How British scientists tracked down the new Covid-19 variant

On December 8, the group, known as the Covid-19 Genomics UK Consortium, found a new variant of the virus, with 23 mutations, in a sample taken from a patient in Kent, near the center of the outbreak in late September. They found the same variant in someone who was tested in London a day later.

Some of the new mutations had the potential to increase the transmissibility of the virus.

“The coming together of the genome data and details from a Kent outbreak led to the most important connection,” said Sharon Peacock, the University of Cambridge microbiologist who leads the genomics team. She said in an email that it was the scientists’ ‘light bulb moment.’

New information continued to pour in and the UK government first expressed concern about the variant publicly on December 14, when Health Secretary Matt Hancock told UK lawmakers it was responsible for 1,000 cases in London and South East England and spread. .

“The initial analysis suggests that this variant is growing faster than the existing variants,” said Mr. Hancock.

In the meantime, scientists took a closer look at the nature of the mutations of the new variants.

Viruses are constantly mutating – although coronaviruses are slower than some other common viruses such as the flu. What was striking in the new variant was that a higher than normal number of mutations affected the code of the amino acids that produce the proteins that make the virus.

One mutation alters the virus’s spike protein in a way that is known to make it easier for the virus to attach to the cell walls and enter the body. Along with two other mutations, the change has the potential to give the variant a potential advantage over previous versions in infecting humans.

It was a variant that had not been seen before – and the number and nature of the mutations were unprecedented, scientists say.

“It’s kind of on a branch, it’s actually quite striking that it’s so different from everything else around it in the UK,” said Dr. Peacock.

At the time of the discovery of the new variant, it accounted for 62% of all recorded cases in London. And infections have continued to rise rapidly.

The latest data shows that the seven-day average of cases from week to Wednesday in the UK was 61% higher than in the previous week, even as the number of cases is declining in the rest of Europe. Hospital admissions and deaths – lagging indicators of the spread of the virus – were 16% and 20% higher, respectively.

“The underlying mechanism” behind the rapid spread “is not fully understood – it may be that the virus is multiplying faster, which means you get a higher viral load, which means you are more infectious,” Peter Horby, president of the New Emerging Respiratory Virus Threats Advisory Group advising the UK government, told lawmakers Wednesday.

Another hypothesis is that it may require a shorter time between exposure and infection, which would lead to a faster transmission. “Or it could mean that the infectivity lasts longer,” said Dr. Horby.

Researchers are now working to answer two crucial questions: Will the new variant cause more serious disease and can it avoid vaccines?

British scientists say they don’t currently have enough evidence to definitively answer either, but are working hard to find out.

On the vaccine, they test blood samples from people who have had the vaccine against the new variant to see if they show a different response from the previous version.

The widely held opinion among scientists and the developers of the Pfizer Inc.

– BioNTech SE vaccine, is that the vaccine produces antibodies that attack a number of different sites on the virus, so the changes in a small area are unlikely to neutralize the vaccine’s potency.

About the severity of the disease caused by the new variant, they are waiting for hospitalization and death data, which counts the number of cases, to tell them more.

As they delved into the new variant, British researchers have been quietly searching for patient zero for the past few weeks. They searched the contacts of the two people who were first identified with the variant, neither of whom was sick, and others who were infected early.

One hypothesis is that the variant originated in a person with a compromised immune system. People with deficient immune systems are often the host when viruses undergo a large number of mutations because the virus can survive in their system for so long.

“Ideally, you would know who the index case was,” said Dr. Peacock. “We don’t know at all if this originated in a patient in the UK or if it was introduced, we can’t categorically say at this point.”

In the week after the new variant was made public, new data and epidemiological modeling made British scientists increasingly convinced that the new variant reproduced faster than its predecessors. Some models suggested it was 50% to 70% more transferable than other versions.

On December 18, as new infections in the region continued to accelerate, a meeting between government officials and scientists troubled the government, prompting a major policy change.

The next day, Prime Minister Boris Johnson announced new lockdowns for regions where the virus was spreading rapidly and cut a planned five-day Christmas relaxation of restrictions to just one day in the rest of the country.

Write to Joanna Sugden at [email protected] and Stephen Fidler at [email protected]