Covid-19: What have we learned about the new variant in the UK?

Is the new variant more infectious?

Yes, according to an analysis of current evidence from the United Kingdom’s New and Emerging Respiratory Virus Threat Advisory Group (NERVTAG). Its December 18 report said that the transmission rate for the variant, known as B.1.1.7 or VUI 202012/01 (variant under investigation, year 2020, month 12, variant 01), was 71% (confidence interval 95% to 67% to 75%), greater than for other variants, and which may also have a higher viral load.1 Although previous variants appeared without clear evidence of a selective advantage, the report noted, the “emergency and subsequent dominance “of this new variant in a period of relatively high prevalence indicated that it has a” selective advantage over other variants “.

When did the new variant appear?

The first known case of this new variant was registered on September 20 and sequenced in early October.2

How long has the government known this?

There has been much speculation about how long the government has known about the new variant and whether it should have acted earlier. At a Science Media Center press conference on December 21, Public Health England epidemiologist Susan Hopkins said it was clear that this variant was important only in December.

“O [SARS-CoV-2] the virus mutates all the time, ”she said. “Even in March, there were eight main strains that were separating. Monitoring virus mutations is how we create the virus family gene tree and track outbreaks.

“In this situation, at the end of November it was clear that the Kent and Medway region of the country in particular was going against the tide of national restrictions and was seeing increases, while on November 20 almost all other parts of the country started to decline.”

Hopkins explained that an initial analysis looked at whether this increase in Kent was related to any specific population group or to outbreaks in the workplace. When this proved not to be the case, PHE reviewed genomic epidemiology to look for changes.

“On December 8, they found that there was a particular variant that had some mutations in the peak protein that came on quickly and was spreading not only in the southeast, but also in parts of London,” she said. “Then, in the next 48 hours, they quickly undertook an investigation looking at the phylogenetic tree and the clinical details of the patients in which the cases arose. They wrote an initial article on December 10, which was submitted to NERVTAG, and it was this article that then initiated further discussions on additional epidemiological modeling and clinical work. “

On December 18, more data was provided to the government, and the next day, the prime minister announced that large parts of south-east England, including London, would enter level 4 restrictions and that the relaxation of the previously announced rules for Christmas would change.

What are the mutations of this variant?

The new variant is defined by 14 mutations resulting in changes in amino acids and three deletions, some of which are believed to influence the transmissibility of the virus in humans.

The World Health Organization reported that one of the identified mutations (N501Y) is altering an amino acid within the six key residues in the receptor-binding domain.3 This same mutation in the receptor-binding domain (N501Y) has also been reported in South Africa South (n = 45), where it emerged independently of the United Kingdom and Australia variant (n = 37). Another significant change is a deletion at position 69/70, which has been found to affect the performance of some diagnostic polymerase chain reaction (PCR) assays that use a target S (peak) gene.

Does this affect the test?

Potentially, but the PCR test has a safety net. Speaking on the BBC Today The radio news program Wendy Barclay, head of the infectious disease department at Imperial College London, said the PCR test was based on three different trials. One of these assays detects the S part or peak of the virus. “One of the ways that this [new virus variant] was detected is that the S part of the test does not seem to work as well in this variant. This is not a problem in terms of number of cases, because we have two other backup pieces that still detect the virus, ”she said.

Less is known about the effect of mutations on lateral flow tests, the rapid response tests that are due to be launched in schools across England in January. An investigation is underway.

Can the new variant affect vaccines?

The message from experts speaking at a Science Media Center briefing on covid-19 was that the new variant would probably not make vaccines ineffective. Peter Openshaw, former president of the British Society for Immunology and professor of experimental medicine at Imperial College London, who participates in NERVTAG, said: “We know that natural infection or vaccination will produce a wide variety of antibody responses. Although it is predicted that some of the mutations that are present in the new variant will affect some of the sites that are recognized by the antibodies, it does not seem likely that it will affect all of them.

“It is clearly important that all of this is tested, and people are working in the labs as we talk to try to get some preliminary answers in the next few days, but it is not a quick science. We have to wait until they can develop the virus and test different sera. Therefore, that information may come out in the coming weeks. “

Are children more susceptible to the new variant?

Yes, compared to the non-variant virus. Speaking at a press conference, Neil Ferguson, director of the Center for Analysis of Global Infectious Diseases at Imperial College London of the Medical Research Council and a member of NERVTAG, said that during the November blockade in England there was a “general change in the distribution of viruses for children – for both variant and non-variant [virus]. ”This was expected, because schools remained open during the blockade, he said, and among those under 15 there were slightly more cases of the variant virus in the community than of the non-variant, although not significantly.

But Barclay, who is also part of NERVTAG, said: “Let’s be clear. We are not saying that this is a virus that specifically attacks children or that it is more specific in its ability to infect children. But we do know that SARS-CoV-2, as it emerged, was not as effective at infecting children as adults. There are many hypotheses [as to why], but one is the expression of the ACE2 receptor which may be different in children. So if the [new variant] the virus is finding it easier to find and enter cells, so that would put children on a more level playing field, if you want. ”

Does the current EPP protect against this?

While this is something that health care professionals are understandably eager to find out, the government has made no mention of any difference regarding the effectiveness of personal protective equipment. The Doctors’ Association UK wrote to Matt Hancock, England’s secretary of health and social care, to highlight his concern about the lack of new guidelines on PPE in light of the increased transmissibility of the new variant. Zainab Najim, the association’s secretary in the UK and a GP registrar, said: “Without a universal policy to vaccinate the front line, the patient facing the team as a priority and without reviewing the current PEP guidelines, we could face disease and avoidable absences of the team in relation to the difficult winter months. We are also concerned that, without escalating the current PEP guidelines, the team itself will be at risk not only of contracting the virus, but also of transmitting it to the vulnerable patient population ”.

Did the variant spread across the UK?

The variant is concentrated in the south east and east of England and in emerging hotspots in the south of Wales and Cumbria. But there are cases of this across the UK, NERVTAG members said.

And outside the UK?

Several countries have confirmed cases of the new variant, including Australia, Denmark, Italy, Iceland and the Netherlands.

Hopkins said that many other countries are likely to report cases soon. She said: “I think it is very likely that it came here. However, it is very likely that it will also be in other countries, because there has been transportation to and from many European countries in the last three months. “

She added that the UK does more genome sequencing (10% of the test samples) than any other European country except Denmark, so it may take some time to know the extent of the variant’s spread. “Denmark probably sequences about 20% now and has increased its sequencing capacity after the mink variant. Most other European countries sequence perhaps 1%, and often much less than that, and many have no sequencing capabilities at all. “

How are other countries responding?

More than 40 countries have stopped all forms of travel to and from the UK to try to reduce the likelihood that the new variant will settle in their populations. Most notably, France closed its border with the United Kingdom, blocking the transport of goods to and from the United Kingdom through the port of Dover. All courier services to Europe (except for the Republic of Ireland) have also been temporarily suspended.

Can the closure of ports affect vaccine stocks?

No, said Transport Secretary Grant Shapps. Speaking to Sky News, he said the disruption to the English Channel ports in Kent “will have no impact on the vaccination program.” 4