San Diego County confirmed 24 new cases involving the variant on Tuesday. In total, the five states have reported more than 30 cases. But in all likelihood, the variant entered the US long before these infections were detected and has been spreading silently for weeks.
None of the infected people have recently traveled outside the US. Charles Chiu, an infectious-disease expert at the University of California, San Francisco, told Business Insider that’s “worrisome because it suggests the virus is circulating in our community now.”
Indeed, the Centers for Disease Control and Prevention confirmed last week that the variant had “been transmitted from person to person in the US.”
Chiu thinks the variant was introduced into the US in early December or shortly afterwards.
“It’s very likely that it’s in every state,” he said.
The variant is not responsible for the majority of US cases
More than 30 countries have reported cases of the mutated strain, which was first detected in Kent and London on September 20 and 21. By mid-November, the strain — which geneticists have named B.1.1.7 — was responsible for 28% of cases in London. Three weeks later, that figure jumped to 62%.
According to Lucy van Dorp, a researcher at University College London’s Genetics Institute, the variant most likely crossed the Atlantic after it hit high frequencies in the UK — probably late in the fall.
If the variant follows the same trend in the US as it did in the UK, she said, it may take a few months for it “reach marked frequencies.”
Nonetheless, public-health officials in Los Angeles are already searching for the variant among the county’s virus samples. Coronavirus hospitalizations and cases have hit unprecedented highs in LA County: Its total infection count doubled from 400,000 to 800,000 in the last month, and the average number of new hospitalizations per day jumped from 790 in early November to about 7,600 on January 2.
No cases involving the variant have been found yet in LA County — all of California’s cases are in San Bernardino and San Diego Counties. But mayor Eric Garcetti told the LA Times that he suspects the new variant is a factor in the recent case spike.
“This happened devastatingly quickly. Everybody I talked to said this acceleration was beyond any model and any expectation, so then people say, ‘What broke down?’ and I’ve got to think it’s partly the strain that was out there,” Garcetti said on Wednesday.
However, based on genetic data collected in the US to date, Chiu said it’s unlikely the strain contributed significantly to the surge in cases.
“It doesn’t appear that this strain is prevalent, at least not currently,” he said, adding, “I think the evidence so far suggests that we’re seeing this in really less than 1% of, of cases. But if this strain is indeed more transmissible, we may start seeing increasing proportion of infections by this strain.”
The more we look, the more we’ll find
Countless versions of the coronavirus are circulating worldwide, each separated by a handful of tiny changes in its genome. To keep tabs on these strains, researchers genetically sequence samples of the virus and track the changes over time.
But the US genetically sequences less than .01% of its coronavirus cases: only 2.5 out of every 1,000. In the UK, by comparison, labs are sequencing 45 out of every 1,000 cases. That’s likely the reason the US missed the new strain’s introduction.
“We’ve done relatively little genomic surveillance in the US compared to the UK. For example, in Connecticut, we’ve sequenced about 0.3% of the cases. In the UK, their goal is 10% of the cases,” Nathan Grubaugh, an epidemiologist at the Yale School of Medicine, told Business Insider.
“So the mutation could be more widespread and we just don’t know it,” he added, also noting that the variant was probably introduced into the US multiple times.
Many public-health officials assumed the variant was in the US many days before cases were found.
“Given the small fraction of US infections that have been sequenced, the variant could already be in the United States without having been detected,” the CDC said on December 22, a week before Colorado officials reported the first case.
Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said on December 21 that the strain was almost certainly in the US already.
“When we start to look for it, we’re going to find it,” Fauci told PBS NewsHour.
The more researchers sequence patients’ samples, the better able they’ll be to spot new strains early, van Dorp said.
“There may be other similar variants elsewhere which have not been detected in other regions of the world due to less intensive sequencing efforts,” she said.
The new variant may be 56% more contagious
The coronavirus typically accumulates two mutations a month, most of which don’t affect its infectiousness or deadliness.
But in the case of B.1.1.7, the virus collected at least 17 mutations at once. Some of those mutations affect the virus’ spike protein, which it uses to invade cells. That could make it easier for it to infect people.
New research suggests the strain is about 56% more contagious than the original virus that emerged in China. The variant has overtaken all other versions of the virus in the UK since late November. By mid-December, six out of every 10 new coronavirus cases in the UK were the new variant.
Given that spread, and how frequently people travel between the US and UK, “the arrival of this variant in the US was expected,” according to the CDC. (There are 16 flights per day from London-Heathrow airport to New York’s JFK airport alone.)
At least 27 countries banned travel from the UK last month; the US did not. But travel bans usually aren’t sufficient to contain a virus’ spread, according to Grubaugh, because the restrictions aren’t airtight — essential travel continues. The bans also came too late: By mid-December, the virus had already been reported in at least eight countries.
“If a country is worried about the new variant being introduced and causing increased local transmission, a more effective plan is to put measures in place to decrease local transmission,” Grubaugh said.
Strict adherence to social distancing and mask wearing “will stop the virus, variant or not,” he added.
This story has been updated with new information about cases in California and Georgia. It was originally published January 5 at 8:04 a.m.
Susie Neilson contributed reporting.