Discovery of COVID-19 variant should signal importance of genome sequencing, scientists say

The British scientists who uncovered a new variant of the virus that causes COVID-19 could be forgiven for feeling somewhat aggrieved at the reaction to their finding.

Instead of being hailed for alerting the world to a dangerous twist in the pandemic, the United Kingdom has been shunned, with more than 40 countries, including Canada, closing their borders to British travellers.

Those involved in the discovery have clapped back and say their work should serve as a wake-up call about the importance of genome sequencing, the painstaking process of monitoring changes in the genetic coding of SARS-CoV-2. They argue it’s only because of Britain’s unique surveillance system, led by a research consortium called COVID-19 Genomics UK (COG-UK), that the variant was found and the world can prepare.

“I think the question for other countries around the world is: What capacity do they have to actually start undertaking some surveillance using genome sequencing to be able to actually get an idea of what’s circulating there?” said Tom Connor, a scientist at Cardiff University who works with the consortium, during a media briefing Tuesday. “Because at the moment you see cases going up in other countries, you see cases going down in other countries, and really, without genome sequence data from those countries, it’s very difficult to know what’s going on there.”

The U.K. isn’t being singled out, though. South Africa also has an advanced sequencing system, and scientists there recently found a similar variant. So many countries have now shut their doors to South African travellers, too. “It is no coincidence that the two places with these interesting variants are both places with the most sequencing coverage,” said Ravindra Gupta, a professor of clinical microbiology at the University of Cambridge. “I think that’s a real lesson for the rest of the world.”

Scientists have long warned that the virus would mutate repeatedly, and Britain began sequencing its genome shortly after the pandemic hit in March. The government set up the genome consortium in April, and it now includes 300 scientists at two dozen public-health agencies, research foundations and universities.

So far the group has sequenced 160,000 genomes of the virus – more than half of all the sequences produced worldwide. Dr. Connor said scientists at Public Health Wales, which is part of the consortium, have done more sequencing in the past week than France has done throughout the pandemic.

“If you are going to find something anywhere, you are going to find it probably here first,” said Sharon Peacock, COG-UK’s director and a professor of public health and microbiology at the University of Cambridge. “And if [a variant] occurs in places that don’t have any sequencing, you’re not going to find it at all.”

COG-UK scientists began looking into the new variant this month after public-health officials noticed a strange phenomenon in Kent, outside London. The infection rate there had not been falling despite a month-long lockdown across England in November that had driven rates down everywhere else. Scientists started looking back through genome sequences and found an extraordinary mutation that first appeared in Kent in late September.

The mutation consisted of 23 changes to the virus, including 17 that altered the genetic coding of the spike protein, which the virus uses to attach to human cells. “That is very, very rare,” said Jeffrey Barrett, a statistical geneticist at the Wellcome Sanger Institute, another COG-UK member. Dr. Barrett said the virus mutates relatively slowly and that researchers normally saw one or two changes a month.

Scientists believe the 17 key mutations have made the virus as much as 70 per cent more transmissible. That could explain why COVID-19 cases have been soaring across Britain this month despite the November lockdown and strict restrictions on social movement. On Tuesday, the U.K. reported 36,804 new cases, the highest daily tally since the pandemic began. The variant has also been found in Denmark and the Netherlands, which also have advanced genome sequencing systems, as well as Italy.

Judith Breuer, a professor of virology at University College London, said there was no evidence the variant causes more illness or increases mortality. Given how quickly the virus has spread, “we would have seen signals by now that it was more deadly.”

There has been some concern that it might increase infections in children, but researchers at COG-UK have yet to determine if that’s happening.

Children have generally been less susceptible to infection and don’t usually get that sick. Wendy Barclay, a virologist at Imperial College, said that may be because the virus attaches to ACE2 receptors, which are found in the lungs and nasal passages, and studies have shown that young children have lower levels of ACE2 in their nasal passages. Dr. Barclay said in a briefing Monday that if the variant makes it easier for the virus to attach to ACE2 receptors, then “children are, perhaps, equally susceptible to this virus as adults.”

Another concern is whether the variant can evade vaccines. So far scientists say that’s unlikely because even 17 mutations aren’t enough to completely throw off the body’s immune system. However, laboratory tests are under way to be certain. And officials at BioNTech, which has made a vaccine with Pfizer, said Tuesday that, if necessary, the vaccine could be adjusted in six weeks to counter the variant.

Dr. Peacock encouraged other countries to study Britain’s success with sequencing. “They can then reflect on whether that’s the investment that they would want to make to get that information,” she said. “This won’t be the last mutation that we’re concerned about. This is going to be an ongoing story.”

Our Morning Update and Evening Update newsletters are written by Globe editors, giving you a concise summary of the day’s most important headlines. Sign up today.