Omicron Origins—Omicron Optimism

The genome of Omicron has taken the community of public health scientists by surprise. Not only are there a large number of mutations, but some of these mutations have not been observed in the many previous genome analyses, thousands of which are being conducted in labs around the world. Among scientists, there are five competing explanations for this situation.

  1. The virus circulated and mutated in a region of the world where there are few scientific labs that might have reported its genome in intermediate states.
  2. A single immune-compromised patient might have harbored the virus for an extended period of “long COVID”, during which the virus mutated while replicating within him.
  3. The virus might have jumped to a mouse host and spread from mouse to mouse, in an environment where different mutations would be favored. The heavily mutated virus must then have jumped back to humans.
  4. The virus leaked from, or was released from, a laboratory in Durban, where experimenters were genetically manipulating the virus.
  5. Vaccinated populations have put intense selection pressure on the virus to evade the vaccine by mutating its spike protein, which is the only part of the virus to which vaccinated individuals have immunity.

As with everything COVID, we’ve seen significant censorship, both in the mainstream press and the medical journals. Three of these theories have been discussed out in the open. But #4 has been relegated to the fringes because scientists are still gunshy about discussing engineered bioweapons; and #5 has similarly been sidelined because it is politically incorrect to say anything bad about vaccines. The irony here is that evolution in vaccinated populations may have led to the emergence of a version of COVID that everyone can live with (see below).

First theory: Omicron was hiding out in darkest Africa

Christian Drosten, a virologist at Charité University Hospital in Berlin, has proposed that the virus evolved its prodigious ability to spread rapidly while hiding out in regions of Botswana and SW Africa. This region of the world has few virology laboratories that would have reported intermediate versions of the virus. In both Botswana and South Africa, just under half the population has been vaccinated (according to Reuters). This might explain the many mutations in the spike protein and Omicron’s ability to infect the vaccinated. (From a news article by Kai Kupferschmidt, published in Science Magazine last month.)

Second theory: Omicron gestated in the slow cooker of a single patient with long COVID

From the same Science article:

Omicron clearly did not develop out of one of the earlier variants of concern, such as Alpha or Delta. Instead, it appears to have evolved in parallel—and in the dark. Omicron is so different from the millions of SARS-CoV-2 genomes that have been shared publicly that pinpointing its closest relative is difficult, says Emma Hodcroft, a virologist at the University of Bern. It likely diverged early from other strains, she says. “I would say it goes back to mid-2020.” That raises the question of where Omicron’s predecessors lurked for more than a year…


Andrew Rambaut of the University of Edinburgh can’t see how the virus could have stayed hidden in a group of people for so long. “I’m not sure there’s really anywhere in the world that is isolated enough for this sort of virus to transmit for that length of time without it emerging in various places,” he says. Instead, Rambaut and others propose the virus most likely developed in a chronically infected COVID-19 patient, likely someone whose immune response was impaired by another illness or a drug. When Alpha was first discovered in late 2020, that variant also appeared to have acquired numerous mutations all at once, leading researchers to postulate a chronic infection. The idea is bolstered by sequencing of SARS-CoV-2 samples from some chronically infected patients.

Third theory: Omicron jumped to a mouse, then back to humans

This study from the Chinese Academy of Sciences (Beijing) cites genetic evidence from the Omicron genome to support the thesis that the virus jumped to mice, then back to humans. The frequency of different kinds of mutations (different amino acid substitutions) is different within the mouse physiology compared to the human physiology. These authors find that the types of mutations found in Omicron are more characteristic of mouse than human physiology.

A creative idea! but perhaps that it is its main weakness: 1) There are a huge number of mutations of every kind when the virus replicates, either in a mouse or a human. The ones that stick are the ones that are adaptive, i.e., the ones that help the virus to replicate or spread more effectively to another host. This is not addressed in the Chinese study. 2) A great many adaptations would be needed for a virus to effectively infect a mouse population. These would have to be established to accomplish the jump into the mouse population, then undone for the virus to jump back to humans. Still, there is some precedent in the known ability of SARS-CoV-2 to infect a herd of white-tailed deer. 3) Both these objections could be obviated if the virus were deliberately passaged through humanized mice in a laboratory.

Fourth theory: Omicron escaped from a gain-of-function laboratory

In April, a laboratory in Durban, South Africa published this paper, describing their genetic modification of the SARS-CoV-2 virus  In November, the Omicron variant was first discovered in the area of Johannesburg / Pretoria, about 600 km away from Durban. Were the two events related? The 501Y mutation which is the subject of the Durban study is present in the Omicron variant, but many of the other mutations listed in the Durban ms are missing from the Omicron genome.

