Recombination in Omicron?

I’ve been curious what the forum thinks about Omicron (besides the fact the name sounds like a Transformer) but I hadn’t come across any information that prompted me to take the time to make a post.

But now I have.

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.

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, said Venky Soundararajan of Cambridge, Massachusetts-based data analytics firm nference, who led the study posted on Thursday on the website OSF Preprints.

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, Soundararajan said.

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 people in whom the recombination that added this ubiquitous set of genes to Omicron might have occurred, Soundararajan said.

Curious what your thoughts are about this or anything related to the omicron variant.


I don’t see anything particularly strange about that hypothesis as SARS-Cov2 is already known to be a recombination-prone virus, with the spike protein being a particularly frequent hotspot (for obvious adaptive reasons).
Recombination between viruses during co-infection is not all that unusual either, and co-infection by multiple respiratory viruses is totally normal. So my two cents here is basically “quite plausible”.


It is an interesting variant mainly due to the numerous mutations it has relative to other variants of concern or interest. It is also likely that these unique insertion “ins214EPE”, arose via recombination following coinfection with another coronavirus or infection of a human/other animal host as the preprint paper, which the Reuter’s article cites, suggests. Future analyses should throw more light but for now its mostly down to speculating.

I found this for @colewd from the omicron preprint paper cited above. Study the Venn diagram and tell me if the members listed had separate origins? Explain how you reached your conclusion.


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.


Reminds you of the furin cleavage site which is also unique to SARS-CoV-2, right? At least the lab leak proponents have gotten a demonstration of nature giving unique insertions to specific lineages such as the one in omicron.


speaking of snippets:
Cells in the lungs and in the gastrointestinal system can harbor SARS-CoV-2 and common-cold coronaviruses simultaneously, according to earlier studies. 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.” -

I tried hard to take a deep dive and understand this sort of science and I got to be honest its like drowning.
All I can say is I hope everyone catches this virus if its mild. I would hope it would be like a natural vaccine causing everyone to develop immunity without dying in the process. Not dying in the process is a plus.
Wasn’t it small pox where they gave people cow pox making a mark on your arm with a bunch of tiny needles and by doing so infected you with a live virus?
Maybe this Omicron will be a wonderful thing rather than a fearful thing. Maybe everyone will want to get that sort of shot in the arm, just on the surface and poof !

Sure, catching and surviving infection with SARS-CoV-2 will confer immunity post-recovery, but that’s a more dangerous route. The safest approach will be to get vaccinated with one of the available effective vaccines. The omicron variant seems to be the most adept at evading the immune system but getting vaccinated at least twice appears to better protect against it. Bottom line: get vaccinated.

Stop fooling around. Many more millions than the current death tally will perish if health authorities took your advice.

SARS-CoV-2 is not the cowpox virus. The former is a lot more dangerous than the latter.

Preliminary data suggests the omicron variant causes milder infection, but there isn’t any anything available from which to draw more certain conclusions. Time and research will tell. In any case, getting vaccinated still remains one of the best ways of reducing one’s risk of falling severely sick due to Covid-19 caused by any SARS-CoV-2 variants of concern.


Overall, BA.1 and BA.2 only share 30 of their 49 and 51 amino acid substitutions. The total number of substitutions and the divergence between the two, even allowing for multiple recombination events, takes a good deal of time, likely extending back well into 2020. Where and how this occurred without discovery for all that time is a serious issue. Unidentified sources for a substantial stretch of sequence clearly indicate that there is a pool of SARS-CoV-2 variant sequences that remain undetected.

The discomfort in discovering an entirely new and widely divergent VOC, with two very different recombinant forms, is very real. Beyond the medical impact of the Omicron variants, there is every reason to believe that this will happen yet again, as it did for Delta and now with Omicron.

Hmm…undetected because they caused mild illness?


Again, I hope the lab leak proponents are seeing a realtime demonstration of how beneficial insertions from “unidentified sources” are finding their way into SARS-CoV-2 in a purely natural fashion. So let’s remind ourselves of the only (and now very weak) evidence for a lab leak: the outbreak was first noted in Wuhan where the WIV is located.

Its more likely due to non-coverage by genomic surveillance. South Africa detected the omicron variant because they focused genome sequencing efforts on the Gauteng region which was experiencing a spike in new cases at the time.

I also share the author’s worries on the high evolvability of SARS-CoV-2. We are going to be in a long fight. The emergence of the omicron variant shows that vaccines alone will not solve our problem. Vaccine usage must be complemented with other measures of disease prevention and control. Sadly we live in a time when misinformation about Covid-19 runs rife, leading to lax behaviour and that will continue to provide time for the virus to adapt to our pharmaceutical strategies to control it. As I said before, it’s gonna be a long fight.

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