The Centers for Disease Control and Prevention’s (CDC) COVID-19 variant tracking estimates suggest that a new subvariant of Omicron is rapidly circulating in the United States.Little is known about the variant, known as BA.2.12.1, except that it may be the most contagious version of SARS-CoV-2 to date, and experts have warned it could trigger new outbreaks across the United States surge of cases.
Since the Omicron variant of SARS-CoV-2 emerged in late 2021, the virus has spread and mutated at an incredible rate. The first iteration of Omicron (B.1.1.529) took just a few weeks to become dominant in the US, before being quickly pushed to prominence by the next sub-variant, BA.1.1.
By March, another iteration of the Omicron called BA.2 had taken over the US. The BA.2 is not a new subtype of the Omicron, but a different iteration of the same bloodline that will appear in South Africa in late 2021.
BA.2 was found to be about 30% more contagious than the previous iteration of Omicron that spread across the United States. But more problematically, BA.2 has the ability to evade previous monoclonal antibody treatments developed to treat COVID-19.
Now, another iteration of the Omicron has been detected and is growing rapidly in the United States. This variant is called BA.2.12.1, and it is a new mutation of unknown origin. While it appeared on the CDC’s variant tracker as early as February, it only exploded nationwide in April.
The latest NowCast modelling by the CDC estimates that BA.2.12.1 accounted for 36.5% of new crown infections in the United States as of the end of April. In the northeastern region of the country, where BA.2.12.1 was first detected, it is now thought to account for 80% of all infections.
The emergence and growth of BA.2.12.1 reflects two other new Omicron subtypes that have been reported in South Africa – BA.4 and BA.5. A recent summary of the characteristics of these new variants by scientist Eric Topol suggests that they are even more infectious than BA.2, and that some of the new mutations may allow them to re-infect those previously infected by earlier iterations of Omicron. Topol noted that BA.4 and BA.5 may be 10% more contagious than BA.2, however BA.2.12.1 may be more contagious, which is 25% more than the previously dominant Omicron variant spread advantage.
A recently released preprint study (not yet peer-reviewed) by scientists from Beijing provides the first robust look at how antibodies from previous Omicron infection interact with BA.4, BA.5 and BA.2.12.1. The findings suggest that all three of these new omicron subtypes may have properties that allow them to evade any immunity that arises from BA.1 infection.
BA.2.12.1 has also been found to harbor some unique mutations that allow it to enhance its ability to enter human cells — essentially raising suspicions that it may be the most infectious variant ever seen.
All of this data is evolving rapidly, and it’s unclear what exactly these Neo-Omicron subtypes will do under real-world conditions. New York City, known as America’s bellwether, has recently seen an increase in COVID-19 hospitalizations.
Officially recorded cases of COVID-19 in New York state reached the highest level since January as of early May. South Africa is battling its own BA.4/BA.5 peak while recording the highest rate of new COVID-19 cases it has seen in months.
So far, there is no evidence that these new variants cause more severe disease than the previous Omicron subtypes. But hospitalizations are rising in New York and South Africa, suggesting that higher infection rates in the community always mean the virus finds the most vulnerable.
Perhaps the biggest question now about these emerging Omicron subtypes is what to do with vaccine boosters for specific variants. Both Moderna and Pfizer are in the advanced stages of experimenting with Omicron-specific mRNA boosters. The two companies now hope to launch the shots later this year, before winter in the northern hemisphere. However, both new vaccines are designed to target the BA.1 subtype of Omicron.
Analyzing preprints of these emerging Omicron subtypes suggests that the immune escape properties of BA.4, BA.5, and BA.2.12.1 may lead to a new round of reinfection. And perhaps a variant-specific vaccine against BA.1 would not be the best option for protecting against these increasingly immune-invasive Ormicon strains.
“This poses a huge challenge to the herd immunity currently established through WT-based vaccination and BA.1/BA.2 infection,” the new study noted, “Likewise, this observation also suggests that Omicron-based BA. 1’s vaccine may not be an ideal antigen to induce broad-spectrum protection against the emerging Omicron sublineage.”
The FDA has scheduled a meeting in late June to lock in a new booster vaccine later this year. Moderna is leading a trial of its BA.1 mRNA booster, and the company plans to deploy the new formulation in August. However, Moderna’s CEO warned that the August date would be pushed back to later in 2022 if a different Omicron sub variant needs to be targeted.