A rising wave of covid-19 cases in the south of England starting in September caused genomic researchers to look more closely. What they found was disturbing: a new virus variant is causing half the cases. Not only does it have a lot of mutations, but several of the genetic alterations are predicted to make possibly significant changes to its spike protein, a part of the virus that plays a key role in infecting cells. 

These were the scientific events which led to an address on Saturday, December 19th, by UK prime minister Boris Johnson, who announced the country was battling a new, faster-spreading, version of the coronavirus.

“It seems that the spread is now being driven by the new variant,” Johnson told the public, announcing new restrictions on movement for the Christmas season, and a total lockdown in London and the south-east. “It does appear that it is passed on significantly more easily.” 

His experts, Johnson said, had made preliminary calculations that the new strain, named ‘VUI – 202012/01 (The first Variant under Investigation in December 2020), 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 due to the new strain. 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 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. 

On Sunday, US Surgeon General Jerome Adams said on CBS News’s “Face the Nation” that there are “no indications” the new variant will impede US vaccination efforts.

In his public comments, Johnson was relaying the findings of an expert body advising his government called the New and Emerging Respiratory Virus Threats Advisory Group, whose assessment was somewhat less alarmist than the prime minister’s version. 

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 super-spreader 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 the variant. 

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 how, and where, the pathogen has been spreading. 

One reason the strain was spotted in the UK might be because 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. 

Distinct signature

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 the southeast of England, where the infection rate has recently quadrupled. Nearly half those cases were found to be caused by the new variant. 

The genetic code of the variant also caught scientists’ attention, for how different it was. According to a preliminary characterizations posted to the website virological.org by the COVID-19 Genomics Consortium UK, the variant possesses a “distinct” genetic signature featuring “an unusually large number of genetic changes” particularly in its spike protein, which the virus uses to invade cells, and which are more likely to alter its function.

The mutations seen in the new variant have all been spotted previously, according to comments posted online by Francois Balloux, a computational biologist at the University of College London, but apparently not in this combination. They include one that increases how well the spike proteins binds to human cells, another linked to escaped from human immune responses, and a third adjacent to a biologically critical component of the pathogen. 

So far in the pandemic, the spreading variants of the virus tend to pick up one or two new mutations a month. The UK scientists say they were surprised to find a variant that has accumulated a unique pattern of more than a dozen changes to important genes, which they suggested were clues the stain might be the result of evolutionary adaptation. adapting. 

Dodging the immune response?

In the UK’s group preliminary report, Andrew Rambaut, at the University of Edinburgh, and his colleagues say they think the variant might have evolved inside a person who is immunocompromised and who became chronically infected with the coronavirus. Such people, in some cases, have been given multiple rounds of treatment with antibody and anti-viral drugs. That could select for viruses which survive the treatment.

If the new strain is able to “evade” the usual immune response, that may also explain why it’s spreading faster, since it would also affect some covid-19 survivors and therefore have more hosts to infect. According to the British scientific reports, four of about 1,000 people infected by the new variant previously had covid-19, although they were not able to say if that figure was out of the ordinary. 

The idea that the covid-19 virus could evolved enough to infect people again, despite immunity to the original germ, would not be a total surprise.  Other coronaviruses, which cause the common cold, are known to reinfect people frequently, possibly because of such shape-shifting.

Another way viruses can change significantly is if they establish themselves in another species—even zoo tigers can catch covid—and then jumped back to people. That was seen in Denmark, which this fall  reported transmission of the covid virus between humans and mink and back again, a situation deemed so dangerous that the country ordered all the mink on commercial fur farms to be culled. 

Now the world will learn if it’s possible to stop the new variant from spreading. That won’t be easy. The existing forms of the covid-19 are already transmitting quickly despite social distancing and masks. If the new variant is really 70% more easily spread, it could soon become the dominant form of the disease. 

British authorities over the weekend faced some criticism that they were raising alarms over the new strain to justify strict lockdown measures before Christmas, including stay at home orders for millions of people. But officials took to the air to encourage people to abide by the restrictions. “The new variant is out of control and we need to bring it under control,” Matt Hancock, the health secretary, told the BBC. He urged his countrymen to “act like you have the virus.” 

By ASNF