The Omicron variant of SARS-CoV-2 diverged from the previous SARS-CoV-2 variants as a result of adaptive evolution, in which beneficial mutations are passed onto future generations through natural selection, rather than through recombination between previous variants, according to a study.
The study, published in the journal Nature, is the first to describe the genomic profile of Omicron and explore the origins of the variant.
“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,” said lead author Maciej Boni, Associate Professor of biology, Pennsylvania State University.
“The latest variant — Omicron — is extraordinary because of the even bigger jump it made in the evolution of its spike protein,” Boni said.
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 neutralisation.
The team analysed all 686 Omicron sequences that were available by December 7, 2021.
They found that Omicron falls within the B.1.1 lineage, which also includes the Alpha variant. However, the team found that Omicron is genetically distinct from Alpha, as well as any other known variants of interest.
Further, 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.
“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,” Boni said.
Additionally, the finding ruled out recombination of previous variants in the origin of Omicron.
“We found no convincing evidence of Omicron being a recombinant of previous SARS-CoV-2 variants,” said Boni.
The team did find that some samples of Omicron displayed weak evidence of having inherited genetic material from a Delta virus, but statistical analyses could not rule out random chance or small sequencing errors as causes of this curious recombination signal.
“Given the recent misinformation suggesting that the Omicron and Delta variants have recombined to create a aDeltacron’ 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.”