A coronavirus variant with some of the same mutations as the highly contagious British variant may have been in the US since October and is already widespread, a re-analysis of more than 2 million tests suggests.
Genome sequencing to confirm if the variant seen in Americans is the same as the so-called B117 variant currently circulating in the UK is underway.
Results are expected in days, but the revelations have raised new questions about where the altered virus came from, including a small possibility that it started in the US, not the UK, or elsewhere. The variant has also been found in at least 17 countries, including South Korea, Spain, Australia, and Canada.
“It wouldn’t be at all surprising if at least some of the cases were B117,” said Eric Topol, head of the Scripps Research Translational Institute in La Jolla, California, who was not involved in the study but whose team confirmed a Californian. . case of the B117 variant on Wednesday.
“It’s probably been at low levels here for a while, but you won’t see it until you look for it.”
The existence of a new and highly transferable Sars CoV-2 variant was announced by the UK Secretary of Health on December 14, after Covid testing labs reported that a growing number of their positive samples were missing a signal from one of the three genes their PCR. use tests to confirm the presence of the virus.
Further sequencing revealed that such “S gene dropout” was the result of mutations in the gene encoding the spike protein the virus uses to gain access to human cells. The variant has been reported to circulate in the UK since September.
The news of the new variant has resulted in multiple countries restricting travel from the UK – or, in the case of the US, requiring travelers to show proof of a negative Covid-19 test in order to enter the country. However, the first known cases in the US were discovered in Colorado and California earlier this week, and it is suspected that this is already widespread.
In the closing hours of December 31, a third US state, Florida, officially reported a case of the variant coronavirus, a man in his 20s in Martin County, north of West Palm Beach, who had no recent travel history, reported Florida health. . department said.
To investigate this, scientists at California-based DNA testing company Helix examined the prevalence of S gene failure in 2 million Covid tests processed by the company in recent months. They saw an increase in S gene dropout among positive samples since early October, when 0.25% of positive tests showed this pattern.
This has grown since then, reaching an average of 0.5% last week – although in Massachusetts, which has the highest number of such samples, it is currently 1.85%, although no cases of the B117 variant have yet been announced in that state .
Further analysis revealed mutations in some of the same regions of the S gene that are also present in the B117 variant – although complete sequencing of the viral genome is needed to confirm whether this is indeed the same variant, or something else.
The coronavirus pandemic has gotten out of control in the US, with the 24-hour death toll in excess of 3,740 earlier this week, signaling the worst day of the outbreak in the nation to date.
Public health experts and Joe Biden, the Democratic president-elect, have warned that the situation will get worse before it gets better, even if vaccines get underway.
Helix is currently working with the U.S. Centers for Disease Control and Prevention (CDC) pending test results on the variant found in the U.S.
‘If we get it [B117 variant], then maybe we can see if it has been introduced once or more in the US, or if it has further mutated, ”said Nicole Washington, associate director of research at Helix, whose research was pre-published and has not yet been published by peers. assessed.
“If all samples have it, then it has probably been here for a while, but if there are only one or two samples, it could be that it was recently introduced and we are just beginning to spread. “
It’s also possible that the variant originated in the US and then spread to the UK – although this is unlikely as the B117 variant appears to be more common in England, Topol said. “However, I don’t think it should be known as the UK variant, because we don’t know where it comes from.”
If B117 is really widespread in the US, then travel bans are unlikely to work, Topol adds, “The variant is likely to become dominant. [within the US] in the coming months, so what we need to do is avoid it through a combination of very strict mitigation measures, including surveillance and testing, and vaccinate as if there is no tomorrow, ”he said. “The vaccines should work well.”
Even if the variant identified by Helix is not B117, the nature of some of the mutations it contains is of concern, as they can increase the virus’s ability to infect human cells, added Ravi Gupta, a professor of clinical microbiology at the University. from Cambridge. , UK, which contributed to the sequence of the B117 variant.
Meanwhile, the US has lagged far behind the goals set by the US government for the number of people it hoped would be vaccinated by the end of 2020.
Top American infectious disease expert Anthony Fauci on Thursday called on the federal government to increase its resources to vaccinate Americans.
As the state’s overworked, underfunded public health departments rushed to administer the vaccines, some seniors waited overnight for their first dose in Florida.
“We would have liked it to run smoothly and have 20 million doses of people… by the end of 2020, that was the projection. It clearly didn’t happen, which is disappointing, ”Fauci told NBC on Thursday.