A new, highly contagious version of the coronavirus has arrived in the US, but scientists cannot track how widespread it is.
The new variant, known as B.1.1.7, was first discovered in the UK and has appeared in at least 45 other countries since Friday. This includes the United States, where it has been reported in dozen of cases in at least eight states: California, Connecticut, Colorado, Georgia, Florida, Texas, Pennsylvania, and New York.
This version of the virus doesn’t seem to cause more serious or deadly infections, and it is still believed that the vaccines, which are now slowly being distributed, will be able to fight them off.
But a much more contagious mutant could exponentially increase the number of infections, causing greater numbers of hospitalizations and deaths if runaway cases are already driving intensive care units across the country beyond capacity.
“Our health infrastructure is already at a breaking point,” Charles Chiu, a laboratory medicine and infectious disease expert at the University of California at San Francisco, told BuzzFeed News. “Introducing a more transferable burden could be enough to upset us.”
In the UK, where the variant is considered widespread, cases are skyrocketing. Fears that seriously ill patients could overwhelm the health system prompted Prime Minister Boris Johnson to put in place tough lockdown measures this week. The Mayor of London declared a “major incident” in the city on Friday, in which 1 in 30 residents are infected with COVID-19 and more than 7,000 people are hospitalized with it. This is a 35% increase from the previous peak of the pandemic in April. At the end of December, the variant accounted for an estimated 60% of the cases.
While only a handful of cases have been confirmed in the United States so far, scientists say any signs point to the variant that is already spreading in communities.
Chius lab discovered some of the first cases of the new variant in California, with at least 30 cases found so far. Based on tests that he and others have carried out, he believes that variant B.1.1.7 is still rare for the time being. But there is no way of knowing for sure how widespread it is or will be, say he and other experts. 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 in testing in the US where we didn’t know where the virus was because we didn’t look,” said Natalie Dean, biostatistician at the University of Florida.
Marc Lipsitch, epidemiologist at Harvard T.H. The Chan School of Public Health called the new variant “a really big deal” and the lack of genomic surveillance in the country as “a major failure of our public health system”.
“Hopefully this will be a wake-up call,” he told reporters on Tuesday.
This means that the country flies in the dark not only to the B.1.1.7 variant, but also to other potentially dangerous ones. Another mutated version of the virus, first discovered in South Africa in mid-December, shares genetic similarities with that found in the UK and is also believed to be more transmissible. It has not yet been discovered in the United States.
Meanwhile, the US recorded 4,000 COVID-19 deaths on Thursday, the highest number ever in a day, bringing the death toll to over 365,000. And the slow spread of COVID-19 vaccines, currently millions of doses behind federal targets, means the number of people infected with the virus – more than 21 million so far – will continue to rise.
“I wouldn’t be surprised if the pandemic continued to spiral out of control,” Chiu said. “I wouldn’t be surprised if this strain eventually becomes the predominant strain when it is more transmissible, which it appears to be.”
It is unclear where variant B.1.1.7 comes from, but it was first discovered in Great Britain in September.
On December 29, the U.S. reported its first confirmed case – a member of the Colorado National Guard – followed by a second likely case that was a colleague.
Cases have now been reported in Florida, California, New York, Georgia, Texas, Connecticut, and Pennsylvania. The 30+ cases in California include two residents of a San Bernardino County household, one of whom came into contact with a symptomatic person from the UK. The Pennsylvanian had “known international exposure” according to the state health department. Of the two unrelated cases reported Thursday in Connecticut, one had recently traveled to Ireland and the other to New York.
To date, most people infected with the variant in the United States have no known travel history. That “really suggests it’s already anchored in the community,” said Angela Rasmussen, a virologist at the Georgetown Center for Global Health Science and Security.
Mutations are a natural by-product of the replication and spread of the coronavirus. These errors in the genetic code usually do not change the way the virus works. But sometimes the changes can give it an evolutionary advantage that allows it to outperform other variants in circulation.
The B.1.1.7 variant has around two dozen changes, including 17 mutations, an unusually high number. Some of them are found in the now infamous spike protein, which enables the coronavirus to attach to and infect human cells.
It is not yet clear which of these mutations make the variant more contagious or how. This version could penetrate cells better or, as some research suggests, deliver very high viral loads that make it easier for people to infect others. To find out, scientists need to conduct studies on cell and animal models.
On Friday, the FDA warned of the possibility that some of these mutations could cause coronavirus tests to report negative results inaccurately. According to the agency, at least two diagnostic tests on the market deal with genetic targets that are now being changed by variant B.1.1.7, although these are not the only targets of the tests.
The good news: The variant is so similar to previous versions of SARS-CoV-2 that scientists are confident it will continue to be recognized by the immune systems of people who have been vaccinated or have recovered from infection.
This is because people typically develop 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 on Mount Sinai. “Even if something changes in a particular region, there are other antibodies that we develop as part of our antibody response that could recognize other parts of the protein as well,” he said.
