A rising wave of covid-19 cases in the south of England has been blamed on a new variant of the virus. The new strain, first detected in September, is now behind half the cases in the region. Genomic researchers have found that not only does the variant have a lot of mutations, but several of the genetic alterations are predicted to make possibly significant changes to the spike protein, a part of the virus that plays a key role in infecting cells.
On Saturday, December 19, UK prime minister Boris Johnson gave a televised press conference in which he announced new restrictions on movement for the Christmas season, and a total lockdown in London and the southeast in response to the sudden spike in cases.
“It seems that the spread is now being driven by the new variant,” Johnson told the public. “It does appear that it is passed on significantly more easily.”
His experts, Johnson said, had made preliminary calculations that the new strain may be up to 70% more transmissible. The immediate result of the leader’s comments was panic. Although there isn’t evidence the new strain is more deadly, by Sunday a number of European countries—including Italy, Ireland, Germany, France, and the Netherlands—were restricting travel to the UK. The UK-France Eurotunnel closed on Sunday night as France shut its borders to travelers from the UK for 48 hours.
Over the weekend, medical experts sought to reassure the public that the new strain, named VUI – 202012/01 (for “first variant under investigation in December 2020”), would not affect vaccination efforts, which began in the UK and the US this month. One reason is that the virus would have to change substantially to “escape” the current vaccine. Even if it does, vaccines can be adjusted to keep up with shape-shifting pathogens, as is the case with the annual flu shot.
It said the variant’s success at spreading exponentially during a national lockdown period gave the group “moderate confidence” that it “demonstrates a substantial increase in transmissibility compared to other variants.”
The situation could prove to be a false alarm. Sometimes virus variants appear to seem to spread more easily but in fact are being propelled by luck, like a superspreader event.
British teams, and some abroad, are now racing to carry out the lab experiments necessary to demonstrate whether the new variant really infects human cells more easily, and whether vaccines will stop it; those studies will involve exposing the new strain to blood plasma from covid-19 survivors or vaccinated people, to see if their antibodies can block it.
Viruses frequently mutate or develop small changes in their genetic code. Since the start of the pandemic, scientists sequencing samples of the coronavirus have been tracking those changes to gain insight into how, and where, the pathogen has been spreading.
One reason the strain was spotted in the UK might be that the country has pursued such “genomic epidemiology” aggressively. For example, British labs contributed fully 45% of the 275,000 coronavirus sequences deposited to the global GISAID database, according to a threat assessment brief from the European Centre for Disease Prevention and Control.
According to the COVID-19 Genomics Consortium UK, the coalition of labs that’s been sequencing viruses, the variant was first spotted on September 20 in Kent and a day later in London.
While mutations in the coronavirus are seen all the time, the new variant raised alarms because it appeared at the same time as a sharp and alarming increase in cases in the southeast of England, where the infection rate has recently quadrupled. Nearly half those cases were found to be caused by the new variant.
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