On December 29, a National Guard in Colorado became the first known case in the United States of a contagious new variant of the coronavirus.
The news was unsettling. The variant, named B.1.1.7, had upset Britain, began to grow in Europe, and threatened to do the same in the United States. And while scientists didn’t know it yet, other mutants began popping up across the country. These included variants that had ravaged South Africa and Brazil that appeared to bypass the immune system, as well as others that were native to California, Oregon, and New York.
This mixture of variants could not have come at a worse time. The nation was at the beginning of a spate of post-vacation cases that would dwarf any previous waves. And the spread of powerful vaccines from Moderna and Pfizer-BioNTech has been botched by chaos and misunderstandings. Scientists warned that the variants – and especially B.1.1.7 – could lead to a fourth wave and that the already strained health system could give way.
That didn’t happen. B.1.1.7 became the predominant version of the virus in the United States and now accounts for nearly three quarters of all cases. But the surge experts feared they were just a slip-up in most of the country. The nationwide total daily new cases began to decline in April and is now down more than 85 percent from horrific highs in January.
“It’s pretty humble,” said Kristian Andersen, a virologist at Scripps Research in La Jolla, California.
Dr. Andersen and other virus watchers still see variants as a potential source of problems in the coming months – especially one that has ravaged Brazil and is growing rapidly in 17 US states. But they are also taking stock of the past few months to better understand how the nation has evaded the variant threat.
Experts point to a combination of factors – masks, social distancing, and other restrictions, and possibly a seasonal decline in infections – that gave tens of millions of Americans crucial time to vaccinate. They also attribute a good dose of serendipity as B.1.1.7 is powerless against the vaccines unlike some of its competitors.
“I think we were lucky to be honest,” said Nathan Grubaugh, an epidemiologist at Yale University. “We are saved by the vaccine.”
After B.1.1.7 appeared at the end of December, new variants with combinations of disruptive mutations came to light. Scientists worried about how competition between the variants might develop.
In January, researchers in California discovered a variant with 10 mutations that was becoming more common there and drifting to other states. Laboratory experiments suggested that the variant of antibody treatment that had worked well against previous forms of the virus could be evaded, and that it was possibly more contagious as well.
In the months that followed, the United States dramatically improved its surveillance for the mutation of the variants. Last week, more than 28,800 virus genomes, nearly 10 percent of all positive test cases, were uploaded to an international online database called GISAID. This clearer picture has allowed scientists to observe how the mutants compete with each other.
The California variant proved a weak competitor, and its numbers fell sharply in February and March. It’s still common in parts of northern California, but it has virtually disappeared from the southern parts of the state and never gained a foothold anywhere else in the country. As of April 24, it made up only 3.2 percent of all virus samples tested in the country, while B.1.1.7 rose to 66 percent.
“B.1.1.7 went to knockout and it’s like ‘Bye bye, California variant’,” said Dr. Andersen.
Across the country, researchers reported in February that a variant called B.1.526 spread quickly in New York and appeared to be a formidable opponent for B.1.1.7. By February, each of these variants was down to about 35 percent of the Dr. Grubaugh’s Connecticut laboratory has grown. But B.1.1.7 has the edge.
Updated
May 16, 2021, 3:46 p.m. ET
In fact, B.1.1.7 seems to have an advantage over almost every variant identified so far. At a congressional hearing on Tuesday, Dr. Rochelle P. Walensky, director of the Centers for Disease Control and Prevention, that B.1.1.7 accounts for 72 percent of cases in the country.
“We really see how B.1.1.7 decisively pushes out other variants,” said Emma Hodcroft, epidemiologist at the University of Bern.
The variants identified in California and New York were found to be only moderately more contagious than older versions of the virus, and much of their initial success may have been luck. The general boom in cases last fall exacerbated what might otherwise have gone undetected.
It is unclear what gives B.1.1.7 an advantage over the others. “Is it the largest of all the variants? It’s hard to tell right now, ”said Angela Rasmussen, virologist at the University of Saskatchewan’s Vaccines and Infectious Diseases Organization. “We need more research to find out what all these combinations of mutations do.” Some of the answers may come from California, where researchers are holding a head-to-head competition in a laboratory and injecting mice with a cocktail of B.1.1.7 and six other variants.
“The idea is to see who will prevail,” said Dr. Charles Chiu, a virologist at the University of California at San Francisco, who was the first scientist to discover the California variant.
In Michigan, one of the few states to see an increase in projected cases this spring, B.1.1.7 found a catch in younger people returning to school and engaging in contact sports.
“Because it’s more transmissible, the virus finds behavioral cracks that normally wouldn’t have been as problematic,” said Emily Martin, an epidemiologist at the University of Michigan.
But in the rest of the country, of course, people became more cautious when faced with the terrible numbers 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 the way it spreads is no different. Most states had at least partial restrictions on indoor eating and introduced mask mandates.
“B.1.1.7 is more transferable but cannot jump through a mask,” said Dr. Hodcroft. “So we can still stop its spread.”
However, other experts are still concerned about how much the virus appears to have defied predictions.
“I can’t necessarily attribute it 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 cycle would have caused it to go back in the middle of winter. “That might make me even more ignorant,” she said.
It is also puzzling why variants that have beaten other countries have not yet become widespread in the United States. B. 1,351 rapidly dominated South Africa and several other African countries late last year. It was first reported in the US on January 28, but it still only accounts for 1 percent of the cases. This may be because it is not ahead of the rapidly expanding B.1.1.7.
“I think that’s because it doesn’t really have much of a transmission benefit,” said William Hanage, an epidemiologist at Harvard TH Chan School of Public Health.
P.1, a variant that is devastating Brazil, got off to a sluggish start in the US but is now estimated to account for more than 10 percent of the country’s cases.
“I think it is a matter of time before the P.1 variant becomes one of the most widespread in the US,” warned Dr. André Ricardo Ribas Freitas, a medical epidemiologist at the Faculdade São Leopoldo Mandic in Brazil.
Still, Nels Elde, an evolutionary biologist at the University of Utah, said the events of the past four months had raised questions about whether it was worth fretting over different variations rather than focusing on the behaviors that can limit them all.
“We split the hair between a handful of mutations here and there, we lost perspective,” he said. “It’s catnip for an inquisitive mind.”
The United States also has a plethora of powerful vaccines that make variants an academic problem rather than a concern for the average person. The vaccines may be slightly less effective against the variants identified in South Africa and Brazil, but prevent serious illness in all known variants.
It is not impossible that the situation could get worse. Only about 35 percent of people in the United States are fully immunized, and protection from the vaccines could wear off by winter. Nobody knows how variants that appear in other parts of the world, like one that has grown in importance in India and is circulating at a low level in the US, will behave here. And even more variants will inevitably appear in places where the virus is widespread, warned Dr. Cobey: “There is still a lot to be done.”
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