The Omicron variant was first detected in Botswana in October 2021 and has quickly spread throughout the world. A large international team of researchers, including Maciej Boni, associate professor of biology, Penn State, was the first to describe the genomic profile of Omicron and explore the origins of the variant.
Credit: Justice Hubane, Unsplash.
Creationist mode: 
A team of scientists led by Maciej Boni, associate professor of biology, Penn State University, USA have discovered how, where and approximately when the omicron variant of the SARS-CoV-2 virus was created.
Of course, being proper scientists they say this was an evolutionary process, but, as any devotee of Creationism's divine sadist will tell you, evolution doesn't happen so all these changes must have been intentionally designed by their beloved malevolence.
We have seen SARS-CoV-2 generate three major variants — Alpha, Delta and Omicron — in about 16 months, which is very surprising because other viruses do not make such repeated big evolutionary leaps. The latest variant — Omicron — is extraordinary because of the even bigger jump it made in the evolution of its spike protein.
The discovery is that omicron (B.1.1.529) is a descendant of the alpha (B.1.1.7) variant, that replaced the original virus at about the beginning of October, 2020 and caused the second major wave of infections. Alpha was of the B.1.1 lineage but was much more transmissible. It was itself replaced by the delta (B.1.617.2) variant which caused the third wave starting in about June, 2021.Associate Professor Maciej Boni
Penn State University.
Penn State University.
Despite expectations that a subsequent variant of concern (VOC) would evolve from delta, the team found that omicron is not closely related to delta, but is a highly modified version of alpha.
The team's findings are published in Nature, sadly behind a paywall. However the abstract can be read here and a PDF is available to download from here.
What this means is that although Omicron belongs to the same lineage as the Alpha variant, it has changed to such a great extent that it is largely unrecognizable as a cousin or nephew of the Alpha variant. When the Omicron genome was first sequenced, it became clear that this virus had the potential to be phenotypically very different from previous SARS-CoV-2 variants that we were familiar with.
This finding led to our conclusion that adaptive evolution played a significant role in the early emergence and establishment of Omicron. This finding suggests that Omicron is likely the result of an evolutionary process that created a highly transmissible virus that partially evades our antibody responses.
The Penn State news release explains:
This finding led to our conclusion that adaptive evolution played a significant role in the early emergence and establishment of Omicron. This finding suggests that Omicron is likely the result of an evolutionary process that created a highly transmissible virus that partially evades our antibody responses.
Maciej Boni
Boni noted that compared to previous variants, Omicron’s spike protein has more than 30 mutations, many of which are known to influence host antibody neutralization.
“Given that Omicron made such a big leap forward evolutionarily speaking, we wanted to investigate why and how this may have happened,” he said.
To do that, the team — which was led by the Centre for Epidemic Response and Innovation in South Africa — analyzed all 686 Omicron sequences that were available by Dec. 7, 2021. They found that Omicron falls within the B.1.1 lineage, which also includes the Alpha variant. Interestingly, the team found that Omicron is genetically distinct from Alpha, as well as any other known variants of interest.
[…]
To determine when the Omicron variant first emerged, the team used a technique, called time-calibrated Bayesian phylogenetic analysis. They estimated that the date when the most recent common ancestor of all Omicrons existed was early October 2021.
Next, the team applied a selection analysis to the 686 Omicron sequences and found evidence of positive natural selection in many genes since the variant split from other B.1.1 lineages.
We found no convincing evidence of Omicron being a recombinant of previous SARS-CoV-2 variants.
Given the recent misinformation suggesting that the Omicron and Delta variants have recombined to create a ‘Deltacron’ super variant, it is important to note that such recombination is in fact possible, but there is currently no evidence that this has occurred,” said Boni. “Additionally, if it does occur, there’s no telling what the properties of such a virus would be in terms of its ability to transmit and/or cause severe disease, among other factors.
This idea that Omicron can partially evade the immune system is supported by other recent findings showing an increased risk of SARS-CoV-2 reinfection associated with the emergence of Omicron. We also know now that the viral load of Omicron is higher in people who are infected, which also contributes substantially to its high transmission rate.
We can’t afford to endure another calendar year with half a million deaths.
Another way viruses can evolve is by 'recombination', where two strains infect the same cell simultaneously, so the resulting genomes of the new virus particles can be a mixture of the two 'parent' viruses. This is often the cause of a large number of changes such as are seen in omicron. However, although recombination between alpha and delta can't be ruled out, the team found the evidence for that was weak and statistical analysis could not rule out random changes.
Given the recent misinformation suggesting that the Omicron and Delta variants have recombined to create a ‘Deltacron’ super variant, it is important to note that such recombination is in fact possible, but there is currently no evidence that this has occurred,” said Boni. “Additionally, if it does occur, there’s no telling what the properties of such a virus would be in terms of its ability to transmit and/or cause severe disease, among other factors.
This idea that Omicron can partially evade the immune system is supported by other recent findings showing an increased risk of SARS-CoV-2 reinfection associated with the emergence of Omicron. We also know now that the viral load of Omicron is higher in people who are infected, which also contributes substantially to its high transmission rate.
We can’t afford to endure another calendar year with half a million deaths.
Maciej Boni
Regarding Omicron’s transmissibility, the team concluded that partial immune evasion was likely a major driver of the rapid spread of omicron in South Africa given that the proportion of the South African population that was immune (either from infection, vaccination or both) was above 60%.That, of course, is the scientific explanation for the emergence of the omicron variant currently causing the latest and largest wave of infections, but, as any Creationists is obliged to believe, all these changes are the result of the Intelligent [sic] designer trying to find better ways to make people sick and keep the death figures high by tweaking its earlier creations in response to things like natural immunity arising in the immune systems it created to protect us from its nasty little parasites, and from immunity caused by the vaccines medical science came up with.
[…]
Boni noted that the current Omicron wave is a reminder to all Americans to keep our COVID-19 vaccinations as current as possible.
Creationist mode: 
That's the Creationist cult's interpretation of the facts, so if you're ever tempted to fall for the Creationist cult's intelligent design hoax, what you need to do is ask yourself why an explanation that makes Creationism's god look like a pestilential sadist who hates its creation is better than an entirely natural one in which no gods were involved, and all the processes are known to science and readily understandable. You might also like to consider the motives of someone who poses as pious but who pushes that view of their god in order to fool people into believing falsehoods.
Reference:
Viana, R., Moyo, S., Amoako, D.G. et al.
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Nature (2022). DOI: 10.1038/s41586-022-04411-y
Viana, R., Moyo, S., Amoako, D.G. et al.
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Nature (2022). DOI: 10.1038/s41586-022-04411-y
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