Warm weather brings tourists to the Isle of Sheppey, a flat, marshy island near the mouth of the River Thames. Each summer, they fill Sheppey’s many caravan parks or flock to villages with seaside attractions geared toward old-school British tourists: pubs and penny arcades, mini-golf, and fish and chips.
Another kind of visitor stays all year round. Clustered in fields and marshes in eastern Sheppey are three prisons holding about 2,500 men. Giant wind turbines stand like sentries outside the lichen-clad walls of HMP Elmley, the largest of the three, where a 52-year-old prison officer named Paul Tottman worked.
On Oct. 28, a Wednesday, he returned home “very angry,” said his wife, Laura. Covid-19 infections among HMP Elmley’s staff and prisoners were rising, and Tottman, who was asthmatic, felt vulnerable. On Thursday, she said, the prison called to tell Tottman that he had been in contact with a Covid-positive person and should self-isolate. Soon, Tottman also tested positive, and was feverish and fighting for breath.
Sheppey had barely been touched by the pandemic’s first wave last spring. This time, the disease tore through the prison and across the island. It hit the Tottman family hard. Laura and their daughter Hattie fell ill, and within a week of his test, Paul was taken to hospital. “Then it started to go downhill,” Laura said.
Sheppey has been prone to invasion ever since Ivar the Boneless and his Viking hordes conquered it in the ninth century. The arrival of a deadlier and more transmissible variant of coronavirus – the B.1.1.7 “variant of concern” – was also swift and destructive. Although scientists say the first known case was later traced elsewhere in the county of Kent, it was Sheppey and its borough of Swale where the variant first took hold.
The new variant quickly spread from Kent across London and southern England, going from an estimated 3% of cases in England at the end of October to 96% at the start of February. The surge pushed Britain’s Covid death toll into six figures; it now stands at 126,000. Two-thirds of those deaths have occurred since Sept. 20, when the variant was first detected.
The so-called Kent or UK variant has now been reported in more than 100 countries. Recent research has shown that it is not only more contagious but also more deadly, although existing vaccines still work against it. The variant’s arrival has fuelled a rise in infections elsewhere in Europe that threatens to outpace sluggish vaccination programs. The U.S. Centers for Disease Control and Prevention predicts it will be America’s dominant variant by the end of this month; experts warn that the country should be bracing for impact and not – as many states are – loosening restrictions.
Although the scientists couldn’t stop the variant’s conquest of Britain, they had become a warning system for the world. And Sheppey had become an improbable breeding ground for a variant that spans the globe.
The Kent variant was identified by the COVID-19 Genomics UK Consortium or COG-UK, a unique scientific endeavor set up last March to explore how genomic research might help tackle the pandemic. Since it emerged in 2019, the coronavirus has mutated thousands of times. These mutations can be tracked by sequencing, or “reading,” their complete set of genetic instructions, or genomes.
Solving the mystery of the Kent variant was a race against time by the COG-UK scientists, who have sequenced almost half of the world’s catalog of Covid-19 genomes. The first case of B.1.1.7 was later traced back to September, but scientists didn’t fully connect it to the surge in cases until December, when they confirmed their fears: The variant was so transmissible, it was leap-frogging restrictions put in place to tackle the virus.
At the time, COG-UK was sequencing about 9,000 samples a week, using leftover swabs from the labs where most of Britain’s Covid-19 tests are processed. For most of last year, that process took about two weeks. But collecting and sequencing genomes are – relatively speaking – the easy part. Much harder is quickly establishing whether a variant is more contagious or deadly – or, in B.1.1.7’s case, both. A range of factors can explain a jump in infections, from a super-spreader event to a change in human behavior as hot weather turns too cold.
Also, although two weeks between swabbing and sequencing is fast by the standards of genomic research, it wasn’t fast enough to keep up with a highly transmissible variant. While scientists puzzled from afar, funeral directors on Sheppey worked 18-hour days to cope with the dead, and Kent’s hospitals filled up with patients who were often too sick to save.
In the end, COG-UK’s scientists relied upon a timely tipoff from a distant colleague and a hack involving Covid tests to zero in on the Kent variant and more quickly confirm how dangerous it was. “There wasn’t some set method for detecting a variant like this,” said Erik Volz, a genetic epidemiologist at Imperial College London and member of COG-UK. “We had to do it on the fly and develop methods as we went.”