Everything You Need to Know About the New COVID Variant

Dado Ruvic / Reuters
A new variant of SARS-CoV-2, the virus that causes COVID-19, is believed to be increasing the spread of the disease in parts of the UK. The government has put new, more stringent coronavirus restrictions on some regions, including London, known as Tier 4. People in Tier 4 areas cannot meet with anyone outside their household on Christmas, while those in the rest of the country can only congregate on Christmas Day itself.
Prime Minister Boris Johnson and his key scientific advisors said the new variant could increase the transmission of COVID-19 by up to 70% and the R or reproductive number by 0.4.
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What is the significance of this new discovery? The interview asked Lucy van Dorp, a microbial genomics researcher and expert on pathogen evolution, some important questions about what we know at this point.
What do we know about this new variant?
The new British variant, known as VUI-202012/01 or line B.1.1.7, was first announced on December 14th by Matt Hancock, the Minister of Health. It was subsequently confirmed by Public Health England and the UK COVID-19 sequencing consortium. When the SARS-CoV-2 databases were searched again, the first sample was taken in Kent on September 20.
The variant carries 14 defining mutations, including seven in the spike protein, the protein that mediates entry of the virus into human cells. This is a relatively large number of changes compared to the many variants we have around the world.
So far, genetic profiles - or genomes - of this variant have been sequenced and shared largely from the UK, but some in Denmark and two cases in Australia. There were also reports of a case in the Netherlands. These countries have all gone to great lengths to genome sequencing, and it is very likely that these observations do not reflect the true distribution of this variant of the virus, which may exist undetected elsewhere. We will know more as more genomes are created and shared.
Thanks to efforts in the UK to share data, genome monitoring and COVID-19 test results, this variant now appears to dominate existing versions of the virus, and potentially responsible for an increasing proportion of cases in parts of the country, particularly regions where we are too have rapidly growing case numbers.
In these cases it is always very difficult to unravel cause and effect. For example, an increase in the incidence of certain mutations may be due to viral lineages whose incidence is increasing simply because they happen to be present in an area where transmission is high, for example due to human activity or the choice of interventions.
While this is still possible, there are clearly enough observations for this variant so far to warrant very careful characterization, monitoring, and intervention to contain transmission.
Is it more dangerous?
Chris Whitty, the chief medical officer, clearly stated that there is so far no evidence that this variant changes the severity of the disease, neither in terms of mortality nor in terms of the severity of cases of COVID-19 among those infected. Work is underway to confirm this.
How do virus mutations occur?
Mutations are a natural part of virus development. In the case of SARS-CoV-2, these mutations can occur due to random errors during virus replication, from antiviral proteins in infected individuals, or from genetic mixing known as recombination. Although there are currently no signs of recombination in SARS-CoV-2.
Most viral mutations are expected to have no effect. For example, when our team examined individual mutation replacement products in more than 50,000 genomes from the first wave of the pandemic, we found none that significantly altered viral fitness - the virus' ability to survive and reproduce.
Every now and then, however, a mutation, or in this case a certain combination of mutations, can bring luck and give the virus a new advantage. Viruses that carry these combinations of mutations can then emerge more frequently through natural selection in the right epidemiological setting.
Where does the variant come from?
We don't know right now. So far, scientists have not identified any closely related viruses to support the theory that the variant was introduced from abroad. The observed mutation patterns are more likely to support a longer period of adaptive evolution, which is most likely in the UK based on current data.
Similar mutation patterns to this one have been observed in the development of SARS-CoV-2 in chronically infected patients with weaker immune systems. The current hypothesis is that such a chronic infection scenario in an individual patient may have played a role in the development of this variant. This is being investigated further.
How many variations of SARS-CoV-2 did we find?
There are many thousands of lines of SARS-CoV-2, which on average differ only in a small number of defining mutations. It remains true that SARS-CoV-2, which is currently in circulation around the world, has little genomic diversity. However, subtleties in the mutations carried in different lineages can be very useful in reconstructing transmission patterns.
For example, work early in the pandemic and use parentage assignments to identify at least a thousand introductions of SARS-CoV-2 in the UK.
On December 16, London was classified in the toughest level 3 of the Covid-19 measures, with a new variant of the coronavirus emerging as a possible cause of rapidly increasing infection rates. Now it's gone to Tier 4.
Why is it different?
It's important to note that many of the mutations that define the UK variant were seen in SARS-CoV-2 before and sometimes quite early in the pandemic.
However, the British variant or lineage is defined by an unusual number and combination of mutations. One of these mutations, N501Y, has previously been shown to increase the virus' binding to receptors in our cells. N501Y was first sequenced in a virus in Brazil in April 2020 and is currently associated with a SARS-CoV-2 variant, the frequency of which is also increasing in South Africa - an independent line from B.1.1.7 that is also cause for concern.
The particular deletions identified in the spike protein of B.1.1.7 have occurred with increasing frequency in several other lineages of the virus and are also observed in chronic infections in which they can alter the antigenicity - recognition by immune antibodies. These deletions may also be linked to other mutations in the coronavirus spike protein binding region, including those seen in mink infections and a mutation that has been shown to play a role in the virus' ability to evade the immune system in humans. B.1.1.7 also contains a truncated ORF8 gene, deletions in this region previously associated with reduced disease severity.
The functional effect of these mutations and deletions, especially in the combination given in B.1.1.7, has yet to be determined. The high number of mutations and the recent increase in the prevalence of this particular variant, as well as the biological relevance of some mutation candidates, underscore the need for detailed investigation.
What does this mean for the vaccine?
At the moment we don't know. While we should rest assured that vaccines stimulate a broad antibody response to the whole spike protein, it is expected that their effectiveness will not be significantly affected by mutations. This is already being tested.
However, there is growing evidence that other types of seasonal coronavirus can escape immunity for extended periods of time.
It is therefore conceivable that we will reach a point where we will need to update our COVID-19 vaccines, as we did with influenza, to reflect the variants in circulation at the time. It is too early to say if this will be the case now, but extensive genome sequencing, data sharing, and standardized reporting on variants will be critical to this effort.
Lucy van Dorp is a Senior Research Fellow in Microbial Genomics at University College London
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