BREAKING! Preprint Study Suggest That Omicron Might Be A Recombined Virus Containing Bits Of Genetic Material From The Common-Cold Virus!

A new preprint study by researchers from nference labs in Bengaluru-India, Massachusetts-USA and Toronto-Canada suggest that the Omicron variant may be a recombined virus containing bits of genetic material from the common-cold virus.

 
The study team hypothesizes that the insertion mutation ins214EPE that has not been previously observed in any other SARS-CoV-2 lineage other than Omicron might have originated as a result of a recombination event involving the SARS-CoV-2 coronavirus and another common human coronavirus that causes the common cold.
 
The study findings are also alarming as it also implies that recombined events involving the SARS-CoV-2 virus and other viruses are easily to achieve and might point to other possible recombined strains emerging especially in human hosts inflicted with other viruses.
 
The study findings were published on a reprint server and are currently being peer reviewed. https://osf.io/f7txy/
 
The sudden emergence of a heavily mutated SARS-CoV-2 variant (B.1.1.529, Omicron) and it’s spread to 6 continents within a week of initial discovery has set off a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its shared or distinctive clinical phenotypes with other SARS-CoV-2 variants.
 
The study team compared the mutations of Omicron with prior variants of concern (Alpha, Beta, Gamma, Delta), variants of interest (Lambda, Mu, Eta, Iota and Kappa), and all 1523 SARS-CoV-2 lineages constituting 5.4 million SARS-CoV-2 genomes. Omicron’s Spike protein has 26 amino acid mutations (23 substitutions, two deletions and one insertion) that are distinct compared to other variants of concern.
 
Importantly whereas most of the substitution and deletion mutations have appeared in previous SARS-CoV-2 lineages, the insertion mutation (ins214EPE) has not been previously observed in any SARS-CoV-2 lineage other than Omicron.
 
The nucleotide sequence encoding for ins214EPE could have been acquired by template switching involving the genomes of other viruses that infect the same host cells as SARS-CoV-2 or the human transcriptome of host cells infected with SARS-CoV-2.
 
There have been recent clinical reports of co-infections in COVID-19 patients with seasonal coronaviruses (e.g. HCoV-229E). https://pubmed.ncbi.nlm.nih.gov/32293646/
 
Furthermore, single cell RNA-sequencing data showing co-expression of the SARS-CoV-2 and HCoV-229E entry receptors (ACE2 and ANPEP) in respiratory and gastrointestinal cells, and HCoV genomes harboring sequences homologous to the nucleotide sequence that encodes ins214EPE, it is plausible that the Omicron insertion could have evolved in a co-
infected individual.
 
Urgently, there is a need to understand the function of the Omicron insertion and whether human host cells are being exploited by SARS-CoV-2 as an ‘evolutionary sandbox’ for host-virus and inter-viral genomic interplay.
 
In our earlier Omicron updates, Thailand Medical News had already warned that the Omicron variant is likely a recombinant strain. ;https://www.thailandmedical.news/news/omega-omicron-variant-updates-variant-now-confirmed-in-13-countries-not-including-countries-in-the-african-continent-with-suspected-cases-now-in-anot">https://www.thailandmedical.news/news/omega-omicron-variant-updates-variant-now-confirmed-in-13-countries-not-including-countries-in-the-african-continent-with-suspected-cases-now-in-anot
 
The study findings suggest that Omicron variant of the virus that causes COVID-19 likely acquired at least one of its mutations by picking up a snippet of genetic material from another virus, possibly one that causes the common cold and was present in the same infected cells of the human host.
 
According to the study team, this genetic sequence does not appear in any earlier versions of the coronavirus, called SARS-CoV-2, but is ubiquitous in many other viruses including those that cause the common cold, and also in the human genome, researchers said.
 
Dr Venky Soundararajan of Cambridge, Massachusetts-based data analytics firm nference, who led the study posted on Thursday on the website OSF Preprints told Thailand Medical News, “By inserting this particular snippet into itself, Omicron might be making itself look ‘more human,’ which would help it evade attack by the human immune system.”
 
He added, “Hence this could also imply that the virus transmits more easily, while only causing mild or asymptomatic disease. Scientists do not yet know whether Omicron is more infectious than other variants, whether it causes more severe disease or whether it will overtake Delta as the most prevalent variant. It may take several weeks to get answers to these questions.”
 
The cells in the lungs and in the gastrointestinal system can harbor SARS-CoV-2 and common-cold coronaviruses simultaneously, according to earlier studies.
 
Alarmingly, such co-infection sets the scene for viral recombination, a process in which two different viruses in the same host cell interact while making copies of themselves, generating new copies that have some genetic material from both "parents."
 
According to the study team, this new mutation could have first occurred in a person infected with both pathogens when a version of SARS-CoV-2 picked up the genetic sequence from the other virus.
 
It was also noted that the same genetic sequence appears many times in one of the coronaviruses that causes colds in people known as HCoV-229E and in the human immunodeficiency virus (HIV) that causes AIDS.
 
The study tea also warned that South Africa, where Omicron was first identified, has the world's highest rate of HIV, which weakens the immune system and increases a person's vulnerability to infections with common-cold viruses and other pathogens. In that part of the world, there are many human candidates in whom the recombination that added this ubiquitous set of genes to Omicron might have occurred.
 
Dr Soundararajan added, "We probably missed many generations of recombinations that occurred over time and that led to the emergence of Omicron.”
 
Further detailed research is needed to confirm the origins of Omicron's mutations and their effects on function and transmissibility. There are competing hypotheses that the latest variant might have spent some time evolving in an animal host.
 
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