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The British B117 variant is circulating in at least 24 states, according to new data from the surveillance of the COVID-19 Centers for Control and Prevention (CDC) variant. The CDC projects that the British variant will become the dominant strain in the United States by March.

From any point of view, the UK appears to be on the crosshairs of COVID-19: Weeks after a new, highly contagious variant emerged that sparked a spike in cases and a new lockdown, Britain is declared to have the world’s highest death rate from coronavirus.

But Britain also has a less secretive weapon: the genome sequencing program that is widely believed to be the most coordinated and advanced any country has ever created. In the grip of the virus, the British have gathered important insights into the behavior and consequences of SARS-CoV-2.

But B117 is also important for what’s missing: In this case, it results in a negative result on certain PCR tests on the spike protein, or S gene.

One of the S gene mutations specific to the variant deletes two amino acids, causing that portion of the PCR test to be negative. The coincidental finding known as target failure of the S gene has become an integral proxy to help track where and when the variant spread in the UK, where about 5% of samples from COVID-19 infected patients are sequenced, said Sharon Peacock. , PhD, executive director and chair of the COVID-19 Genomics UK Consortium.

The same tactic could prove valuable for doctors overwhelmed by cases and deaths, but lacking high-level sequence information about the virus, Peacock said. Medscape Medical News. A British report released on Friday stated that there was a “realistic possibility” that the variant had a higher death rate than other SARS-CoV-2 cases.

“In this particular variant, the deletion of the genome causes one part of the diagnostic test to fail,” explains Peacock. “Some targets are positive, but these are negative. In the UK, this has been used as a substitute marker.”

Targeting Unseen Enemies

B117 isn’t the only variant producing these results, Peacock warns, “but in screening for it, you can think about it.”

“Because the UK ranks about 5% of the cases they detect, this gives them very important clues about what’s going on there,” says Anderson Brito, PhD, a virologist and postdoctoral researcher at Yale University School of Public Health in New Haven. , Connecticut, where investigators created a special PCR test to detect the B117 variant.

Brito, who lived in the UK for 4 years while studying for a doctorate at Imperial College London, said a “major advantage” was a more integrated process for collecting and sequencing samples. Important information – including date and place of collection – is included with each sample, which encourages not only sorting, but also an epidemiological perspective.

“They weren’t in the dark at all,” said Brito Medscape Medical News. “I don’t think any other country in the world knows better which lineage of the virus is circulating.”

CDC launches the file SPHERES a consortium in May 2020 to coordinate the sequencing of the SARS-CoV-2 genome across the United States.

But the American genome effort was “not concentrated,” said Brito, whose lab detected the first two cases of the British variant in Connecticut on January 6. “We had difficulty getting samples, because they were decentralized to a level where there was little coordination between hospitals and research centers. They were not as connected as in the UK. If we only get samples and have no collection date and no origin information, for example, it is at basically useless. “

Global genome collaboration incl GISAID, an international database where researchers share new genomes of various coronaviruses. By mid-January, the United States had shipped about 68,000 sequences to GISAID, added about 3,000 new samples each week and expects more from commercial laboratories in the coming days, according to the CDC.

“The UK must have been much more looking for variants when they emerged,” says Gigi Gronvall, PhD, immunologist and senior scholar at the Johns Hopkins Center for Health Security in Baltimore. “The US has now changed it.”

Warning From British Scientists to the World

Despite these genomic achievements, some British scientists say they are sorry too, hoping they would know how fast SARS-CoV-2 actually spread a year ago, when it hit western Europe.

That information is critical not only for prevention efforts, but because the virus is sure to mutate more quickly the more people become infected, says Igor Rudan, MD, PhD, director of the Center for Global Health Research at the University of Edinburgh in the UK.

“Italy showed us how fast it is spreading and how deadly it is for the very old and people with many comorbidities,” said Rudan, who is also the editor in chief of Journal of Global Health. “We hope we know it is spreading so fast, and we hope we know the threshold of cases we can allow to be infected before the virus mutates.”

More mutations meant more new strains of SARS-CoV-2, Rudan said Medscape Medical News. “We have reached that threshold now and will see more of these mutations,” he said.

Despite its current struggles, Britain is trying to go beyond tracking the spread of its new variant and trying to identify new mutations that might change the way the virus behaves.

Three features of each of the variants that emerged were very important, explains Peacock: Is it more contagious? Is it more deadly? And does that bypass the natural or vaccine-induced ability of immunity to protect people from infection?

“We need to sort the people who come to the hospital who are sick,” said Peacock, also a professor of public health and microbiology at the University of Cambridge, UK. “Also, if anyone gets infected after they’ve gotten sick or got vaccinated, we really want to know what it looks like” genomically.

SARS-CoV-2 has recorded more than 4000 mutations, Peacock said. But “knowing that viruses mutate all the time is not reason enough not to look. We really wanted to know whether mutations cause changes in amino acids, and whether they can cause functional changes,” he said.

However, for now, experts say they are relieved that the British strain does not appear to be able to avoid the COVID-19 vaccine or make it less effective.

“Although mutations are common, those that can change the virus code are rare,” explains Brito. If necessary, the vaccine can be changed to replace the spike gene sequence “in a matter of weeks,” he said. “We’ve done this for flu vaccine. Every year, we have to monitor the variants of the virus in circulation to develop a vaccine that covers most of these viruses. If we end up doing it for SARS-CoV-2, I won’t be surprised. “

But the increase in variant-triggered infections will require more people to be vaccinated before herd immunity can be achieved, Rudan warned. “If it spreads faster, we need to vaccinate maybe 85% of people vs 70% to achieve herd immunity,” he said.

One lesson the COVID-19 pandemic brings with it “is to always be vigilant about what happens next,” said Peacock. Although confident about the genome effort in Britain to date, he and his colleagues feel they are still trying to fully understand the evolutionary changes of the virus.

“We’re ahead of the curve right now, but we want to be ahead of the curve,” said Peacock. “It is very important to be ahead of what might happen because we don’t know how the virus will develop.”

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