A large international research team published a study in Nature on January 7, 2022, revealing that the SARS-CoV-2 Omicron variant diverged from previous variants through adaptive evolution—beneficial mutations were passed on through natural selection rather than recombination between earlier variants. This was the first study to describe Omicron's genomic features and explore its origins.

Dr. Maciej Boni, Associate Professor of Biology at Penn State University and a co-author, noted: "We have seen SARS-CoV-2 produce three major variants—Alpha, Delta, and Omicron—within approximately 16 months, which is surprising because other viruses do not undergo such large evolutionary jumps. Omicron is extraordinary because of the even larger leap in its spike protein evolution."

Unlike previous variants, Omicron carries more than 30 mutations in the spike protein, many known to affect neutralization by host antibodies. The team analyzed all 686 Omicron sequences available as of December 7, 2021, and found that Omicron belongs to the B.1.1 lineage (the same lineage as Alpha) but is genetically distinct from Alpha and all other known variants.

Using time-calibrated Bayesian phylogenetic analysis, they estimated that the most recent common ancestor of all Omicron variants existed in early October 2021. Selection analyses revealed evidence of positive natural selection across multiple genes since Omicron diverged from other B.1.1 lineages.

Dr. Boni concluded: "This finding suggests that adaptive evolution played a major role in Omicron's emergence and establishment. Omicron likely resulted from an evolutionary process that created a highly transmissible virus capable of partially evading our antibody responses." The study found no convincing evidence that Omicron originated from recombination of previous variants.

Regarding transmissibility, the team concluded that partial immune evasion is likely a major driver of Omicron's rapid spread in South Africa, given the population's immunity level of over 60% from infection, vaccination, or both. Dr. Boni added: "We now also know that Omicron viral loads are higher in infected individuals, which significantly contributes to its high transmissibility." He emphasized the importance of maintaining COVID-19 vaccination: "We cannot afford another year with 500,000 deaths."