Where did Omicron come from? Three key theories | Hacker News Reader

Where did Omicron come from? Three key theories

nature.com

38 pointspseudolus38 comments

>Ahead of that report, scientists are investigating three theories. Although researchers have sequenced millions of SARS-CoV-2 genomes, they might simply have missed a series of mutations that eventually led to Omicron. Alternatively, the variant might have evolved mutations in one person, as part of a long-term infection. Or it could have emerged unseen in other animal hosts, such as mice or rats

There is another theory, that Omicron is from a lab leak (or we might say "another" lab leak, but I don't want to jump to conclusions about that).

From what I've read about this, and how Omicron is lacking the signs of natural evolution (specifically having branched off a strangely early strain of COVID and having a suspiciously low count of silent mutations which are expected in natural evolution) they truly have some gall to leave this theory out of their list.

Considering how many animal pool reservoirs there are it seems pretty likely that this variant came from such a reservoir and then hopped back into the human population where we first saw it, South Africa.

Absolutely sounds plausible, but it seems odd to leave out another competing reasonable theory if the intent is to survey the various theories. Certainly they know stuff I don’t, though.

>Absolutely sounds plausible, but it seems odd to leave out another competing reasonable theory if the intent is to survey the various theories.

To be fair, even the article suggests that "whichever idea a researcher favours 'often comes down to gut feeling rather than any sort of principled argument'", that "they are all fair game" and "everyone has their favourite hypothesis."

So there are a lot of reasonable theories out there; at what point do they stop adding other theories to the article without upsetting someone that certain theories were ommitted?

>Certainly they know stuff I don’t, though.

Maybe that's why they had the "gall" to not mention it?

> Maybe that's why they had the "gall" to not mention it?

Maybe. Could be other reasons as well, like circling the wagons to protect their preferred work approaches and their colleagues. It’s not like this isn’t a known phenomenon in virology.

> then hopped back into the human population

How likely is that? Do you think Omicron got very lucky, or are we just very lucky that (if the animal reservoir theory is correct) it only happened with Omicron?

Somehow doing so without the expected number of silent mutations. Off by an order of magnitude. Yeah not sure how that could happen.

> or we might say "another" lab leak, but I don't want to jump to conclusions about that)

I think we're good now. When Newsweek is finally admitting the thing that got 1000s of people vilified it's now part of TheScience(TM)

That's technically a variant of emerging from other hosts.. although I suppose it could have been grown on tissue culture and not animal models.

>having a suspiciously low count of silent mutations which are expected in natural evolution

AIUI the low dN/dS isn't too far out of line with other variants.

Yeah! Didn’t they say it evolved in rats? Hmm.. I wonder where they use rats? Yet nobody wants to say it.

Option 4: lab leak.

Now, I don't know if there's any evidence for/against this. Most people don't understand how these things work. But, if you're going to write an article stating all hypotheses... You best state them all and then procede to arguing for/against each one. Not even acknowledging that omicron could be artificial is poor practice.

We've already been through this once yelling "bats!". I understand people needed comfort at that time, and I agree that talking about a lab leak at the start of the pandemic could cause people to point fingers instead of working together to solve the issue. But, we're not there anymore.

We need to list all theories and rigurously reject each incorrect one.

My understanding from listening to virologists (this week in virology podcast) is that bats or similar animals are still the most likely culprit. Not that lab leak is impossible, but just that animal spillover still seems most likely.

I wonder if there's a group of people who are uniquely motivated to prove, or convince, that COVID is not a lab leak...

It's been pointed out that a couple decades ago, we had this notion "conflict of interest": that someone too close to an issue is a poor choice to report on that issue, because everyone is influenced by their own self-interest. But now we have turned that idea completely on its head! We demand to hear only the opinions of "the experts"; who are in fact the same people who we used to describe as having a conflict of interest!

Virology is far too complicated for non-experts to have any chance of finding a valid answer. We simply need to watch for and be careful of conflicts of interest. Any good expert, especially academic, knows the importance of disclosing conflicts and for bias, well, we can only hope that there are enough diverse experts that they will catch that.

I don't know why you're being downvoted. This issue is at the center of this controversy and many others that have nothing to do with COVID. You don't even have to accept the lab origin hypothesis to recognize the problems.

It is absolutely not most likely. What is likely is that they want to hold safe opinions. Spend even a little bit of time looking into lab leak theory and you’ll see.

Are you a virologist? Because I was relaying information from virologists.

We'll probably never know for sure. But my point was not: "HEY, this was a lab leak!". My point is that it's no longer the time to skip over various theories for fear of impact. Just drop it in there and debunk it as it should be debunked if it's wrong. Skimming over the option without mention suggests the article is cherry picking.

The main problem with the bat hypothesis is that with SARS and MERS, wild animal populations that very closely matched those coronaviruses were quickly found. For example, with SARS it was very quickly identified that there were SARS infected civets in the animal markets SARS spread from, and then scientists went to the places in the wild were these civets were caught and also found SARS infected civets in the wild. The SARS they found in civets in the wild had a 99.8% sequence similarity with human SARS.