Many scientists are convinced, based on its genetic signature, that the original Alpha strain of COVID was engineered in a bioweapons laboratory. Normally, the spike protein of a virus is just evolved to latch firmly onto a host cell. But in the case of the COVID virus, the spike protein does a lot of nasty things as well, including blood clots and damage to nerves and arteries. The spike protein seems on its face to be designed for toxicity.

Ironically, the early Nature Medicine article that tried to put the lab-origin theory to rest claimed only that the spike protein was not fully optimized to bind to human cells, QED. (When Dr Fauci’s emails were FOIAed, we learned that Fauci himself had commissioned this article, and that its authors included suspects for channeling NIAID funding of bioweapons research to China.) So now it appears that the spike protein was designed as a compromise between optimal infectivity and optimal toxicity.

If Omicron is engineered, then perhaps it has been designed as an antidote rather than a weapon. Omicron seems to spread so fast that it has rapidly displaced Delta in the African population where it originated, and yet it is causing remarkably mild illness and few if any deaths.

All of these four stories have adherents and there is logic behind them. Any may turn out to be correct. But there is a simpler hypothesis, which involves no extra assumptions, but relies only on the principles of natural selection. The main weakness of this hypothesis is that the number of mutations in Omicron and the rate of evolution seem to be anomalously high; but perhaps it is being ignored because of publishing taboos.

Fifth theory: Omicron evolved to evade the vaccine

Viruses always evolve toward higher transmission rates and lower fatality rates. The higher transmission rate is what allows it to out-compete other variants and spread through the population. The lower fatality rate is less obvious—viruses can spread better if the host is feeling well and circulating in the population; and if the host dies, the virus dies with him.

The Omicron variant seems to be an unusually large step in both directions. This is the reason that most epidemiologists are looking for a specialized explanation for its origin. A more mundane explanation is the pressure to adapt that has been created in vaccinated populations. Communities with high vaccination rates have created an ideal environment for the Corona virus to mutate. All parts of the virus are mutating all the time, but not all help the virus to be successful. If the spike protein mutates, this can throw the vaccinated immune system off the scent, because vaccination produces a highly focused immune response to the (Wuhan original) spike protein.Dr Geert vanden Bossche prominently predicted that this would happen early in the distribution of the COVID vaccines.

The Omicron variant demonstrates that vanden Bossche got this exactly right. It includes 37 new mutations in the area of the spike protein, and Omicron has largely evaded the vaccines. Vaccinated people are as likely or more likely to get Omicron compared to unvaccinated.

Vanden Bossche anticipated tragic consequences for all of humanity, but this does not seem to be what is happening. Rather, this cloud has a silver lining. As mentioned above, the spike protein is the toxic payload of the COVID virus, responsible for most of the damage that the virus does to blood vessels and neurons. (It appears that the spike protein was engineered for this purpose in a gain-of-function experiment.) As the spike protein has mutated, it has become less toxic. As a result, the Omicron variant is far milder than original Wuhan COVID. The Omicron mortality rate, according to UK figures, is only 1/10 as high. (The UK has had 10,866 Omicron cases and 14 deaths for a mortality rate of 0.0013. For comparison, the 2-year total of COVID deaths and cases in the UK was 148,000/11,800,000 = 0.013, almost exactly ten times higher.)

Unknowns and the Future

We know historically that the natural immunity of a recovered patient provides the best immunity we know.  People (mostly Chinese) who recovered from SARS eighteen years ago seem to have full immunity to COVID, though the two viruses are substantially different. This should mean that Omicron sweeps through the population, and many, many people will recover after a mild and abbreviated illness, with permanent immunity to all forms of COVID. This would be the dawn of herd immunity and the end of COVID. The question is whether recovering from Omicron will provide full immunity to future variants. We see that recovery from past variants does not provide sufficient immunity to protect against Omicron. Is this because Omicron is an exception to the general rule about robust immunity in recovered patients? Or is it an artifact of faulty testing, people who have been told that they recovered from COVID when they really had the flu? Or is it an artifact of vaccination after recovery, which seems to be counter-productive, narrowing some of natures’s robust, acquired immunity?

Meanwhile, CDC press releases and mainstream reports are using Omicron as a booster for the fear-porn industry, citing exploding “case” statistics while ignoring the simultaneous drop in “death” statistics. Pfizer is developing a new mRNA vaccine for Omicron, which they plan to release in March. Will they double down on their tragic mistake in basing the vaccine on the toxic spike protein? Or will the new vaccine be derived from a less dangerous part of the virus?  We have reason to hope that Omicron will spell the end of COVID, but only time will tell.