A coronavirus variant detected in California this winter rapidly became dominant in the state over five months and now makes up more than half of the infections in 44 counties, according to new research from scientists who believe this version of the virus should be declared a “variant of concern warranting urgent follow-up investigation.”
The United States has been ramping up scrutiny of the shape-shifting virus, and scientists have identified many genetically distinct variants, but there is continued uncertainty and debate over which of these mutations are significant and to what extent. The variant identified in California has emerged as potentially the first homegrown “variant of concern” in the United States, though it has not yet been designated that by the Centers for Disease Control and Prevention.
The variant contains a mutation that scientists suspect is enhancing the virus’s ability to bind to human receptor cells. If truly more transmissible, as the new study contends, the California variant joins a growing list of virus variants circulating in the United States as the country continues to emerge from the devastating winter wave of infections, hospitalizations and deaths.
Those key metrics have been trending in a positive direction since peaking in January. Whether the variants can significantly slow, or even reverse, those trends is unknown. Forecasts must take into account multiple variables, including vaccination rates, continued mutation of the virus and the unpredictability of human behavior.
But evidence from other countries suggests that highly transmissible variants can be suppressed through public health interventions, such as mask-wearing, social distancing and restrictions on gatherings, and by broadening immunity through vaccination campaigns.
“Fundamentally, it doesn’t change the direction we are going, which is we want to hold cases down to where we can get the pandemic under control. Simply having a more infectious variant circulating is not going to be the end of the world,” said Charles Chiu, a professor of laboratory medicine and infectious diseases at the University of California at San Francisco School of Medicine, and the senior scientist behind the new research.
The study has not been peer-reviewed. It will be submitted for publication soon, Chiu said. But his team’s conclusion is consistent with what has been seen multiple times across the planet: The virus is not static but rather mutating as it circulates in the human species and gets better at infecting cells or collides with natural and vaccine-induced immunity.
A separate study from scientists at the University of Washington, posted Monday to the preprint server BioRxiv and not yet peer-reviewed, found that a mutation known as L452R in the California variant gives the virus an advantage in binding to receptors in human cells. The authors write that “the positive selection for this mutation became particularly strong only recently, possibly reflecting viral adaptation to the containment measures or increasing population immunity.”
The CDC is tracking the spread in the United States of three other variants — first identified in the United Kingdom, South Africa and Brazil. Greg Armstrong, head of a genomic surveillance program at the CDC, noted in a webinar Saturday that the variant detected in California might be more transmissible, and said there were other variants in the United States that scientists are keeping an eye on.
A variant can potentially have a competitive advantage against other virus variants and be more transmissible or even more lethal. But scientists face a challenge in determining whether a spike in cases reflects some property of a variant or simply happenstance — a situation in which the variant was in the right place at the right time, riding a wave of infections driven by other factors. That could potentially be the case in California.
Separately, researchers have identified a mutation in a spot on the virus called Q677, which initially was detected in variants in Louisiana and New Mexico. It has popped up independently in seven variants in what appears to be a case of “convergent evolution.” Scientists worry when a specific mutation keeps appearing in scattered locations, because it suggests that this genetic change reliably gives the virus an advantage.
“The whole issue of convergent evolution . . . that’s the signature of trouble, and that’s why I’m worried about Q677,” Francis S. Collins, director of the National Institutes of Health, said in an interview.
The new California research contends that the variant, which goes by two names, B.1.427 and B.1.429, has spread widely because it is more transmissible. The research drew on multiple lines of evidence — each of which on its own might be considered circumstantial but that collectively provide a picture of a virus that is unusually contagious.
In laboratory experiments, researchers created a version of the virus and found that it was more efficient at infecting cells and lung tissue growing in a dish.
They also found that the amount of virus in people’s noses was significantly higher for people infected with the variant than for others.
One concern has been that a more-transmissible variant could prolong the pandemic and make it harder to reach herd immunity. But cases are coming down even in countries where variants have taken over.
“Even when we’re seeing a surge of cases due to this variant, overall, the cases have been going down since the holidays,” Chiu said. “It’s a promising sign, actually — even though this new variant is more than 50 percent of cases, we’re not seeing the surge we might be worried about.”
He said that while it is hard to know for certain, he does not think the variant was responsible for the winter surge in cases in the state. He said it is possible it may have contributed to the surge in the northern part of the state.
Much concern has focused on whether variants could evade vaccines. The new research indicates that the California variant partially impedes the effectiveness of antibodies at neutralizing the virus in a dish. The reduction was modest, however.
Early data from vaccine clinical trials has suggested that, even when vaccines lose some of their effectiveness when confronting a variant, they still afford protection, particularly against severe disease outcomes.
The study by Chiu and his colleagues found a hint that the variant is associated with an increased risk of severe disease, but that data is far from conclusive. The researchers examined the cases of 324 people who were treated at UCSF hospitals and clinics and found that 69 were infected with the variant. There was a higher risk of death among those patients.
But the overall number of deaths in the study was low, with seven deaths among people infected with the variant and five among those who did not have the variant. The deaths were also during a period when there was a surge of infections in Northern California, making it hard to distinguish “between whether the variant is inherently more virulent or whether the higher risk of severe disease is related to other factors,” including a strained health-care system.
Most variants of the coronavirus “will be inconsequential, but as we have seen some may enhance the ability of the virus to spread more rapidly, or to change the character of the infection,” Michael J. Buchmeier, a virologist at the University of California at Irvine, said in an email. He urged the public to continue to take precautions against the virus, adding, “Testing and sequencing is needed to localize and quarantine any infected individuals to prevent further propagation of the variant virus into the population.”