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It’s not a unique quirk, but like many other Covid-19 tests, Helix searches for three extracts from the virus genome. One of these extracts is on the S gene, which codes for the virus advanced protein allowing infection. The B.1.1.7 variant has a six-letter deletion on this section of the S gene. So the test for an infected person always comes back positive, but without the S gene signal. Scientists have dubbed it “gene drop. S ”or“ S gene target failure ”, abbreviated SGTF. This can be a useful shortcut for estimating the extent of circulation of B.1.1.7 in an area, but since other harmless variants also have the same deletion, the only way to know for sure is to sequence.
After the UK sounded the alarm on B.1.1.7 at the end of December, Helix began sending each SGTF sample to Illumina for sequencing. At the time, they found around 100 cases of S gene drop every 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, all of the S gene dropouts are B.1.1.7. It is no longer possible to sequence them all, because there are simply too many of them – at least in these two places, which represent about 50% of the tests carried out by Helix. “In Florida, we see B.1.1.7 now accounting for about 15 percent of all new Covid-19 cases,” says Lee. “Six weeks ago it was less than 1%.”
The Florida Department of Health did not respond to WIRED’s questions. But the fate of that state over the next few weeks may be an indicator of what is to come for the rest of the United States. According to the CDC, the prevalence of B.1.1.7 is still low – approaching 1 percent – across the country. But Helix data suggests other hot spots are starting to emerge, most notably in Georgia, Texas, and Pennsylvania. This means that the decisions that government officials in these areas make in the days and weeks to come regarding the reopening of schools and businesses will be crucial. Actions to slow the spread of more contagious variants are more effective during the early stages of circulation.
“Because we caught this early, it gives us precious time to try to reduce current levels of transmission and to vaccinate as many people as possible,” Gangavarapu says. These two parameters, he says, are what will dictate whether or not the United States sees a significant spike due to the new bloodlines. “It’s a race against time,” he continues. “If we don’t do these things, an even bigger wave than the one we saw this winter is possible. If you open everything now, it’s almost guaranteed. “
Gangavarapu says his team of collaborators found a lot of B.1.1.7 in circulation. But so far, their sequencing efforts haven’t captured either of the two variants believed to be the best performers of immune evasion – the B.1.351 and P.1 variants, found in South Africa and Brazil respectively. . According to CDC data, only a handful of them have been reported in the United States so far, mostly in people who have recently returned from a trip. But imports are not the only thing to worry about. There are also local variations.
Jeremy Kamil is among those looking for them. A virologist at Louisiana State University Health Sciences Center Shreveport, Kamil normally studies the cytomegalovirus family, but starting last spring, he joined forces with Vaughn Cooper, the director of the Center for Evolutionary Biology and Medicine at the University of Michigan who performs microbial sequencing. startup, to set up genomic surveillance for SARS-CoV-2 in Louisiana. For months, they sequenced hundreds of randomly collected coronavirus test samples across the state, looking for anything unusual. On January 27, Kamil noticed exactly that – a batch of samples all containing a mutation he had never seen before. When he took a closer look, he saw that each of the mutant viruses were closely related – they were all from the same genetic line. And although this line was quite young, only going back in early December in its data, it was becoming more and more common every day.
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