How British researchers tracked the new Covid-19 variant

LONDON – British public health officials were mystified. Nationwide restrictions drove down the spread of coronavirus across large parts of the country in late November. But in one part of south-east England, infections increased inexplicably.

Epidemiologists set out to investigate, first assuming that there had been some sort of super-spreading incident, or that people were ignoring rules of social distance in the workplace, in illegal house parties, or elsewhere. They found nothing. Stumped, they approached a team of researchers monitoring mutations in the virus’ genome.

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 compilation of genome data and details of an outbreak in Kent led to the key link,” said Sharon Peacock, a microbiologist at the University of Cambridge who heads the genome research team. She said in an e-mail that it was the researchers’ “pear moment”.

Out of control

The UK increased the restrictions after announcing a new variant of coronavirus that appears to be more transmissible.

Two-week percentage change in new daily confirmed Covid-19 cases

Note: Luxembourg change calculated using data for 10 December; Spain from 9 December.

Source: Johns Hopkins CSSE

New information continued to flow in, and the British government first raised concerns about the variant publicly on December 14, when Health Secretary Matt Hancock told British lawmakers it had been 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,” Hancock said.

Meanwhile, researchers dug deeper into the nature of the mutations of the new variants.

Viruses mutate all the time – though coronavirus is slower than some other common viruses like the flu. What happened in the new variant was that a larger than normal number of mutations affected the code of the amino acids that produce the proteins that produce the virus.

A mutation alters the virus’ spike protein in a way that has been known to make it easier for the virus to attach to cell walls and enter the body. Together with two other mutations, the change has the potential to give the variant a possible advantage over previous versions of human infection.

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

“It’s a bit out on a branch, it’s actually really striking that it’s so different from everything else around it in the UK,” said Drs. Peacock.

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

The latest data shows that the seven-day average of cases in the week to Wednesday across the UK increased 61% compared to the previous week, although the number of cases is declining in most of the rest of Europe. Admissions and deaths – lagging indicators of virus spread – increased by 16% and 20%, respectively.

“The underlying mechanism” that drives the rapid spread “is not entirely clear – it may be because the virus replicates faster, which means you get higher viral loads, which means you are more contagious,” Peter Horby, chairman of the new Emerging Respiratory Virus Threats The advisory group advising the UK government told lawmakers on Wednesday.

Public health announcements outside Victoria Station in London on Tuesday.


Photo:

Victor Szymanowicz / Zuma Press

Another hypothesis is that it may be that it takes less time between being exposed and being contagious, which will lead to faster transmission. “Or it could mean that the infection lasts longer,” said Dr. Horby.

Researchers are now working on answering two important questions: Will the new variant cause more serious illness, and will it be able to avoid vaccines?

British scientists say they do not have enough evidence at the moment to either answer definitively, 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 compared to what was developed in the previous version.

Footage shows empty supermarket shelves while trucks with cargo are stuck at the border after France imposed a travel ban on Britain following the spread of a new coronavirus strain. Other countries have also excluded passengers from the UK Photo: Neil Hall / EPA / Shutterstock

The widespread perception among researchers and developers of Pfizer Inc.

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

About the severity of the disease caused by the new variant, they wait for hospitalization data and death data, which delayed cases count, to tell them more.

As they have immersed themselves in the new variant, British researchers have spent the last few weeks quietly in search of patient zero. They have sifted through the contacts of the two people who were the first to be identified with the variant, where neither of them was ill, 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 often host when viruses undergo a large number of mutations because the virus is able to survive in their system for so long.

“In an ideal situation, you would know who the index case was,” said Dr. Peacock. “We do not know at all whether this has occurred in a patient in the UK or whether it has been introduced, we can categorically not tell it at the moment.”

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

On December 18, as new infections in the region continued to accelerate, a meeting between officials and researchers alerted the government, leading to a marked shift in policy.

The following day, Prime Minister Boris Johnson announced new lockdowns for regions where the virus spread rapidly, cutting a planned five-day Christmas easing 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]

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