New subvariant of Covid-19 spreading rapidly in the United States

First came omicron, then came its highly contagious subvariant, BA.2. That subvariant gave rise to its own subvariants, whose share of new coronavirus cases in the United States is growing.
The coronavirus is constantly mutating. While some variants seem to vanish, causing little ripples of surges in their wake, others have kept driving large outbreaks. Experts say a new form, BA.2.12.1, is spreading rapidly and will likely in the next weeks become the dominant form of the virus in the United States. There’s no indication yet that causes more severe disease.
In the week ending Saturday, BA.2.12.1 made up about 36% of all new cases in the United States, according to estimates the Centers for Disease Control and Prevention. That’s up from 26% of cases the week before, and 16% of infections during the second week in April. (The latest figures are rough estimates, subject to revision as more data comes in. Genetic sequencing of the virus is performed on a portion of samples across the country.)
First detected in the United States New York state health officials in April, BA.2.12.1 is spreading more rapidly than the first versions of the omicron variant, which caused a huge surge in cases over the winter. This version descends from BA.2 and appears to have spread even more quickly, although the reasons are still under investigation.
Indeed, the virus seems to keep finding ways to spread more easily. “Omicron was more transmissible than delta, which was more transmissible than alpha,” said Kra Queen, director of viral genomics and surveillance at Louisiana State University. BA2.12.1 is building on that trend, she added, “and that’s why it’s taking over now, especially in the Northeast.”
New cases in New York have increased, although they remain far below the horrific numbers seen earlier in the pandemic. Yet a number of counties have become hot spots, reminding state health officials that the coronavirus will not surrender regardless of general pandemic fatigue.
Queen expects rising infections to spread from the Northeast to the South then the West, driving more outbreaks. “We’re already seeing it here in Louisiana,” said Queen, who oversees genetic analysis for the virus at the university. “Our most recent sequencing runs of community samples have all been BA.2.12.1, and those samples are from mid-April.”
Reports of new cases nationally have doubled in the past month as omicron subvariants have spread, according to a New York Times database. In the past two weeks, cases overall have increased 50%.
But reported cases are likely an undercount of the virus’s true spread, since access to at-home tests has increased and the results are often not officially reported.
Still, virtually every reported infection across the nation is from an omicron subvariant, and although BA.2 is still the dominant form, BA.2.12.1 is quickly gaining ground.
Dr. Rochelle Walensky, director of the CDC, said last week that the agency was beginning to focus on BA.2.12.1 in addition to BA.2.
“Epidemiologically, it doesn’t appear as if we’re seeing more severe disease in places that are having more cases,” she said. “So we are not anticipating more severe disease from some of these subvariants, but we are actively studying it.”
Hospitalizations have risen more slowly than new cases — up 18% in two weeks — but those rates tend to trail increases in cases. Deaths have decreased 17% in the past two weeks.
Still, early research suggests that BA.2.12.1 evades the body’s immune defenses more adroitly than previous versions of the coronavirus, and that seems to account in some measure for its rapid spread. “In two weeks, it will probably be everywhere,” said Massimo Caputi, a professor of biomedical science at Florida Atlantic University.
But the subvariant is finding more opportunities as well. Taj Azarian, a genomic public health researcher at the University of Central Florida, said he believes the recent surge is mostly due to “the great unmasking.”
“We’re in this phase of pandemic fatigue and complacency,” he said. “And while we need to balance the weight of mental health with the risk of contraction, as a result we’ve seen an uptick not only in the omicron variant but other respiratory illness.”