-authors analyzed the dynamics of viral dissemination and its evolution over time in Brazil, the United States and India, for the period included between February and August 2021.

The analysis showed an increase in the number of mutation sites in the viral genome, especially in the spike protein, configuring what the researchers call convergent evolution, which means that different variants undergo identical mutations that confer advantages such as evading the host immune system or binding to human cells more efficiently.

“We show that the vast majority of mutations result from this phenomenon,” said Carla Torres Braconi, professor at EPM-UNIFESP and co-principal investigator of the 2021 study.

Braconi is affiliated with a group of researchers working on a project supported by FAPESP and led by Luiz Mário Ramos Janini, professor at EPM-UNIFESP and the other co-author of the VMY item.

Nine directional spike mutation sites were detected before February 2021, followed by 14 between that date and July. With the spread of the Delta variant, more mutations of the spike protein were observed, as well as signs of recombination, one of the factors that can lead to the emergence of new variants.

Recombination is a rearrangement of genetic material, in particular by joining together segments of DNA from different strains. Signs of recombination involving Omicron have also been observed.

In December, researchers analyzed 146 Omicron whole genome sequences from Australia, Austria, Belgium, Botswana, Canada, England, Germany, Hong Kong, Israel, Italy and South Africa. Evidence for recombination was found when the sequences of Beta, Delta, and Omicron were aligned, suggesting that co-circulation of multiple variants may enhance recombination events.

“An increase in virus circulation increases the likelihood that the same individual will be infected by different variants, leading to this exchange of genetic material between variants,” said Danilo Rosa Nunes, first author of the 2021 paper. Nunes doing research for a doctorate. at EPM-UNIFESP.

The researchers now plan to study how the blood serum and plasma of vaccinated patients respond to the different variants with the mutations they have identified. “We want to use serum neutralization tests to find out if these individuals are able to neutralize the different variants, including Omicron,” Braconi said.

Another possible next step would be to use computer models to try to predict what each mutation changes in the spike protein and its ability to invade human cells.

By combining the results of these experiments, researchers could elucidate the effects of these mutations shared by several variants, so that they can serve as targets for even more effective future vaccines.

As researchers acknowledge, it is not yet possible to be sure that currently available vaccines will work against future new strains of SARS-CoV-2, so it remains essential to maintain social distancing, wear face coverings effective faces and complete the course of vaccination in order to slow down the process of viral evolution and minimize the risk of new mutations promoting immune evasion.

Scientists Unveil World’s First Molecular-Level Analysis of Omicron Spike Protein

More information:
Robert Andreata‐Santos et al, From Alpha to Omicron variants of SARS‐CoV‐2: What can their evolutionary signatures tell us?, Journal of Medical Virology (2022). DOI: 10.1002/jmv.27555

Danilo Rosa Nunes et al, Deep phylogenetics-based cluster analysis reveals novel and shared mutations in SARS-CoV-2 variants following directional and convergent evolution, medRxiv (2021). DOI: 10.1101/2021.10.14.21264474

Quote: Omicron has mutations detected in previous variants, which explains the effectiveness of the vaccine, according to scientists (2022, February 8) retrieved on February 9, 2022 from -mutations-previous-variants-vaccine .html

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Sara H. Byrd