Absence of evidence is not evidence of absence, yes. But take another look at the phylogenetic tree. Those are huge gaps. See also this article describing how good South Africa is at spotting and sequencing variants."The reality is that southern Africa is a top international powerhouse of COVID-19 surveillance." https://www.businessinsider.com/how-southern-africa-detected...

The hypothesis is that it could have originated in a different country and was only identified after it arrived in South Africa.

Yes, this is true. But it's also somewhat narrow.

Consider this: days after the successful sequencing of Omicron, similar cases were reported in dozens of countries, having arrived there just before or just after the announcement. We know, that it's "just before," because references are being kept and re-analyzed in those cases, and none of the countries with the resources for genomic surveillance has any data on earlier strains in the phylogenic tree.

It is simply very unlikely (not impossible, but if you're in London and hear hoof beats, it's probably a horse, not a zebra), that Omicron could have developed over 33 N and a superset of S mutations without ever popping up in any surveillance. South Africa, especially, is a key surveillance player. They're often much more granular than even European key players like the UK, Germany, or France.

A strain with this level of infectivity doesn't linger in one hospital. From the looks of the genome, that part (infectivity) would have developed before immune evasion. Having a highly infective strain evolve would ring alarm bells in labs the world around.

I guess it's pretty non debatable that Omicron started its World Dominance Tour in October or November 2021. To get there, it had to undergo a massive sequence of events making it as far removed from α.7 as it is. So we can state, with some certainty, that it evolved in isolation and broke free shortly before being discovered.

If we now consider the possible origins, wild zoonotic, single origin immune compromised, or accidental leak from research, the latter doesn't sound so improbable anymore. Again, horse, not zebra.

But, the point is it was growling so fast you wouldn't expect it to show up in other places until the "knee" of the exponential showed up there as well. SA being just a couple of weeks ahead is a lifetime for Omicron.

100% agreed. Again, this is a possibility, not a certainty. But I'd be loath to dismiss it, just as I am not willing to dismiss a reservoir origin. In the end, the author does make a good point: we need mandatory disclosures of GoF research and a general ban on GoF financing of labs who aren't working in full disclosure mode.

Ideally, we should not have this discussion because the GoF leak is impossible. Sadly, as secretive as this research is, as much money as we funnel into labs in China and Russia, and as reluctant as oversight authorities (such as the WHO) are to even consider leaks, the best response would be a general ban on GoF and GoF financing.

There is a belief that Omicron originated in South Africa, but some growing evidence that it was present elsewhere earlier, but only either detected or first identified early on in South Africa.

This is the first link in a search for same:

https://www.cbsnews.com/news/omicron-variant-covid-in-europe...

Either way, it may be wrong to assume SA is point of origin, so any follow-on assumptions may be comparably flawed.

> absence of samples showing the step-by-step evolution

Sounds much like the "missing link" gotcha that creationists loved to deploy.

And even if they did do genomic analysis - it's entirely plausible the results are sitting in a hospital database somewhere instead of uploaded to the international gene surveillance repository.

Plausible, yes. If the data exists, it should be made public. The article still mostly just makes a hypothesis and makes the argument that this is something that should be seriously investigated, not that the author has determined without a doubt that this is a lab leak.

Sure - but what are the chances that whichever hospitals did the sequencing even know they're in possession of the intermediate data? The OPs' method of "just asking questions" is really bad science and feels a whole lot like the God of the Gaps argument style that Creationists are so fond of using.

I'm not sure the best way to judge the quality of a scientific argument is whether it 'feels like good science.'

While the author is obviously only scratching the surface in an article targetted at non-scientists, the several PhDs he cites make decent arguments that are based on a little more than feelings. It would probably be more in line with the ideal of 'good science' to actually investigate the possibilities presented than dismiss them from emotional associations.

It is a worrying trend that the way science feels is increasingly more important than the actual evidence (or lack thereof). One could even describe the current attitude towards science outside of scientitific institutions as religious.

And the reason not all of these spread fast is obviously that one mutation (or combination) impacts the spread rate more than the 30+other mutations in isolation... Although after enough conversations I've found this too needs spelling out in plain English...

Yeah but since spring 2020? This variant slept without getting replaced by other more contagious variants? That doesn't seem likely.

The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa?

Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps.

> The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa?

You're pointing out distinctions that do not make any relevant or substantial differences to the argument.

> Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps.

With lack of information, ideas that have the less assumptions and concepts tend to be true than their counterparts who require many possible sub-hypotheses and concepts. GoF happen and lab leaks happen and the genetic histogram and the genes makes make this hypothesis the more likely one. The opposite require many hypothetical actors (mouses, immunosuppressed patients, back and forth between geographically distant places and all the combinations thereof) to account for it "hiding" since spring 2020.

> especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons.

Nobody blamed nobody here. GoF research happens everywhere.

