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Updated December 4th, 2021 at 14:36 IST

Omicron COVID-19 variant likely picked up genetic material of common cold virus: Study

Spike protein sequences from Omicron and Wuhan SARS-CoV- 2 sequences show two different insertions and former seems to be a recombination of common cold virus.

Reported by: Zaini Majeed
Omicron
Image: AP | Image:self
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Omicron variant B.1.1.529 of the novel coronavirus SARS-CoV-2’s lineage may have likely acquired at least one of its mutations by picking the genetic material from the virus that causes the common cold known as HCoV-229E, and in the human immunodeficiency virus (HIV) that causes AIDS, researchers at the Cambridge, Massachusetts-based data analytics firm have found. The genetic sequence of Omicron common with the human genome and virus that cause common cold does not appear in any earlier versions of the coronavirus that spread in 2020, said the study published on the website OSF Preprints.

According to the scientists it became increasingly important to study the characterization of the mutational profile of Omicron as it spread to at least 6 continents within a week and raised global public health alarm. South Africa has the highest rate of HIV where common cold viruses and other pathogens can interact, and such recombination resulting in a ubiquitous set of genes as seen in Omicron is possible. The mutational burden of Omicron is higher in the Spike protein, scientists have found. “This gives rise to the plausibility of such cells in co-infected individuals being exploited as sites of genomic interplay between different viruses,” the study purports. 

Profile of Omicron necessary first step in interpreting variant's transmissibility 

It is necessary to interpret its shared or distinctive clinical phenotypes with other SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Lambda, Mu, Eta, Iota, and Kappa) researchers said, adding that the genome of Omicron is found to be distinct compared to other variants of concern (VOC). Omicron’s Spike protein has 26 amino acid mutations, as per the scientists, that may have been acquired by template switching involving the genomes of other viruses. 

“Thoroughly characterizing the mutational profile of Omicron is the necessary first step to begin interpreting its shared or distinctive clinical phenotypes, sensitivity or resistance to existing vaccines,” said the scientists in the study published on website OSF Preprints.

Spike protein sequences from Omicron and the Wuhan SARS-CoV- 2 sequences show two different insertions. By inserting this particular common cold virus snippet into itself, Omicron might be making itself look "more human," which would help it evade attack by the human immune system, said scientist Venky Soundararajan, as quoted by OSF Preprints. "We probably missed many generations of recombinations" that occurred over time and that led to the emergence of Omicron, Soundararajan added. Researchers however say that further studies will be necessary to understand whether this insertion may help SARS-CoV-2 escape T-cell immunity that fights off the infection. 

This novel insertion mutation implies that the virus might spread more easily, and may cause mild or asymptomatic COVID-19 disease. However, the virulence of the Omicron is not yet known and more research is needed. A statistical analysis done by South African scientists appears to suggest that the Omicron variant might overtake delta and become the ‘most dominant variant’ by 2022.  

"You have to vaccinate to reduce the odds that other people, who are immunocompromised, will encounter the SARS-CoV-2 virus," researcher Soundararajan said in the study.

Earlier studies have also shown that cells in the lungs and in the gastrointestinal system might harbour SARS-CoV-2 and common-cold coronaviruses simultaneously. The viral recombination of Omicron is a result of the process in which two different viruses, in this case, coronavirus’ variant B.1.1.529 and common cold virus in the same host cell interact and make copies of themselves giving rise to a genetic material that hosts cells from both the parents. South Africa, the country where Omicron was first identified, has the world's highest rate of HIV that weakens the immune system and hence elevates the chances of infections with common-cold viruses and other pathogens at the time time. 

Image: AP

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Published December 4th, 2021 at 14:36 IST

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