An Extra-Contagious Coronavirus Variant Is In The US — But No One Knows How Widespread It Is

A new, highly contagious version of the coronavirus has arrived in the United States, but scientists have no way to track how widespread it is.

The new variant, known as B.1.1.7, was first detected in the United Kingdom and, as of Friday, has cropped up in at least 45 other countries. That includes the US, where it has been reported in dozens of cases across at least eight states: California, Connecticut, Colorado, Georgia, Florida, Texas, Pennsylvania, and New York.

This version of the virus does not appear to cause infections that are more severe or deadly, and the vaccines now slowly being distributed are still believed to be capable of fending it off.

But a much more contagious mutant could exponentially drive up the number of infections and cause greater numbers of hospitalizations and deaths at a time when out-of-control caseloads are already pushing ICUs across the country beyond capacity.

“Our healthcare infrastructure is already at a breaking point,” Charles Chiu, a laboratory medicine and infectious diseases expert at the University of California, San Francisco, told BuzzFeed News. “The introduction of a more transmissible strain might be enough to tip us over.”

In the UK, where the variant is believed to be widespread, cases are skyrocketing. Fears that severely ill patients would overwhelm the healthcare system spurred Prime Minister Boris Johnson to impose strict lockdown measures this week. The mayor of London on Friday declared a “major incident” in the city, where 1 in 30 residents are infected with COVID-19 and more than 7,000 people are hospitalized with it, up 35% from the previous peak of the pandemic in April. As of late December, the variant accounted for an estimated 60% of cases.

While only a handful of cases have been confirmed in the US so far, scientists say that all signs point to the variant already spreading within communities.

Chiu’s lab detected some of the first cases of the new variant in California, where at least 30 cases have been found so far. Based on testing done by him and others, he believes that the B.1.1.7 variant is still rare for now. But there is no way of knowing with certainty how prevalent it is or will be, he and other experts say. Unlike the UK and other countries, the US does not have a robust, centralized surveillance system for identifying genetic variants of the virus.

“This reminds me of the early situation with testing in the US, where we didn’t know where the virus was because we weren’t looking,” said Natalie Dean, a biostatistician at the University of Florida.

Marc Lipsitch, an epidemiologist at the Harvard T.H. Chan School of Public Health, called the new variant “a really big deal” and the country’s lack of genomic surveillance “a huge failing of our public health system.”

“Hopefully this will be a wake-up call,” he told reporters Tuesday.

That leaves the country flying in the dark not just to the B.1.1.7 variant, but other possibly dangerous ones as well. Another mutated version of the virus, first detected in South Africa in mid-December, shares genetic similarities with the one found in the UK and is also believed to be more transmissible. It has not been spotted in the US yet.

Meanwhile, the US recorded 4,000 COVID-19 deaths on Thursday, its highest single-day count so far, which brought its total death toll to more than 365,000. And the slow distribution of COVID-19 vaccines, currently millions of doses behind federal targets, means that the number of people infected with the virus — more than 21 million so far — will continue to climb.

“I wouldn’t be surprised if the pandemic continues to remain out of control,” Chiu said. “I wouldn’t be surprised to see this strain eventually become the predominant strain if it is more transmissible, which appears to be the case.”

Where the B.1.1.7 variant originated is unclear, but it was first detected in the UK in September.

On Dec. 29, the US reported its first confirmed case — a Colorado National Guard member — followed by a second probable case who was a colleague.

Cases have since been reported in Florida, California, New York, Georgia, Texas, Connecticut, and Pennsylvania. California’s 30-plus cases include two residents of a household in San Bernardino County, one of whom came into contact with a symptomatic person traveling from the UK. The Pennsylvanian had “known international exposure,” according to the state health department. Of the two cases reported Thursday in Connecticut, which were not related to each other, one had recently traveled to Ireland and the other to New York.

But so far, most of the people infected with the variant in the US have not had any known travel history. That “really suggests that it’s already entrenched in the community,” said Angela Rasmussen, a virologist at the Georgetown Center for Global Health Science and Security.

Mutations are a natural byproduct of the coronavirus replicating and spreading. These errors in the genetic code usually don’t change how the virus functions. But sometimes the changes can give it an evolutionary advantage, enabling it to outcompete other variants in circulation.

The B.1.1.7 variant has about two dozen changes, including 17 mutations, an unusually high number. Some of them are in the now-infamous spike protein that enables the coronavirus to bind to and infect human cells.

It’s not clear yet which of these mutations make the variant more contagious or how. This version could be better at entering cells, or as some research suggests, it could yield very high viral loads that make it easier for people to infect others. To find out, scientists will need to conduct studies in cell and animal models.

On Friday, the FDA warned of the possibility that some of these mutations could cause coronavirus tests to inaccurately report negative results. At least two diagnostic tests on the market, according to the agency, look at genetic targets that are now altered by the B.1.1.7 variant, although those are not the tests’ only targets.

The good news: the variant is similar enough to previous versions of SARS-CoV-2 that scientists are confident it will still be recognized by the immune systems of people who have gotten vaccinated or have recovered from infections.