> Give the science time and we might start to fill in the gaps.

Science is not beholden to your worldview. Filling the gaps is part of the scientific method, by the way.

All I'm saying is that my bias is towards this virus being a natural phenomenon and I think waiting for the full context will settle the case. Jumping to conclusions on the basis of flimsy evidence mainly serves political agendas. We simply will not know for a long time, months or years, where Omicron came from and that's uncomfortable, but we have to sit with that.

If you DO want to get conspiratorial, you can watch this 2001 Bush administration pandemic simulation where China blames the US for a smallpox lab leak. It's pretty amusing to me to watch the US administration astounded by their luck of COVID-19 first being identified in China try to flip the script on their simulated exercise. My feeling is this Omicron theory is trying to breathe life back into the original lab leak theory by proxy.

https://www.youtube.com/watch?v=we7Map5Pho0

I don’t understand how natural origin is your “bias” while everyone else is “jumping to conclusions”. There’s a lack of conclusive evidence for either scenario. And politics aside, SARS has leaked before resulting in deaths… no conspiracy required!

That's true Delta leaked in Taiwan, but that was a preexisting natural strain. Smallpox's last fatality also was a lab leak. However, most gain of function experiments use test harasses that can't infect humans or can't replicate. It's not impossible, but it's hard to have any conclusion at all at this early date with very little evidence.

The virus is infecting so many people and changes so rapidly that a natural explanation will not be surprising in the least. New variants have been expected. I think people are surprised at how bad the new variants have been, but anyone following the scientific literature wouldn't be taken completely off guard.

You seem to have caught some memes which don't make you see things rationally.

> The opposite require many hypothetical actors (mouses, immunosuppressed patients, back and forth between geographically distant places and all the combinations thereof) to account for it "hiding" since spring 2020

If you ever implied that closeness of outbreak of the Wuhan variant to the Wuhan lab the same should make you incredibly suspicious about this being a lab leak, since there is such lab nearby. So it would require an actor in another country to "breed" this variant and import it into South Africa/have agents spread it world wide and someone funding and green lighting what would a be case of international bio terrorism or even bio warfare.

As for accounting for those factors. Africa is an incredible diverse places with Nomads and hyper dense slums, with untreated large scale AIDS and healthcare systems as South Africa has and also a poorly understood and explored flora and fauna.

Does it seem that implausible that some combination of immuno compromised tribes/rural human and animals caught the old variant and didn't interact with the new variants from western civilization for less than two years? I don't think so.

As for the low number of silent mutations. I can not imagine how the lab leak theory would account for that, if it was designed why would there a low number of silent mutations and not an average number or none and if it was due to GoF why would a lab environment have less silent mutations then a "natural" one?

AFAIK we have almost no data on variants in some African capitals let alone people in rural/tribal areas or surveillance of animals. Maybe along its evolutionary it was a variant that has an advantage in sparsely populated areas so we didn't notice a large part of its history because it wasn't competitive in cities with other variants.

There are many possible explanations but the lack of lab is kinda blow for a lab leak theory and your political goal of less GoF-Research is only compatible with a lab leak and not any other form of lab caused (philanthropist/evil government developing and releasing this variant) explanation.

Such gaps in phylogenetic trees actually happen all the time.

Gaps can appear if there are (1) missing data or (2) a big change such as a transposition or elision event. Neither are the case for our coronavirus data. For (1) we have a good random sampling of the population as a whole so it is exceedingly unlikely we would not see intermediate changes and for (2) the overall structure has not changed dramatically--we are looking at the accumulation of point mutations over the course of 18 months. So while gaps can and do occur, we would not expect this to occur naturally in the situation we are observing today with coronavirus.

Gaps also appear because evolution is not a smooth process, and once in a while a large number of mutations are selected for. We see the same type of pattern even in vitro. Moreover, mutations are not always well described by gaussian processes: the rate of mutation can be seen as having a fat tailed distribution.

That's not the way it works.

Mutations has to be incremental because most mutations are not viable or doesn't provide any reproductive gain. Having multiple functional mutations all at once happening in a very short amount of time and being naturally selected in big enough number of infections is very very improbable.

> mutations are not always well described by gaussian processes: the rate of mutation can be seen as having a fat tailed distribution

I'm sorry if I have to be blunt, but you have no idea of what you are talking about.

I’m a biochemist.

Other viruses are not scanned and studied for other variants like Covid-19 is and Omicron is the only outlier by a large margin.

Sure and if it had arisen in Europe then those questions would have to be asked. But it's a safe assumption that very little analysis is happening in southern central Africa. It doesn't seem that outrageous that a parallel line has been percolating there for quite some time and only recently gained a mutation or two that allowed it to shoot to stratospheric levels.

Even in Europe I wouldn't find it all that difficult to believe. We see the same sort of pattern, qualitatively speaking, even in well controlled in vitro experiments.