The coronavirus is receding across the United States. The pandemic is still raging, mind you, with over 70,000 new cases still being reported every day. But since the post-holiday peak in mid-January, the seven-day average of new cases has fallen nearly 64 percent. The number of hospital admissions has also fallen. And with vaccines accelerating, there’s a glimmer of hope that this downward trend could be the start of COVID’s long slide into containment, at least in the US and other wealthy countries that have the sails.
But retreating doesn’t always mean defeat. And the emergence of several worrisome new coronavirus variants with new tricks to spread faster or evade immune responses offers another possibility: that the current postponement will only be temporary. Public health experts are urging governments to prepare for a potential new wave of infections, fueled by variants like B.1.1.7, which has already been identified in more than 1,200 U.S. cases and in nearly every state , according to data from the U.S. Centers for Disease Prevention and Control.
That’s more than double the number reported two weeks earlier. But the real number is probably much higher. How much higher? Nobody knows. That’s because the only way to determine which version of the coronavirus is causing an infection is by sequencing the genome. In this country, that should be easy enough – the US is a sequencing superpower. It has dozens of academic institutions and huge commercial labs with the capacity to crank out genomes in no time. But the federal government’s response during much of the pandemic did not include a plan to mobilize America’s DNA mappers into a coordinated coronavirus monitoring corps. SARS-CoV-2 monitoring, well, bad.
Late last year, the CDC finally got the green light to roll out additional programs and funding to change that. Since then, the US has ramped up sequencing from about 3,000 viral genomes per week to more than 7,000. But scientists say it’s still not close enough. And we’re running out of time to catch up. Because as Congress debates a bill that could provide the necessary infusion of funds to build out the genomic surveillance system the US should have had all along, variants — both the ones scientists know to worry about and the ones they have not yet discovered – are expanding their territory.
“Right now in the US we see a doubling of B.1.1.7 every 10 days,” said Karthik Gangavarapu, a computer biologist at the Scripps Institute in La Jolla, California. He’s part of a team of researchers tracking the rapid spread of the extra-infectious lineage, which is still sometimes referred to as the “British variety.”
In a study posted online earlier this month, the team analyzed more than 200 viral genomes of the B.1.1.7 lineage collected from around the country, and they found that the variant most likely arrived in the U.S. in November, a month. before it was first discovered here. They then calculated how quickly the variant spread in the months of December and January: between 35 and 45 percent faster than existing American species. Although it has not yet been published in a peer-reviewed journal, the data provides the first hard evidence to support a forecast released in January by the CDC, which predicts that B.1.1.7 will be the dominant variant in the US by the end of March. would become.
“What we’ve seen in recent weeks is that things are basically evolving the way we thought they would,” said William Lee, the vice president of science at Helix and a co-author on the study. Helix, a lab testing company headquartered in San Diego, in partnership with parent company Illumina, is one of three commercial labs contracted by the CDC to perform genomic surveillance of SARS-CoV-2. Technically, Illumina does the sequencing and Helix provides the viral material, recovered from nasal swabs that the company uses to test for coronavirus. And because of a quirk in the design of the test, Helix can easily mark the samples that are likely to contain B.1.1.7.
Meet the S gene
It’s not a unique quirk, but like many other COVID-19 tests, Helix hunts for three fragments of the virus’s genome. One of those fragments is located on the S gene, which codes for the virus’s infection-promoting spike protein. The B.1.1.7 variant just happens to have a six letter deletion on that part of the S gene. So the test for a person infected with it still comes back positive, but lacks the S gene signal. Scientists have called it “S gene loss” or “S gene target failure,” SGTF for short. It can be a useful shortcut to estimate how widespread B.1.1.7 is circulating in an area, but because other harmless variants have the same deletion, the only way to know for sure is to determine the order.
After the UK sounded the alarm over B.1.1.7 in late December, Helix began sending each SGTF sample to Illumina for sequencing. At the time, they found about 100 cases of S gene loss every day. And most of them turned out not to be B.1.1.7. But now, Lee says, in places like Florida and Southern California, all S gene dropouts are B.1.1.7. It’s no longer feasible to rank them all because there are just too many of them — at least in those two locations, which represent about 50 percent of the tests Helix performs. “In Florida, we see that B.1.1.7 now represents about 15 percent of all new COVID-19 cases,” Lee says. “Six weeks ago it was less than 1 percent.”
The Florida Department of Health did not respond to WIRED’s questions. But that state’s fate in the coming weeks could foreshadow what’s to come for the rest of the US. According to the CDC, the prevalence of B.1.1.7 is still low — nearly 1 percent — nationwide. But Helix’s data suggests other hot spots are starting to emerge, including in Georgia, Texas and Pennsylvania. That means the decisions government officials in those areas make in the coming days and weeks regarding reopening schools and businesses will be critical. Actions to slow the spread of more contagious variants are most effective during the earliest stages of circulation.
“Because we discovered this so early, it gives us precious time to try to reduce the current levels of transmission and vaccinate as many people as possible,” Gangavarapu said. Those two metrics, he says, will determine whether the US will see a major spike as a result of the new lineages. “It’s a race against time,” he continues. “If we don’t do those things, an even bigger wave is possible than what we’ve seen this winter. If you open everything up now, it will almost certainly happen.”
Gangavarapu says his team of collaborators has found a lot of B.1.1.7 in circulation. But so far, their sequencing efforts have not caught either of the two variants suspected of being the top immune evasion artists — the B.1.351 and P.1 variants, discovered in South Africa and Brazil, respectively. According to CDC data, only a handful of these have been reported in the US so far, mostly in people who have recently returned from a trip. But imports aren’t the only thing you need to worry about. There are also homegrown variants.
Jeremy Kamil is one of the people looking for them. Kamil, a virologist at Louisiana State University Health Sciences Center Shreveport, normally studies the cytomegalovirus family, but since last spring he joined forces with Vaughn Cooper, the director of the Center for Evolutionary Biology and Medicine at the University of Michigan, who is a microbial sequencing runs startup, to set up genomic surveillance for SARS-CoV-2 in Louisiana. For months, they tracked hundreds of coronavirus test samples randomly collected from across the state, looking for anything unusual. On January 27, Kamil noticed just that: a batch of monsters that all contained a mutation he hadn’t seen before. When he looked more closely, he saw that each of the mutated viruses was closely related — they all belonged to the same genetic lineage. And while that lineage was quite young, in his records dating only to early December, it was becoming more common every day.
Kamil uploaded the genomes to an online database called GISAID, which is used by researchers around the world. The next day, scientists at the University of New Mexico contacted him. They had found the same variant in their state. Meanwhile, Cooper searched the database looking for more viruses with the same mutation — a genetic alteration that changes the 677th amino acid in the coronavirus spike protein. He found more, not just in Louisiana and New Mexico, but also North Carolina, Massachusetts, and eight other states. The researchers realized they needed a phylogenist to get their viral family tree in order, so they enlisted the help of Emma Hodcroft of the University of Bern in Switzerland. Within a week, her team had tracked the emergence of seven new variants in the US, each of which had individually developed the same mutation.
The researchers described this pattern as an example of “convergent evolution” in a preprint posted Sunday. “It’s a pretty strong indication of an adjustment, even though we don’t yet know what that adjustment is,” said Cooper, a co-author of the study, which has not yet been peer-reviewed.