LONDON — All at once, the coronavirus seemed to change.
For months, Dr. Steven Kemp, an infectious disease expert, had been scanning a global library of coronavirus genomes. He was studying how the virus had mutated in the lungs of a patient struggling to shake a raging infection in a nearby Cambridge hospital, and wanted to know if those changes would turn up in other people.
Then in late November, Dr. Kemp made a startling match: Some of the same mutations detected in the patient, along with other changes, were appearing again and again in newly infected people, mostly in Britain.
Worse, the changes were concentrated in the spike protein the virus uses to latch onto human cells, suggesting that a virus already wreaking havoc around the world was evolving in a way that could make it even more contagious.
“There’s a load of mutations that occur together at the same frequency,” he wrote on Dec. 2 to Dr. Ravindra Gupta, a Cambridge virologist. Listing the most troubling changes, he added: “ALL of these sequences have the following spike mutants.”
The two researchers did not yet know it, but they had found a new, highly contagious coronavirus variant that has since stampeded across Britain, shaken scientists’ understanding of the virus and threatened to set back the global recovery from the pandemic.
Word raced through a consortium of British disease scientists, longtime torchbearers in genomics who had helped to track the Ebola and Zika epidemics. They gathered on Slack and on video calls, comparing notes as they chased down clues, among them a tip from scientists in South Africa about yet another new variant there. Still others have since emerged in Brazil.
For nearly a year, scientists had observed only incremental changes in the coronavirus, and expected more of the same. The new variants forced them to change their thinking, portending a new phase in the pandemic in which the virus could evolve enough in time to undermine vaccines’ effectiveness.
But the road to its discovery was laid down to little acclaim in March, when Britain decided to begin sequencing coronavirus samples en masse. The country produces half the world’s inventory of coronavirus genomes, providing an unparalleled view of how the virus changes, and how people brought it into Britain last year and are now carrying the variant out.
For Britain, the discovery came too late to prevent a punishing new wave of Covid-19 that has put its hospitals on the brink of having to deny lifesaving care. The variant was already spreading fast, abetted by the government’s lax restrictions during the fall and early winter.
But Britain sounded an alarm for the world, allowing countries to close their borders and start frantically searching for a variant they otherwise might not have noticed for months. British scientists quickly published studies that convinced skeptics of its potency.
“The U.K.’s got many things wrong about this pandemic, mainly not learning lessons about the importance of reacting early,” said Neil Ferguson, an epidemiologist and government adviser. “But the U.K. has a fairly unparalleled surveillance system for Covid. We can monitor very small changes…