In January, researchers in California discovered a variant with 10 mutations that was growing more common there and had drifted into other states. Laboratory experiments suggested that the variant could dodge an antibody treatment that had worked well against previous forms of the virus, and that it was perhaps also more contagious.
In the months that have followed, the United States has drastically improved its surveillance of how the variants mutate. Last week more than 28,800 virus genomes, almost 10 percent of all positive test cases, were uploaded to an international online database called GISAID. That clearer picture has enabled scientists to watch how the mutants compete.
The California variant turned out to be a weak competitor, and its numbers dropped sharply in February and March. It is still prevalent in parts of Northern California, but it has virtually disappeared from southern parts of the state and never found a foothold elsewhere in the country. By April 24, it accounted for just 3.2 percent of all virus samples tested in the country, as B.1.1.7 soared to 66 percent.
“B.1.1.7 went in for the knockout, and it’s like, ‘Bye bye, California variant,’” Dr. Andersen said.
On the other side of the country, researchers reported in February that a variant called B.1.526 was spreading quickly in New York and appeared to be a formidable adversary for B.1.1.7. By February, each of those variants had grown to about 35 percent of the samples collected by Dr. Grubaugh’s lab in Connecticut. But B.1.1.7 came out on top.
In fact, B.1.1.7 seems to have the edge over nearly every variant identified so far. At a congressional hearing on Tuesday, Dr. Rochelle P. Walensky, the director of the Centers for Disease Control and Prevention, said B.1.1.7 made up 72 percent of cases in the country.
But in the rest of the country, people naturally became more cautious when confronted with the horrifying toll of the virus after the holidays. B.1.1.7 is thought to be about 60 percent more contagious than previous forms of the virus, but its mode of spread is no different. Most states had at least partial restrictions on indoor dining and instituted mask mandates.
“B.1.1.7 is more transmissible, but it can’t jump through a mask,” Dr. Hodcroft said. “So we can still stop its spread.”
But other experts are still discomfited by how much the virus seems to have defied predictions.
“I can’t necessarily ascribe it just to behavior,” said Sarah Cobey, an evolutionary biologist at the University of Chicago. Respiratory viruses sometimes go through seasonal cycles, but it’s not clear why the coronavirus’s cycle would have caused it to decline in the middle of winter. “That makes me feel maybe even more ignorant,” she said.
Also puzzling is why variants that pummeled other countries have not yet spread widely in the United States. B.1.351 rapidly dominated South Africa and some other African countries late last year. It was first reported in the United States on Jan. 28, but still accounts for only 1 percent of cases. That may be because it can’t get ahead of the fast-spreading B.1.1.7.
“I think that is because it doesn’t really have much transmission advantage,” said William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health.
