As the United Kingdom became the world leader in coronavirus genome sequencing

Viral sequencing, which produces a kind of barcode for the virus, has emerged in recent months as fundamental to the global search for versions of the pathogen that are best suited to infect humans, evade vaccines, and possibly kill. Virus variants first identified in the UK, South Africa and Brazil have raised concern among experts.

The variant that the sequencers discovered in the UK, which is now the dominant variety in the country, has a mutation that seems more capable of binding to human cells. Studies suggest that it is 50% more transmissible than the previous prevalent variant, while other research suggests that it could be at least 30% more lethal.

New viral variants are more likely to be seen in the UK than anywhere else. As of January 29, the UK had submitted 44%, or approximately 190,000, of the genomes found in a global library managed by the Global Non-Profit Initiative to share all influenza or Gisaid data. That is, around 5.1% of the nearly four million cases detected in the UK

The United States is rapidly increasing its sequencing capabilities, but only a handful of other countries have contributed more than 1% to the library, meaning that scientists’ understanding of where and how the virus is mutating is erratic. .

This represents a weakness in the global response to the pandemic: the rapid detection of new variants allows governments to adjust restrictions and limit travel from countries where new problematic variants prevail. It can also help vaccine developers update their vaccines.

The UK says it plans to address this weakness by exporting its experience to countries with limited sequencing capabilities.

Half of the genome sequences in the UK were generated at the Wellcome Sanger Institute, the Cambridgeshire facility that stores, classifies, displays and sequences the genomes of Covid-19 positive test byproducts from five major UK laboratories.

The United States has increased its contribution to the global coronavirus genome database since December and has so far accounted for 20% of the total. About 0.3% of Covid-19 cases in the United States have been evaluated.

Anthony Fauci, President Biden’s chief medical adviser for the Covid-19 pandemic, told CBS Sunday that U.S. authorities must expand genomic surveillance to identify variants of the virus.

Britain’s capabilities are based in part on history. British scientists discovered the double helix of DNA and were part of the international team that first sequenced the human genome.

“The UK was one of the first countries in the world to recognize the need for an infrastructure for viral genomic sequencing and we supported it with a large investment long before Covid emerged,” the Health Secretary said on Tuesday. Matt Hancock.

The National Health Service, statewide and rich in data from the country, is also closely linked to an extensive network of researchers from its universities and the pharmaceutical industry.

However, large-scale sequencing of the coronavirus in the United Kingdom hardly left the field.

On March 4, when the UK had four known cases of Covid-19, microbiologist Sharon Peacock called on the phone with a group of other scientists who agreed with her that sequencing the virus genome to control mutations would be vital to tracking its spread. country and identify the origin of the shoots.

They found opposition. Some scientists thought that large-scale genome sequencing of a virus that mutates more slowly than others, such as the flu, would be useless.

“At the time, there were people who said there wouldn’t be enough mutational difference to make this worthwhile,” said Dr Peacock, who is now director of Covid-19 Genomics UK, a network set up to track the coronavirus family tree.

On March 11, the same day that the World Health Organization declared a global pandemic, Dr. Peacock held a meeting in London at the Wellcome Trust with 19 more people, including clinical virologists, technologists, human genome sequencing experts and vaccinologists, to eliminate a large-scale coronavirus sequencing plan.

“It wasn’t like a standard scientific meeting, it was a huge debate about how we could do this,” Dr. Peacock recalled. At the end of the day, they had a plan and presented it to the English Chief Scientist on March 18th. It was accepted and awarded £ 20 million, equivalent to $ 27 million, on 1 April to establish COG-UK.

“This was a superior pace to perfection and this has been the case ever since, but I am delighted that our consortium of over 600 people can contribute to our understanding of the diseases,” he added.

However, the country’s success in discovering variants seems to be due more to serendipity than to strategy.

The UK genomic sequencing production scale – which has assessed up to 10% of all positive coronavirus tests in the UK at some point in the pandemic – was intended to identify superspander events where sequences appear. identical, closely related to their predecessors at the same time.

When an RNA virus like the one causing Covid-19 replicates inside a new host, errors in its genetic code can be made. Most don’t matter, some are corrected and corrected and sometimes no mistakes are made. But some of the errors or mutations are numerous or important to change the virus to affect its biology, and in rare cases give it an advantage over its predecessors.

Coronaviruses mutate more slowly than some other viruses like the flu, so initially scientists didn’t think there would be enough mutations to make large-scale genomic sequencing worthwhile.

But because the virus has infected so many people (more than 100 million worldwide so far), it has had many opportunities to mutate. Some changes, including one of the UK variant that is now present in at least 64 countries, confer evolutionary advantages over their ancestors that make this version of the virus more transmissible.

The new variant caught the attention of experts in November, when a version with a large number of significant changes from its predecessor began to accumulate in a corner of the south-east of England, creating an outcrop of identical genomes. which flashed red on the screens of the genomists.

Initially, sequencers did not know if the variant was gaining prominence due to widespread violation of coronavirus restrictions or if it was the cause of savings in new cases, Jeffrey Barrett, director of the Covid-19 Genomics Initiative at the Wellcome Sanger Institute , he said at an online seminar this month.

In the last week of November, it became clear that in exactly the same place where the mutant genomes congregated, Covid-19 cases were accelerating in the community despite compliance with a national blockade.

Going back through the genome databases, the sequencers found the first occurrence of the highly mutated variant on September 20 in Kent, in the south-east of England, and another a day later in London. Geographical comparison of cases with genomes allowed virus detectives to say with a high degree of certainty that the correlation was not a coincidence and designated the virus as a concern.

Write to Joanna Sugden to [email protected]