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What We Know About the Omicron Clan of Virus Variants: QuickTake

July 8, 2022, 12:04 AM

The global spread of SARS-CoV-2 has spawned a plethora of virus variants, each competing to more efficiently spread and evade the antibodies people generated from past infections and vaccinations. The highly transmissible omicron variant sent daily cases of Covid-19 to new heights early this year and its subvariants continue to evolve, driving fresh outbreaks. That’s challenging the achievement of community protection via so-called herd immunity, prompting the development of updated vaccines as well as testing the public’s tolerance for pandemic-mitigation efforts like booster shots, frequent testing and mask-wearing.

1. How is omicron evolving?

Omicron, also known as BA.1, was first identified in southern Africa late last year. It’s characterized by some 30 mutationsin the gene for the spike protein, which gives the coronavirus its crown-like appearance and allows it to invade cells. Changes there can make the pathogen less recognizable to the antibodies the immune system makes in response to vaccination or a case of Covid, increasing the risk of infection in such cases. Over time, subvariants of the original omicron strain have evolved, with the “fittest” superseding earlier versions. Several have been shown to cause different patterns of symptoms and may carry different risks of persistent or “long-haul” symptoms.

Explainer: Alpha, Delta and More. Why Virus Variants Cause Alarm: QuickTake

2. What about these subvariants?

Scientists divide omicron viruses broadly into five branches that descend from an ancestor strain. These are BA.1, BA.2, BA.3, BA.4 and BA.5. Each comprises a different constellation of genetic mutations that affect antibody evasion, infectivity and possibly virulence. In the US, one of BA.2’s descendants -- BA.2.12.1 -- predominated until it was superseded by BA.5, which accounted for more than half of new cases in the US and globally by early July. BA.4, which shares similar mutations with BA.5 in the spike protein, is also spreading, though at a slower pace, the World Health Organization said in a July 6 report. Transmission of both subvariants has coincided with an increase in cases that’s led to a jump in hospitalizations and ICU admissions in several regions. Still, available evidence doesn’t indicate they’re associated with a change in severity, the WHO said. The emergence of BA.2.75, first detected in India, has some eight additional spike protein mutations compared with BA.2, from which it evolved. The genetic changes have raised concern that BA.2.75 might be able to escape the immunity conferred by a previous BA.2 infection.

3. What’s the concern?

Omicron viruses are more transmissible than delta, the variant that became dominant worldwide in mid-2021, and each major subvariant appears more infectious still. Detailed analysis of omicron and its subvariants by scientists in Japan in late May found BA.2.12.1, BA.4 and BA.5 share a common mutation in the spike protein that’s associated in lab studies with a greater propensity to infect the lower lungs, where the virus can cause more severe disease. The so-called L452 mutation, which was also detected in delta, may make these strains more virulent than a BA.1 or BA.2 infection -- although there’s no evidence yet to indicate that’s the case. A study by scientists in China released ahead of publication in Nature on June 17 found that BA.2.12.1, BA.4 and BA.5 were more adept at evading antibodies than BA.1. They also reduce the neutralizing activity of the monoclonal antibody therapies casirivimab and imdevimab, according to WHO. Still, the monoclonal antibody treatment bebtelovimab and cilgavimab could effectively neutralize, or block, all three.

4. How effective are current vaccines?

Broadly, omicron variants reduce the effectiveness of immunity generated by a primary vaccination series. Booster doses, especially using a mRNA shot from Moderna Inc. or Pfizer Inc. and BioNTech SE substantially improve protection against symptomatic disease and infection, though the benefit diminishes over time. More studies are needed to assess the duration of effectiveness of boosters beyond six months, according to the WHO.

5. What are the caveats?

Although some of the newer omicron variants have caused local spikes in Covid cases, hospitalizations aren’t going up at nearly the same rate they did during previous waves. This suggests that the immunity generated from prior infections and vaccination is protecting against severe illness in some people. Still, even mild infections in vaccinated individuals can lead to long Covid in some cases, which means vaccination alone may not be enough to reduce the long-term health consequences of the pandemic.

The Reference Shelf

  • Related QuickTakes on whether Covid is becoming endemic, flurona (flu + coronavirus), virus testing, Covid treatments, vaccine mandates, omicron risk to kids, and the risks of flying amid the spread of omicron.
  • The New York Times tracks omicron and other SARS-CoV-2 variants.
  • The journal Science focuses on BA.2.
  • Bloomberg Intelligence’s Sam Fazeli and Bloomberg Opinion’s Therese Raphael discuss BA.2.
  • CDC information on variants.
  • The journal Nature provides a guide to the tangled omicron family.
  • Omicron’s impact in South Africa is discussed in Science Translational Medicine.

(Updates with BA.2.75)

To contact the reporter on this story:
Jason Gale in Melbourne at

To contact the editors responsible for this story:
Brian Bremner at

Paul Geitner, Michelle Fay Cortez

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