That’s because people typically mount broad immune responses that target more parts of the virus than a single region of the spike protein, said Harm van Bakel, a geneticist at the Icahn School of Medicine at Mount Sinai. “Even if there is a change in one particular region, there are still other antibodies we develop as part of our antibody response that would be able to recognize other parts of the protein as well,” he said.

Even if a mutated version of the virus in the future is sufficiently different, vaccines can also be adjusted to protect against different strains. As Rasmussen pointed out: “Before people start freaking out, they should keep in mind we deal with this every single year with influenza.”

As for just how much more contagious this variant is than previous ones, a modeling study out of London in December estimated it is roughly 56% more transmissible. Supposing that a person infected with the original SARS-CoV-2 virus would ordinarily infect around one additional person on average, individuals carrying the new variant could instead spread it to around 1.5 people. The cumulative effect of this is significant: If each infection leads to 1.5 new cases per week, then in about two weeks, there would be twice the number of cases as normal.

That’s why the variant’s arrival is stoking heated debates over whether vaccine doses should be cut in half or delayed in order to get them to people faster. Despite scant data about how effective a single dose would be, some scientists argue that it is better to have some protection rather than none at all. Others, including top FDA officials, fear that deviating from the authorized dosing schedule could wreak further havoc.

The UK has adopted a stretched-out vaccine schedule as an emergency response to the surge. As part of the stringent national lockdown, the country has also taken the drastic step of also closing schools and universities.

In the US, where new cases and deaths are at record highs, a more contagious virus will mean more stress on a healthcare system already struggling to treat patients. In Southern California, available ICU capacity has bottomed out at 0% and first responders in Los Angeles are being instructed not to transport patients unlikely to survive.

“If we don’t change our control measures, once it becomes common it will accelerate transmission considerably,” Lipsitch said.

Scientists could know a lot more about how widespread the variant is in the US — if they were given the resources to look.

Early research indicates that the variant is strongly correlated with a change in one of the virus’s genes, the S gene. Spotting this change in a patient’s viral sample appears to be a useful cue to then genetically sequence it and root out more cases.

Rapid and widespread sequencing is what enabled the UK to quickly detect this and other variants. In March, the government invested 20 million pounds into forming the COVID-19 Genomics UK Consortium (or COG-UK) — a coordinated national program that analyzes samples from hospitals and other testing sites across the country and tracks genetic changes in the virus.

It has sequenced about 10% of all UK infections to date, and can process 5,000 samples a week, according to Joshua Quick, a University of Birmingham researcher affiliated with the group. “Having rapid genome sequencing capacity increases the chance of detecting existing or new variants or making interventions such as quarantining cases of the variant,” he said by email.

By comparison, the US has sequenced less than 1% of its cases — about 51,000 of 17 million, according to a CDC report in late December. Lipsitch said the UK is “five years or so ahead of us in terms of genomic surveillance and really knowing the genetics of the pathogens and circulating in their country.”

The US’s closest equivalent to COG-UK is SPHERES, a CDC-led patchwork of laboratories across health agencies, universities, and sequencing centers.

Russ Corbett-Detig, an evolutionary geneticist at the University of California, Santa Cruz, said that the scientists involved are highly collaborative and share methods and datasets. But he and some other researchers say that unlike the UK consortium, it does not have a clear mandate. “What we desperately need is more sequencing in the US,” Corbett-Detig said.

SPHERES “doesn’t really have the infrastructure or the resources or the funding that’s needed to do widespread national surveillance,” said Chiu, whose UCSF lab is also part of the consortium, adding that it costs his lab about $200 to sequence each sample, not including labor.

“We literally need money,” he said. “My lab, we have the capacity of doing 300 genomes a week, basically. If we had more resources, we could end up doing thousands of genomes.”

The CDC did not return requests for comment. Its website says that it is launching a strain surveillance program that, when fully implemented this month, will have each state send the CDC at least 10 samples biweekly for sequencing. On Wednesday, the California sequencing companies Illumina and Helix announced that they would collaborate with the agency to increase national genomic surveillance and track the emergence of the B.1.1.7 variant.

Meanwhile, some states and cities are taking it upon themselves to heighten their monitoring efforts. California’s public health department is asking healthcare providers to submit samples for sequencing from COVID-19-positive people who are likely suspects. But regional monitoring is often limited. In Los Angeles, which reported nearly 12,000 new cases on Wednesday alone, health officials said they are sequencing just 30 to 35 samples every few days. New York’s state public health laboratory is ramping up its sequencing efforts and has analyzed more than 870 samples in the last two weeks, a representative said. For the past week, New York has been reporting an average of more than 14,000 cases a day.

Until the US can develop a better system to monitor for variants, scientists say it’s a good sign that the same public health measures can still protect people. The virus still spreads through airborne droplets and smaller aerosol particles, and to a lesser extent, physical contact with infected surfaces.

So the efforts to reduce transmission remain the same: social distancing, masking, cooperating with contact tracing, staying home as much as possible, avoiding indoor gatherings, hand-washing, and getting vaccinated as soon as possible.

But in the face of an even more threatening adversary, Americans will need to take the risks much more seriously than they have so far.

“People need to understand this is no longer a theoretical concern,” Rasmussen said. “This is an imminent concern.”

Dan Vergano and Stephanie Baer contributed reporting to this story.