Even if a mutated version of the virus is sufficiently different in the future, vaccines can also be adapted to protect against different strains. As Rasmussen pointed out, “Before people freak out, consider that we deal with influenza every year.”
How much more contagious this variant is than previous ones was estimated in a model study from London in December that it is about 56% more transmissible. Assuming that one person infected with the original SARS-CoV-2 virus would normally infect one more person on average, people wearing the new variant could instead transmit it to around 1.5 people. The cumulative effect of this is significant: if each infection resulted in 1.5 new cases per week, in about two weeks there would be twice as many cases as normal.
Because of this, the arrival of the variant leads to heated debates over whether vaccine doses should be halved or delayed in order to get them to people faster. Despite little data on how effective a single dose would be, some scientists argue that it is better to have some protection than none at all. Others, including senior FDA officials, fear that deviating from the approved dosage schedule could wreak further havoc.
The UK has adopted an extended vaccination schedule as an emergency response to the surge. As part of the strict national lockdown, the country has also taken the drastic step of closing schools and universities as well.
In the United States, where new cases and deaths are reaching record highs, a more contagious virus puts more stress on a health system that is already struggling to treat patients. In Southern California, available ICU capacity has bottomed out at 0% and first responders in Los Angeles are instructed not to move patients who are unlikely to survive.
“If we don’t change our controls, it will speed up the transmission significantly once it becomes common,” Lipsitch said.
Scientists could know a lot more about how widespread the variant is in the US – if they got the resources to look it up.
Early research shows that the variant is strongly correlated with a change in one of the virus’ genes, the S gene. Recognizing this change in a patient’s virus sample appears to be a useful clue, then genetically sequencing it and eradicating more cases.
Thanks to rapid and widespread sequencing, the UK was able to quickly identify these and other variants. In March, the government invested £ 20 million to create 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.
According to Joshua Quick, one of the group’s researchers at the University of Birmingham, the company has so far sequenced around 10% of all infections in the UK and can process 5,000 samples per week. “Fast genome sequencing capacity increases the chance of identifying existing or new variants or interventions such as quarantining cases of the variant,” he said via email.
For comparison, the US has sequenced less than 1% of its cases – about 51,000 out of 17 million according to a CDC report in late December. Lipsitch said the UK is “about five years ahead of us in terms of genomic surveillance and knowledge of the genetics of the pathogens and how they spread in their country”.
The closest U.S. equivalent to COG-UK is SPHERES, a CDC-led patchwork of laboratories from health authorities, universities and sequencing centers.
Russ Corbett-Detig, an evolutionary geneticist at the University of California at Santa Cruz, said the scientists involved are very collaborative and share methods and data sets. But he and several other researchers say that unlike the UK consortium, it doesn’t have a clear mandate. “What we urgently need is more sequencing in the US,” said Corbett-Detig.
SPHERES “doesn’t really have the infrastructure, resources, or funds to do full national surveillance,” said Chiu, whose UCSF lab is also part of the consortium, adding that sequencing each sample is about US $ 200 -Dollars costs. without work.
“We literally need money,” he said. “My laboratory, we basically have the capacity to produce 300 genomes a week. If we had more resources, we could end up producing thousands of genomes. “
The CDC has not returned any requests for comment. Its website states that a strain monitoring program will be launched and if fully implemented this month, each state will send at least 10 samples to the CDC for sequencing every two weeks. On Wednesday, California-based sequencing companies Illumina and Helix announced that they would work with the agency to improve national genome surveillance and track the emergence of variant B.1.1.7.
In the meantime, some states and cities are taking it upon themselves to step up their surveillance efforts. The California Department of Health is asking healthcare providers to submit samples for sequencing of COVID-19 positive individuals who are likely to be suspects. However, regional surveillance is often limited. In Los Angeles, where nearly 12,000 new cases were reported on Wednesday alone, health officials said they only sequence 30 to 35 samples every few days. The state health laboratory in New York is stepping up sequencing efforts and has analyzed more than 870 samples in the past two weeks, a representative said. For the past week, New York has reported an average of more than 14,000 cases a day.
Until the US can develop a better system for monitoring variants, scientists say this is a good sign that the same public health measures can continue to protect people. The virus still spreads through airborne droplets and smaller aerosol particles and, to a lesser extent, through physical contact with infected surfaces.
So efforts to reduce transmission remain the same: social distancing, masking, collaborative tracing, staying home as much as possible, avoiding indoor gatherings, washing hands, and getting vaccinated as soon as possible.
But in the face of an even more threatening adversary, Americans must take the risks much more seriously than before.
“People need to understand that this is no longer a theoretical problem,” said Rasmussen. “This is an imminent problem.”
Dan Vergano and Stephanie Baer contributed to this story.
January 8, 2021, 7:06 p.m.
This story has been updated to include an FDA warning about the possibility of false negative test results due to the new coronavirus variant.