If someone was to find coronavirus infected bats with a similarly high sequence similarity to COVID-19 it would take a lot of wind out of the sails of the lab leak hypothesis. But it's been two years now, and that hasn't happened. This doesn't prove or disprove the wild animal hypothesis, but the longer we go without a high sequence similarity match to animals in the wild the less plausible that hypothesis seems.

This report seems to indicate that it took years before the origin of SARS was discovered and that it was still being debated even 10 years later.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747529/

Stupid idea: create artificial virus that spreads faster than natural one but without negative health effects.

Nobody would admit that, but that could potentially be most efficient way to combat a future global pandemic (assuming people keep sabotaging the system by not cooperating).

I dunno, nobody even does this for computer viruses, which have a lot less ethical downside.

The FBI did something similar once: https://nakedsecurity.sophos.com/2021/04/14/fbi-hacks-into-h...

Hard for it to spread faster than a respiratory bug unless it has some symptoms - coughs etc. The version of that idea that is feasible is intentional innoculations, which is basically a live attenuated vaccine.

Well, a virus can be contagious without symptoms. COVID in particular starts spreading before symptoms suggesting you could have respiratory virus without people even being aware they are infected. And we know most people are not even aware they were sick or they had only mild symptoms.

The issue with COVID is that some people are hit hard and a lot of people develop hard to detect complications.

If you could modify the virus to avoid complications and avoid hitting some people very hard, you could have pretty effective way to innoculate population.

The thing you are after is a virus that has same basic spike protein for your immune system to recognize and only enough mechanism to multiply itself.

Yes, COVID replicates in the nose quite a bit pre-symptoms but for it to out-compete the actual very fit active strains, which are turning your upper respiratory tract into a virus factor, it would be difficult to ensure no symptoms. Also, of course you are only a few mutations away at any one time from an unpredictably virulent version; there is no guarantee that the trajectory of viral evolution is toward less virulence.

> The thing you are after is a virus that has same basic spike protein for your immune system to recognize and only enough mechanism to multiply itself.

The version of that that is feasible is a viral vector vaccine e.g., ChAdOx1.

But a virus can't replicate itself. It has to hijack (and kill) the hosts cells in order to replicate.

There are limits to how fast a virus can spread from person to person, and how quickly it can spread through a population. An intentional policy of inoculation is faster. That’s why vaccination works to reduce the incidence of even very contagious diseases like measles. Human logistics can pretty easily outrun the disease.

It’s also easier to control dosage with inoculation, and therefore control for side effects. A naturally reproducing virus, even one that begins benign, can infect different people with varying severity, and change via mutation over time.

That's why I mentioned populations sabotaging the system.

I know this might sound like a radical idea, but vaccinations can only be effective when people are actually getting vaccinated.

It took over a year and a half to come close to vaccinating everyone. Omicron infected the world in something like 2 months. Your statement that "An intentional policy of inoculation is faster" is clearly wrong.

Not saying this is a good idea though.

In the U.S. there have been about 75 million cases reported (this includes Omicron), while about 211 million people have received a full dose of vaccine.

This has nothing to do with your statement on how fast we are able to deploy a vaccine vs infect population with a virus.

Obviously, vaccine is preferable IF people were getting vaccinated.

Also, it is normal for viruses to infect vaccinated people. The point of most vaccines is not to protect any single person, it is to protect the population. This happens by making it difficult for the virus to find a new host.

When enough people are not vaccinated the virus is perfectly "happy" to mostly spread through unvaccinated population and hit the vaccinated population in the process.

Think about this way: imagine a town densely built with wooden houses.

Any fire would quickly consume entire town.

Now imagine replacing 25% of wooden houses with brick houses.

The fire will still consume entire town and it will still consume most or all of the brick houses.

Does this mean that brick houses spread fire as readily as wooden ones?

This is not necessarily the case, it depends on how contagious the disease is.

The UK managed to vaccinate approximately 700-900K people per day during the recent drive.

During the same time period we had approximately 200,000 confirmed cases (via test) per day. The general consensus is that the real number of infections approached 1 million.

It's not impossible to imagine that if the R rate were a bit higher the virus could spread faster.

You do have the issue that it won't reach people locked indoors, but then again vaccination doesn't reach all people either.

Also, if some people elect to be locked indoors they are also probably safe from the original deadly virus.

I mean the crafted virus would have to be significantly more transmissible than the deadly one it tries to outpace.

Seems to be the one of the most efficient ways to combat a virus.

Someone wrote a worm that went around patching the vulnerabilities that another worm was using. This fix made things worse, as this second worm was using more of the network as it spread than the worm it was trying to eradicate.

I'm worried that we'll make a super fast spreading but mild virus, then it'll mutate.

It seems implausible to me that we could engineer a virus that was able to replicate in humans prolifically enough to be spread person to person but not cause any damage.

My understanding is that viruses replicate by hijacking human cells and I don't think those cells survive the ride.

Feeling sick is usually your immune system reacting and killing off the virus. If it didn't react at all, the virus would eventually kill enough cells to kill the host.

The only way to not get sick from a viral infection is for your immune system to react quickly before the virus spreads too much, which would kill the virus before the host had enough of it to start shedding it and become infective to others.

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