It’s not a specific quirk, but like many other Covid-19 experiments, Helix hunts for three fragments of the virus’s genome. One of these fragments is the S gene, which codes for virus-enabled spike proteins. The variant B.1.1.7 happens to have a six-letter deletion of that part of the S gene. So the test for a person on it is still coming back positive, but misses the gene mark S. Scientists have called it “S gene dropout” or “S gene target failure,” SGTF for short. It can be a useful shortlist for estimating the extent of B.1.1.7 circulation in an area, but because other innocuous variables have the same elimination, it is the only way to know for sure.
After the UK switched off the alarm over B.1.1.7 in late December, Helix began sending all SGTF samples to Illumina for ordering. Back then, they found about 100 instances of S gene release per day. And most of them did not turn out to be B.1.1.7. But now, says Lee, in places like Florida and Southern California, the S. gene release is B.1.1.7. It’s not impossible to order them now, because there are too many – at least in those two places, which represents about 50 percent of the tests that Helix performs. “In Florida, we see B.1.1.7 now representing about 15 percent of new Covid-19 cases,” Lee said. “Six weeks ago, it was less than 1 per cent.”
The Florida Department of Health did not respond to WIRED questions. But what has happened to that state over the next few weeks may be affecting the future for the rest of the U.S. According to the CDC, the frequency of B.1.1.7 remains low – at nearly 1 percent – nationwide. But Helix data shows that other hotspots are starting to appear, including in Georgia, Texas, and Pennsylvania. That means that the decisions that government officials will make in these areas in the coming days and weeks regarding the opening of schools and businesses will be crucial. Actions to reduce the spread of more infectious variables are more effective in the earliest circulation stages.
“Because we have found this early, that gives us valuable time to try to bring down the normal transmission rates and give the vaccine to so many people,” says Gangavarapu. It is these two metrics, he says, that determine whether the U.S. is seeing a big spike because of the new series. “It’s a race against time,” he continues. “If we don’t do these things, an even bigger wave than we’ve seen this winter is possible. If you open everything now, that’s almost certain it will happen. ”
Gangavarapu says his team of colleagues has found enough B.1.1.7 in circulation. But so far, their sequencing efforts have failed to capture one of the two suspected versions as the best eviction artists – the B.1.351 and P.1 versions, found in South Africa and Brazil, respectively. According to CDC data, very little of that has been reported in the U.S. so far, mostly in people who have recently returned from traveling. But imports are not the only concern. There are also rural changes.
Jeremy Kamil is one of the people watching them. A virologist at Louisiana Shreveport State University’s Center for Health Sciences, Kamil usually examines the cytomegalovirus family, but beginning last spring, he teamed up with Vaughn Cooper, director of the Center for Mean Biology -growth and Medicine at the University of Michigan that runs a microphone sequence startup, to establish a genomic study for SARS-CoV-2 in Louisiana. For months, they followed hundreds of samples from randomly collected coronavirus tests from across the state, looking for anything unusual. On January 27, Kamil noticed just that – a batch of symbols with a mutation he had never seen before. Looking closer, he saw that each of the mutant viruses was closely linked – they all belonged to the same genetic line. And while that line was very young, going back straight to the beginning of December in its data, it was becoming more common every day.